@article{fransson_effects_2021,
	title = {Effects of x-ray free-electron laser pulse intensity on the {Mn} {Kβ1},3 x-ray emission spectrum in photosystem {II}—{A} case study for metalloprotein crystals and solutions},
	volume = {8},
	issn = {2329-7778},
	url = {https://doi.org/10.1063/4.0000130},
	doi = {10.1063/4.0000130},
	abstract = {In the last ten years, x-ray free-electron lasers (XFELs) have been successfully employed to characterize metalloproteins at room temperature using various techniques including x-ray diffraction, scattering, and spectroscopy. The approach has been to outrun the radiation damage by using femtosecond (fs) x-ray pulses. An example of an important and damage sensitive active metal center is the Mn4CaO5 cluster in photosystem II (PS II), the catalytic site of photosynthetic water oxidation. The combination of serial femtosecond x-ray crystallography and Kβ x-ray emission spectroscopy (XES) has proven to be a powerful multimodal approach for simultaneously probing the overall protein structure and the electronic state of the Mn4CaO5 cluster throughout the catalytic (Kok) cycle. As the observed spectral changes in the Mn4CaO5 cluster are very subtle, it is critical to consider the potential effects of the intense XFEL pulses on the Kβ XES signal. We report here a systematic study of the effects of XFEL peak power, beam focus, and dose on the Mn Kβ1,3 XES spectra in PS II over a wide range of pulse parameters collected over seven different experimental runs using both microcrystal and solution PS II samples. Our findings show that for beam intensities ranging from ∼5 × 1015 to 5 × 1017 W/cm2 at a pulse length of ∼35 fs, the spectral effects are small compared to those observed between S-states in the Kok cycle. Our results provide a benchmark for other XFEL-based XES studies on metalloproteins, confirming the viability of this approach.},
	number = {6},
	urldate = {2024-11-25},
	journal = {Structural Dynamics},
	author = {Fransson, Thomas and Alonso-Mori, Roberto and Chatterjee, Ruchira and Cheah, Mun Hon and Ibrahim, Mohamed and Hussein, Rana and Zhang, Miao and Fuller, Franklin and Gul, Sheraz and Kim, In-Sik and Simon, Philipp S. and Bogacz, Isabel and Makita, Hiroki and de Lichtenberg, Casper and Song, Sanghoon and Batyuk, Alexander and Sokaras, Dimosthenis and Massad, Ramzi and Doyle, Margaret and Britz, Alexander and Weninger, Clemens and Zouni, Athina and Messinger, Johannes and Yachandra, Vittal K. and Yano, Junko and Kern, Jan and Bergmann, Uwe},
	month = nov,
	year = {2021},
	pages = {064302},
}

In the last ten years, x-ray free-electron lasers (XFELs) have been successfully employed to characterize metalloproteins at room temperature using various techniques including x-ray diffraction, scattering, and spectroscopy. The approach has been to outrun the radiation damage by using femtosecond (fs) x-ray pulses. An example of an important and damage sensitive active metal center is the Mn4CaO5 cluster in photosystem II (PS II), the catalytic site of photosynthetic water oxidation. The combination of serial femtosecond x-ray crystallography and Kβ x-ray emission spectroscopy (XES) has proven to be a powerful multimodal approach for simultaneously probing the overall protein structure and the electronic state of the Mn4CaO5 cluster throughout the catalytic (Kok) cycle. As the observed spectral changes in the Mn4CaO5 cluster are very subtle, it is critical to consider the potential effects of the intense XFEL pulses on the Kβ XES signal. We report here a systematic study of the effects of XFEL peak power, beam focus, and dose on the Mn Kβ1,3 XES spectra in PS II over a wide range of pulse parameters collected over seven different experimental runs using both microcrystal and solution PS II samples. Our findings show that for beam intensities ranging from ∼5 × 1015 to 5 × 1017 W/cm2 at a pulse length of ∼35 fs, the spectral effects are small compared to those observed between S-states in the Kok cycle. Our results provide a benchmark for other XFEL-based XES studies on metalloproteins, confirming the viability of this approach.

@incollection{shevela_photosystem_2021,
	title = {Photosystem {II}},
	copyright = {Copyright © 2021 John Wiley \& Sons, Ltd.},
	isbn = {978-0-470-01590-2},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9780470015902.a0029372},
	abstract = {Photosystem II (PSII) of plants, algae and cyanobacteria is a specialised protein complex that uses light energy to transfer electrons from water to plastoquinone, producing molecular oxygen and reduced plastoquinone. The PSII complex includes a peripheral antenna containing chlorophyll and other pigments to absorb light, a reaction centre that utilises the excitation energy transferred to it for charge separation, cofactors that stabilise the charge pair via electron transfer reactions, a Mn4CaO5 cluster that oxidises water, and a binding pocket where plastoquinone is reduced. The electrons and protons that PSII extracts from water are employed in the overall photosynthetic process for the reduction of CO2, which provides the chemical energy for most life on Earth. PSII is the only known biological source of O2 produced from water and is responsible for the molecular oxygen in the atmosphere. Key Concepts Photosystem II (PSII) is a membrane-embedded pigment–protein complex, containing more than 20 subunits and approximately 100 cofactors. The PSII antenna and the PSII reaction centre are distinct protein complexes. Light is absorbed by chlorophyll, carotenoid and phycobilin pigments in the antenna and the excitation energy is rapidly transferred to the reaction centre. At the reaction centre, light-induced charge separation takes place resulting in the formation of a chlorophyll cation and a pheophytin anion that are approximately 10 Å apart; this charge separation is rapidly stabilised by the transfer of the charges to more distant cofactors with smaller differences in redox potentials. The oxidation of water occurs at the Mn4CaO5 cluster, which is embedded in the two protein subunits D1 and CP43 on the luminal side of PSII. To oxidise two molecules of water, four oxidising equivalents must be accumulated in the Mn4CaO5 cluster by four consecutive light-induced charge separations. Water oxidation by PSII occurs at the Mn4CaO5 cluster, likely via oxo-oxyl radical coupling in the so-called S4 state. Hydrogen-bonding networks surrounding the Mn4CaO5 cluster are crucial for its catalytic activity, as well as its structural flexibility. Bicarbonate ions play regulatory roles for electron transfer through PSII. The electrons and protons extracted from water by PSII drive the reduction of NADP+ via Photosystem I, and the production of ATP, respectively.},
	language = {en},
	urldate = {2024-10-16},
	booktitle = {{eLS}},
	publisher = {John Wiley \& Sons, Ltd},
	author = {Shevela, Dmitry and Kern, Jan F and Govindjee, Govindjee and Whitmarsh, John and Messinger, Johannes},
	year = {2021},
	doi = {10.1002/9780470015902.a0029372},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/9780470015902.a0029372},
	keywords = {chlorophyll, electron transport, oxygen evolution, photosynthesis, primary photochemistry, reaction centre, solar energy conversion, water oxidation},
	pages = {1--16},
}

Photosystem II (PSII) of plants, algae and cyanobacteria is a specialised protein complex that uses light energy to transfer electrons from water to plastoquinone, producing molecular oxygen and reduced plastoquinone. The PSII complex includes a peripheral antenna containing chlorophyll and other pigments to absorb light, a reaction centre that utilises the excitation energy transferred to it for charge separation, cofactors that stabilise the charge pair via electron transfer reactions, a Mn4CaO5 cluster that oxidises water, and a binding pocket where plastoquinone is reduced. The electrons and protons that PSII extracts from water are employed in the overall photosynthetic process for the reduction of CO2, which provides the chemical energy for most life on Earth. PSII is the only known biological source of O2 produced from water and is responsible for the molecular oxygen in the atmosphere. Key Concepts Photosystem II (PSII) is a membrane-embedded pigment–protein complex, containing more than 20 subunits and approximately 100 cofactors. The PSII antenna and the PSII reaction centre are distinct protein complexes. Light is absorbed by chlorophyll, carotenoid and phycobilin pigments in the antenna and the excitation energy is rapidly transferred to the reaction centre. At the reaction centre, light-induced charge separation takes place resulting in the formation of a chlorophyll cation and a pheophytin anion that are approximately 10 Å apart; this charge separation is rapidly stabilised by the transfer of the charges to more distant cofactors with smaller differences in redox potentials. The oxidation of water occurs at the Mn4CaO5 cluster, which is embedded in the two protein subunits D1 and CP43 on the luminal side of PSII. To oxidise two molecules of water, four oxidising equivalents must be accumulated in the Mn4CaO5 cluster by four consecutive light-induced charge separations. Water oxidation by PSII occurs at the Mn4CaO5 cluster, likely via oxo-oxyl radical coupling in the so-called S4 state. Hydrogen-bonding networks surrounding the Mn4CaO5 cluster are crucial for its catalytic activity, as well as its structural flexibility. Bicarbonate ions play regulatory roles for electron transfer through PSII. The electrons and protons extracted from water by PSII drive the reduction of NADP+ via Photosystem I, and the production of ATP, respectively.

@article{kwong_electrochemical_2021,
	series = {Sustainable {Energy} and {Environmental} {Protection}},
	title = {Electrochemical {N2} reduction at ambient condition – {Overcoming} the selectivity issue via control of reactants’ availabilities},
	volume = {46},
	issn = {0360-3199},
	url = {https://www.sciencedirect.com/science/article/pii/S0360319921024678},
	doi = {10.1016/j.ijhydene.2021.06.184},
	abstract = {Ammonia production via the electrochemical N2 reduction reaction (NRR) at ambient conditions is highly desired as an alternative to the Haber-Bosch process, but remains a great challenge due to the low efficiency and selectivity caused by the competing hydrogen evolution reaction (HER). Herein we investigate the effect of availabilities of reactants (protons, electrons and N2) on NRR using a FeOx-coated carbon fiber paper cathode in various electrochemical configurations. NRR is found viable only under the conditions of low proton- and high N2 availabilities, which are achieved using 0.12 vol\% water in LiClO4-ethyl acetate electrolyte and gaseous N2 supplied to the membrane-electrode assembly cathode. This results in an NRR rate of 29 ± 19 pmolNH3 s−1 cm−2 at a Faradaic efficiency of 70 ± 24\% at the applied potential of −0.1 V vs. NHE. Other conditions (high proton-, or low N2-availability, or both) yield a lower or negligible amount of ammonia due to the competing HER. Our work shows that promoting NRR by suppressing the HER requires optimization of the operational variables, which serves as a complementary strategy to the development of NRR catalysts.},
	number = {59},
	urldate = {2024-10-16},
	journal = {International Journal of Hydrogen Energy},
	author = {Kwong, Wai Ling and Wågberg, Thomas and Messinger, Johannes},
	month = aug,
	year = {2021},
	keywords = {Ammonia, Electrocatalysis, H evolution reaction, Haber-Bosch method, N reduction reaction},
	pages = {30366--30372},
}

Ammonia production via the electrochemical N2 reduction reaction (NRR) at ambient conditions is highly desired as an alternative to the Haber-Bosch process, but remains a great challenge due to the low efficiency and selectivity caused by the competing hydrogen evolution reaction (HER). Herein we investigate the effect of availabilities of reactants (protons, electrons and N2) on NRR using a FeOx-coated carbon fiber paper cathode in various electrochemical configurations. NRR is found viable only under the conditions of low proton- and high N2 availabilities, which are achieved using 0.12 vol% water in LiClO4-ethyl acetate electrolyte and gaseous N2 supplied to the membrane-electrode assembly cathode. This results in an NRR rate of 29 ± 19 pmolNH3 s−1 cm−2 at a Faradaic efficiency of 70 ± 24% at the applied potential of −0.1 V vs. NHE. Other conditions (high proton-, or low N2-availability, or both) yield a lower or negligible amount of ammonia due to the competing HER. Our work shows that promoting NRR by suppressing the HER requires optimization of the operational variables, which serves as a complementary strategy to the development of NRR catalysts.

@article{ibrahim_reply_2021,
	title = {Reply to {Wang} et al.: {Clear} evidence of binding of {Ox} to the oxygen-evolving complex of photosystem {II} is best observed in the omit map},
	volume = {118},
	shorttitle = {Reply to {Wang} et al.},
	url = {https://www.pnas.org/doi/10.1073/pnas.2102342118},
	doi = {10.1073/pnas.2102342118},
	number = {24},
	urldate = {2024-10-16},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Ibrahim, Mohamed and Moriarty, Nigel W. and Kern, Jan and Holton, James M. and Brewster, Aaron S. and Bhowmick, Asmit and Bergmann, Uwe and Zouni, Athina and Messinger, Johannes and Yachandra, Vittal K. and Yano, Junko and Dobbek, Holger and Sauter, Nicholas K. and Adams, Paul D.},
	month = jun,
	year = {2021},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	pages = {e2102342118},
}

@article{keable_room_2021,
	title = {Room temperature {XFEL} crystallography reveals asymmetry in the vicinity of the two phylloquinones in photosystem {I}},
	volume = {11},
	copyright = {2021 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-021-00236-3},
	doi = {10.1038/s41598-021-00236-3},
	abstract = {Photosystem I (PS I) has a symmetric structure with two highly similar branches of pigments at the center that are involved in electron transfer, but shows very different efficiency along the two branches. We have determined the structure of cyanobacterial PS I at room temperature (RT) using femtosecond X-ray pulses from an X-ray free electron laser (XFEL) that shows a clear expansion of the entire protein complex in the direction of the membrane plane, when compared to previous cryogenic structures. This trend was observed by complementary datasets taken at multiple XFEL beamlines. In the RT structure of PS I, we also observe conformational differences between the two branches in the reaction center around the secondary electron acceptors A1A and A1B. The π-stacked Phe residues are rotated with a more parallel orientation in the A-branch and an almost perpendicular confirmation in the B-branch, and the symmetry breaking PsaB-Trp673 is tilted and further away from A1A. These changes increase the asymmetry between the branches and may provide insights into the preferential directionality of electron transfer.},
	language = {en},
	number = {1},
	urldate = {2024-10-16},
	journal = {Scientific Reports},
	author = {Keable, Stephen M. and Kölsch, Adrian and Simon, Philipp S. and Dasgupta, Medhanjali and Chatterjee, Ruchira and Subramanian, Senthil Kumar and Hussein, Rana and Ibrahim, Mohamed and Kim, In-Sik and Bogacz, Isabel and Makita, Hiroki and Pham, Cindy C. and Fuller, Franklin D. and Gul, Sheraz and Paley, Daniel and Lassalle, Louise and Sutherlin, Kyle D. and Bhowmick, Asmit and Moriarty, Nigel W. and Young, Iris D. and Blaschke, Johannes P. and de Lichtenberg, Casper and Chernev, Petko and Cheah, Mun Hon and Park, Sehan and Park, Gisu and Kim, Jangwoo and Lee, Sang Jae and Park, Jaehyun and Tono, Kensuke and Owada, Shigeki and Hunter, Mark S. and Batyuk, Alexander and Oggenfuss, Roland and Sander, Mathias and Zerdane, Serhane and Ozerov, Dmitry and Nass, Karol and Lemke, Henrik and Mankowsky, Roman and Brewster, Aaron S. and Messinger, Johannes and Sauter, Nicholas K. and Yachandra, Vittal K. and Yano, Junko and Zouni, Athina and Kern, Jan},
	month = nov,
	year = {2021},
	note = {Publisher: Nature Publishing Group},
	keywords = {Biochemistry, Bioenergetics, Photosynthesis, Structural biology},
	pages = {21787},
}

Photosystem I (PS I) has a symmetric structure with two highly similar branches of pigments at the center that are involved in electron transfer, but shows very different efficiency along the two branches. We have determined the structure of cyanobacterial PS I at room temperature (RT) using femtosecond X-ray pulses from an X-ray free electron laser (XFEL) that shows a clear expansion of the entire protein complex in the direction of the membrane plane, when compared to previous cryogenic structures. This trend was observed by complementary datasets taken at multiple XFEL beamlines. In the RT structure of PS I, we also observe conformational differences between the two branches in the reaction center around the secondary electron acceptors A1A and A1B. The π-stacked Phe residues are rotated with a more parallel orientation in the A-branch and an almost perpendicular confirmation in the B-branch, and the symmetry breaking PsaB-Trp673 is tilted and further away from A1A. These changes increase the asymmetry between the branches and may provide insights into the preferential directionality of electron transfer.

@article{hussein_structural_2021,
	title = {Structural dynamics in the water and proton channels of photosystem {II} during the {S2} to {S3} transition},
	volume = {12},
	copyright = {2021 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-021-26781-z},
	doi = {10.1038/s41467-021-26781-z},
	abstract = {Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89 Å structure obtained by averaging all the S states and refining the data of various time points during the S2 to S3 transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, which is essential in shuttling substrate waters and protons.},
	language = {en},
	number = {1},
	urldate = {2024-10-16},
	journal = {Nature Communications},
	author = {Hussein, Rana and Ibrahim, Mohamed and Bhowmick, Asmit and Simon, Philipp S. and Chatterjee, Ruchira and Lassalle, Louise and Doyle, Margaret and Bogacz, Isabel and Kim, In-Sik and Cheah, Mun Hon and Gul, Sheraz and de Lichtenberg, Casper and Chernev, Petko and Pham, Cindy C. and Young, Iris D. and Carbajo, Sergio and Fuller, Franklin D. and Alonso-Mori, Roberto and Batyuk, Alex and Sutherlin, Kyle D. and Brewster, Aaron S. and Bolotovsky, Robert and Mendez, Derek and Holton, James M. and Moriarty, Nigel W. and Adams, Paul D. and Bergmann, Uwe and Sauter, Nicholas K. and Dobbek, Holger and Messinger, Johannes and Zouni, Athina and Kern, Jan and Yachandra, Vittal K. and Yano, Junko},
	month = nov,
	year = {2021},
	note = {Publisher: Nature Publishing Group},
	keywords = {Bioenergetics, Structural biology, X-ray crystallography},
	pages = {6531},
}

Light-driven oxidation of water to molecular oxygen is catalyzed by the oxygen-evolving complex (OEC) in Photosystem II (PS II). This multi-electron, multi-proton catalysis requires the transport of two water molecules to and four protons from the OEC. A high-resolution 1.89 Å structure obtained by averaging all the S states and refining the data of various time points during the S2 to S3 transition has provided better visualization of the potential pathways for substrate water insertion and proton release. Our results indicate that the O1 channel is the likely water intake pathway, and the Cl1 channel is the likely proton release pathway based on the structural rearrangements of water molecules and amino acid side chains along these channels. In particular in the Cl1 channel, we suggest that residue D1-E65 serves as a gate for proton transport by minimizing the back reaction. The results show that the water oxidation reaction at the OEC is well coordinated with the amino acid side chains and the H-bonding network over the entire length of the channels, which is essential in shuttling substrate waters and protons.

@article{ekspong_solar-driven_2021,
	title = {Solar-{Driven} {Water} {Splitting} at 13.8\% {Solar}-to-{Hydrogen} {Efficiency} by an {Earth}-{Abundant} {Electrolyzer}},
	volume = {9},
	url = {https://doi.org/10.1021/acssuschemeng.1c03565},
	doi = {10.1021/acssuschemeng.1c03565},
	abstract = {We present the synthesis and characterization of an efficient and low cost solar-driven electrolyzer consisting of Earth-abundant materials. The trimetallic NiFeMo electrocatalyst takes the shape of nanometer-sized flakes anchored to a fully carbon-based current collector comprising a nitrogen-doped carbon nanotube network, which in turn is grown on a carbon fiber paper support. This catalyst electrode contains solely Earth-abundant materials, and the carbon fiber support renders it effective despite a low metal content. Notably, a bifunctional catalyst–electrode pair exhibits a low total overpotential of 450 mV to drive a full water-splitting reaction at a current density of 10 mA cm–2 and a measured hydrogen Faradaic efficiency of ∼100\%. We combine the catalyst–electrode pair with solution-processed perovskite solar cells to form a lightweight solar-driven water-splitting device with a high peak solar-to-fuel conversion efficiency of 13.8\%.},
	number = {42},
	urldate = {2024-10-16},
	journal = {ACS Sustainable Chemistry \& Engineering},
	author = {Ekspong, Joakim and Larsen, Christian and Stenberg, Jonas and Kwong, Wai Ling and Wang, Jia and Zhang, Jinbao and Johansson, Erik M. J. and Messinger, Johannes and Edman, Ludvig and Wågberg, Thomas},
	month = oct,
	year = {2021},
	note = {Publisher: American Chemical Society},
	pages = {14070--14078},
}

We present the synthesis and characterization of an efficient and low cost solar-driven electrolyzer consisting of Earth-abundant materials. The trimetallic NiFeMo electrocatalyst takes the shape of nanometer-sized flakes anchored to a fully carbon-based current collector comprising a nitrogen-doped carbon nanotube network, which in turn is grown on a carbon fiber paper support. This catalyst electrode contains solely Earth-abundant materials, and the carbon fiber support renders it effective despite a low metal content. Notably, a bifunctional catalyst–electrode pair exhibits a low total overpotential of 450 mV to drive a full water-splitting reaction at a current density of 10 mA cm–2 and a measured hydrogen Faradaic efficiency of ∼100%. We combine the catalyst–electrode pair with solution-processed perovskite solar cells to form a lightweight solar-driven water-splitting device with a high peak solar-to-fuel conversion efficiency of 13.8%.

@article{lichtenberg_exchange_2021,
	title = {The exchange of the fast substrate water in the {S2} state of photosystem {II} is limited by diffusion of bulk water through channels – implications for the water oxidation mechanism},
	volume = {12},
	issn = {2041-6539},
	url = {https://pubs.rsc.org/en/content/articlelanding/2021/sc/d1sc02265b},
	doi = {10.1039/D1SC02265B},
	abstract = {The molecular oxygen we breathe is produced from water-derived oxygen species bound to the Mn4CaO5 cluster in photosystem II (PSII). Present research points to the central oxo-bridge O5 as the ‘slow exchanging substrate water (Ws)’, while, in the S2 state, the terminal water ligands W2 and W3 are both discussed as the ‘fast exchanging substrate water (Wf)’. A critical point for the assignment of Wf is whether or not its exchange with bulk water is limited by barriers in the channels leading to the Mn4CaO5 cluster. In this study, we measured the rates of H216O/H218O substrate water exchange in the S2 and S3 states of PSII core complexes from wild-type (WT) Synechocystis sp. PCC 6803, and from two mutants, D1-D61A and D1-E189Q, that are expected to alter water access via the Cl1/O4 channels and the O1 channel, respectively. We found that the exchange rates of Wf and Ws were unaffected by the E189Q mutation (O1 channel), but strongly perturbed by the D61A mutation (Cl1/O4 channel). It is concluded that all channels have restrictions limiting the isotopic equilibration of the inner water pool near the Mn4CaO5 cluster, and that D61 participates in one such barrier. In the D61A mutant this barrier is lowered so that Wf exchange occurs more rapidly. This finding removes the main argument against Ca-bound W3 as fast substrate water in the S2 state, namely the indifference of the rate of Wf exchange towards Ca/Sr substitution.},
	language = {en},
	number = {38},
	urldate = {2024-10-16},
	journal = {Chemical Science},
	author = {Lichtenberg, Casper de and Kim, Christopher J. and Chernev, Petko and Debus, Richard J. and Messinger, Johannes},
	month = oct,
	year = {2021},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {12763--12775},
}

The molecular oxygen we breathe is produced from water-derived oxygen species bound to the Mn4CaO5 cluster in photosystem II (PSII). Present research points to the central oxo-bridge O5 as the ‘slow exchanging substrate water (Ws)’, while, in the S2 state, the terminal water ligands W2 and W3 are both discussed as the ‘fast exchanging substrate water (Wf)’. A critical point for the assignment of Wf is whether or not its exchange with bulk water is limited by barriers in the channels leading to the Mn4CaO5 cluster. In this study, we measured the rates of H216O/H218O substrate water exchange in the S2 and S3 states of PSII core complexes from wild-type (WT) Synechocystis sp. PCC 6803, and from two mutants, D1-D61A and D1-E189Q, that are expected to alter water access via the Cl1/O4 channels and the O1 channel, respectively. We found that the exchange rates of Wf and Ws were unaffected by the E189Q mutation (O1 channel), but strongly perturbed by the D61A mutation (Cl1/O4 channel). It is concluded that all channels have restrictions limiting the isotopic equilibration of the inner water pool near the Mn4CaO5 cluster, and that D61 participates in one such barrier. In the D61A mutant this barrier is lowered so that Wf exchange occurs more rapidly. This finding removes the main argument against Ca-bound W3 as fast substrate water in the S2 state, namely the indifference of the rate of Wf exchange towards Ca/Sr substitution.

@article{de_lichtenberg_d1-v185n_2021,
	title = {The {D1}-{V185N} mutation alters substrate water exchange by stabilizing alternative structures of the {Mn4Ca}-cluster in photosystem {II}},
	volume = {1862},
	issn = {0005-2728},
	url = {https://www.sciencedirect.com/science/article/pii/S0005272820301699},
	doi = {10.1016/j.bbabio.2020.148319},
	abstract = {In photosynthesis, the oxygen-evolving complex (OEC) of the pigment-protein complex photosystem II (PSII) orchestrates the oxidation of water. Introduction of the V185N mutation into the D1 protein was previously reported to drastically slow O2-release and strongly perturb the water network surrounding the Mn4Ca cluster. Employing time-resolved membrane inlet mass spectrometry, we measured here the H218O/H216O-exchange kinetics of the fast (Wf) and slow (Ws) exchanging substrate waters bound in the S1, S2 and S3 states to the Mn4Ca cluster of PSII core complexes isolated from wild type and D1-V185N strains of Synechocystis sp. PCC 6803. We found that the rate of exchange for Ws was increased in the S1 and S2 states, while both Wf and Ws exchange rates were decreased in the S3 state. Additionally, we used EPR spectroscopy to characterize the Mn4Ca cluster and its interaction with the redox active D1-Tyr161 (YZ). In the S2 state, we observed a greatly diminished multiline signal in the V185N-PSII that could be recovered by addition of ammonia. The split signal in the S1 state was not affected, while the split signal in the S3 state was absent in the D1-V185N mutant. These findings are rationalized by the proposal that the N185 residue stabilizes the binding of an additional water-derived ligand at the Mn1 site of the Mn4Ca cluster via hydrogen bonding. Implications for the sites of substrate water binding are discussed.},
	number = {1},
	urldate = {2024-10-16},
	journal = {Biochimica et Biophysica Acta (BBA) - Bioenergetics},
	author = {de Lichtenberg, Casper and Avramov, Anton P. and Zhang, Minquan and Mamedov, Fikret and Burnap, Robert L. and Messinger, Johannes},
	month = jan,
	year = {2021},
	keywords = {EPR, Manganese cluster, O-O bond formation, Photosystem II, Substrate water exchange, Water oxidation},
	pages = {148319},
}

In photosynthesis, the oxygen-evolving complex (OEC) of the pigment-protein complex photosystem II (PSII) orchestrates the oxidation of water. Introduction of the V185N mutation into the D1 protein was previously reported to drastically slow O2-release and strongly perturb the water network surrounding the Mn4Ca cluster. Employing time-resolved membrane inlet mass spectrometry, we measured here the H218O/H216O-exchange kinetics of the fast (Wf) and slow (Ws) exchanging substrate waters bound in the S1, S2 and S3 states to the Mn4Ca cluster of PSII core complexes isolated from wild type and D1-V185N strains of Synechocystis sp. PCC 6803. We found that the rate of exchange for Ws was increased in the S1 and S2 states, while both Wf and Ws exchange rates were decreased in the S3 state. Additionally, we used EPR spectroscopy to characterize the Mn4Ca cluster and its interaction with the redox active D1-Tyr161 (YZ). In the S2 state, we observed a greatly diminished multiline signal in the V185N-PSII that could be recovered by addition of ammonia. The split signal in the S1 state was not affected, while the split signal in the S3 state was absent in the D1-V185N mutant. These findings are rationalized by the proposal that the N185 residue stabilizes the binding of an additional water-derived ligand at the Mn1 site of the Mn4Ca cluster via hydrogen bonding. Implications for the sites of substrate water binding are discussed.

@article{boniolo_electronic_2021,
	title = {Electronic and geometric structure effects on one-electron oxidation of first-row transition metals in the same ligand framework},
	volume = {50},
	issn = {1477-9234},
	url = {https://pubs.rsc.org/en/content/articlelanding/2021/dt/d0dt03695a},
	doi = {10.1039/D0DT03695A},
	abstract = {Developing new transition metal catalysts requires understanding of how both metal and ligand properties determine reactivity. Since metal complexes bearing ligands of the Py5 family (2,6-bis-[(2-pyridyl)methyl]pyridine) have been employed in many fields in the past 20 years, we set out here to understand their redox properties by studying a series of base metal ions (M = Mn, Fe, Co, and Ni) within the Py5OH (pyridine-2,6-diylbis[di-(pyridin-2-yl)methanol]) variant. Both reduced (MII) and the one-electron oxidized (MIII) species were carefully characterized using a combination of X-ray crystallography, X-ray absorption spectroscopy, cyclic voltammetry, and density-functional theory calculations. The observed metal–ligand interactions and electrochemical properties do not always follow consistent trends along the periodic table. We demonstrate that this observation cannot be explained by only considering orbital and geometric relaxation, and that spin multiplicity changes needed to be included into the DFT calculations to reproduce and understand these trends. In addition, exchange reactions of the sixth ligand coordinated to the metal, were analysed. Finally, by including published data of the extensively characterised Py5OMe (pyridine-2,6-diylbis[di-(pyridin-2-yl)methoxymethane])complexes, the special characteristics of the less common Py5OH ligand were extracted. This comparison highlights the non-innocent effect of the distal OH functionalization on the geometry, and consequently on the electronic structure of the metal complexes. Together, this gives a complete analysis of metal and ligand degrees of freedom for these base metal complexes, while also providing general insights into how to control electrochemical processes of transition metal complexes.},
	language = {en},
	number = {2},
	urldate = {2024-10-16},
	journal = {Dalton Transactions},
	author = {Boniolo, Manuel and Chernev, Petko and Cheah, Mun Hon and Heizmann, Philipp A. and Huang, Ping and Shylin, Sergii I. and Salhi, Nessima and Hossain, Md Kamal and Gupta, Arvind K. and Messinger, Johannes and Thapper, Anders and Lundberg, Marcus},
	month = jan,
	year = {2021},
	note = {Publisher: The Royal Society of Chemistry},
	pages = {660--674},
}

Developing new transition metal catalysts requires understanding of how both metal and ligand properties determine reactivity. Since metal complexes bearing ligands of the Py5 family (2,6-bis-[(2-pyridyl)methyl]pyridine) have been employed in many fields in the past 20 years, we set out here to understand their redox properties by studying a series of base metal ions (M = Mn, Fe, Co, and Ni) within the Py5OH (pyridine-2,6-diylbis[di-(pyridin-2-yl)methanol]) variant. Both reduced (MII) and the one-electron oxidized (MIII) species were carefully characterized using a combination of X-ray crystallography, X-ray absorption spectroscopy, cyclic voltammetry, and density-functional theory calculations. The observed metal–ligand interactions and electrochemical properties do not always follow consistent trends along the periodic table. We demonstrate that this observation cannot be explained by only considering orbital and geometric relaxation, and that spin multiplicity changes needed to be included into the DFT calculations to reproduce and understand these trends. In addition, exchange reactions of the sixth ligand coordinated to the metal, were analysed. Finally, by including published data of the extensively characterised Py5OMe (pyridine-2,6-diylbis[di-(pyridin-2-yl)methoxymethane])complexes, the special characteristics of the less common Py5OH ligand were extracted. This comparison highlights the non-innocent effect of the distal OH functionalization on the geometry, and consequently on the electronic structure of the metal complexes. Together, this gives a complete analysis of metal and ligand degrees of freedom for these base metal complexes, while also providing general insights into how to control electrochemical processes of transition metal complexes.

@article{edesi_root_2021,
	title = {Root {Rot} {Resistance} {Locus} {PaLAR3} {Is} {Delivered} by {Somatic} {Embryogenesis} ({SE}) {Pipeline} in {Norway} {Spruce} ({Picea} abies ({L}.) {Karst}.)},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/12/2/193},
	doi = {10.3390/f12020193},
	abstract = {Research Highlights: The Norway spruce somatic embryogenesis (SE) pipeline is suitable for multiplication of material with root rot resistance traits. Background and Objectives: Heterobasidion root rot is the economically most severe forest pathogen in Europe, reducing the benefit of planting elite forest material. In this study, the SE-propagation ability of elite Norway spruce material carrying root rot resistance traits was studied. Materials and Methods: We analyzed the presence of the root rot resistance locus PaLAR3B among 80 Finnish progeny-tested Norway spruce plus-trees used for SE-plant production as well as in 241 SE lines (genotypes) derived from them. Seven full-sib families with lines having either AA, AB, or BB genotype for PaLAR3 locus were further studied for their SE-plant propagation ability. Results: The results indicate that 47.5\% of the studied elite trees carry the PaLAR3B allele (45\% are heterozygous and 2.5\% homozygous). The resistance allele was present among the SE lines as expected based on Mendelian segregation and did not interfere with somatic embryo production capacity. All embryos from PaLAR3 genotypes germinated well and emblings were viable in the end of first growing season. However, in three families, PaLAR3B homo- or heterozygotes had 23.2\% to 32.1\% lower viability compared to their respective hetero- or PaLAR3A homozygotes. Conclusions: There is no trade-off between root rot resistance locus PaLAR3B and somatic embryo production ability, but the allele may interfere with Norway spruce embling establishment.},
	language = {en},
	number = {2},
	urldate = {2024-10-16},
	journal = {Forests},
	author = {Edesi, Jaanika and Tikkinen, Mikko and Elfstrand, Malin and Olson, Åke and Varis, Saila and Egertsdotter, Ulrika and Aronen, Tuija},
	month = feb,
	year = {2021},
	note = {Number: 2
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {genomic selection, root rot resistance, somatic embryogenesis, vegetative propagation},
	pages = {193},
}

Research Highlights: The Norway spruce somatic embryogenesis (SE) pipeline is suitable for multiplication of material with root rot resistance traits. Background and Objectives: Heterobasidion root rot is the economically most severe forest pathogen in Europe, reducing the benefit of planting elite forest material. In this study, the SE-propagation ability of elite Norway spruce material carrying root rot resistance traits was studied. Materials and Methods: We analyzed the presence of the root rot resistance locus PaLAR3B among 80 Finnish progeny-tested Norway spruce plus-trees used for SE-plant production as well as in 241 SE lines (genotypes) derived from them. Seven full-sib families with lines having either AA, AB, or BB genotype for PaLAR3 locus were further studied for their SE-plant propagation ability. Results: The results indicate that 47.5% of the studied elite trees carry the PaLAR3B allele (45% are heterozygous and 2.5% homozygous). The resistance allele was present among the SE lines as expected based on Mendelian segregation and did not interfere with somatic embryo production capacity. All embryos from PaLAR3 genotypes germinated well and emblings were viable in the end of first growing season. However, in three families, PaLAR3B homo- or heterozygotes had 23.2% to 32.1% lower viability compared to their respective hetero- or PaLAR3A homozygotes. Conclusions: There is no trade-off between root rot resistance locus PaLAR3B and somatic embryo production ability, but the allele may interfere with Norway spruce embling establishment.

@article{hu_genome_2021,
	title = {Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn},
	volume = {12},
	copyright = {2021 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-021-21380-4},
	doi = {10.1038/s41467-021-21380-4},
	abstract = {Sweet corn is one of the most important vegetables in the United States and Canada. Here, we present a de novo assembly of a sweet corn inbred line Ia453 with the mutated shrunken2-reference allele (Ia453-sh2). This mutation accumulates more sugar and is present in most commercial hybrids developed for the processing and fresh markets. The ten pseudochromosomes cover 92\% of the total assembly and 99\% of the estimated genome size, with a scaffold N50 of 222.2 Mb. This reference genome completely assembles the large structural variation that created the mutant sh2-R allele. Furthermore, comparative genomics analysis with six field corn genomes highlights differences in single-nucleotide polymorphisms, structural variations, and transposon composition. Phylogenetic analysis of 5,381 diverse maize and teosinte accessions reveals genetic relationships between sweet corn and other types of maize. Our results show evidence for a common origin in northern Mexico for modern sweet corn in the U.S. Finally, population genomic analysis identifies regions of the genome under selection and candidate genes associated with sweet corn traits, such as early flowering, endosperm composition, plant and tassel architecture, and kernel row number. Our study provides a high-quality reference-genome sequence to facilitate comparative genomics, functional studies, and genomic-assisted breeding for sweet corn.},
	language = {en},
	number = {1},
	urldate = {2024-03-22},
	journal = {Nature Communications},
	author = {Hu, Ying and Colantonio, Vincent and Müller, Bárbara S. F. and Leach, Kristen A. and Nanni, Adalena and Finegan, Christina and Wang, Bo and Baseggio, Matheus and Newton, Carter J. and Juhl, Emily M. and Hislop, Lillian and Gonzalez, Juan M. and Rios, Esteban F. and Hannah, L. Curtis and Swarts, Kelly and Gore, Michael A. and Hennen-Bierwagen, Tracie A. and Myers, Alan M. and Settles, A. Mark and Tracy, William F. and Resende, Marcio F. R.},
	month = feb,
	year = {2021},
	note = {Publisher: Nature Publishing Group},
	keywords = {Agricultural genetics, Evolutionary biology, Plant breeding},
	pages = {1227},
}

Sweet corn is one of the most important vegetables in the United States and Canada. Here, we present a de novo assembly of a sweet corn inbred line Ia453 with the mutated shrunken2-reference allele (Ia453-sh2). This mutation accumulates more sugar and is present in most commercial hybrids developed for the processing and fresh markets. The ten pseudochromosomes cover 92% of the total assembly and 99% of the estimated genome size, with a scaffold N50 of 222.2 Mb. This reference genome completely assembles the large structural variation that created the mutant sh2-R allele. Furthermore, comparative genomics analysis with six field corn genomes highlights differences in single-nucleotide polymorphisms, structural variations, and transposon composition. Phylogenetic analysis of 5,381 diverse maize and teosinte accessions reveals genetic relationships between sweet corn and other types of maize. Our results show evidence for a common origin in northern Mexico for modern sweet corn in the U.S. Finally, population genomic analysis identifies regions of the genome under selection and candidate genes associated with sweet corn traits, such as early flowering, endosperm composition, plant and tassel architecture, and kernel row number. Our study provides a high-quality reference-genome sequence to facilitate comparative genomics, functional studies, and genomic-assisted breeding for sweet corn.

@article{yost_situ_2021,
	title = {An \textit{in situ} and morphometric study of maize (\textit{{Zea} mays} {L}.) cob rondel phytoliths from {Southwestern} {North} {American} landraces},
	volume = {35},
	issn = {2352-409X},
	url = {https://www.sciencedirect.com/science/article/pii/S2352409X2030523X},
	doi = {10.1016/j.jasrep.2020.102732},
	abstract = {We present the first comprehensive computer-assisted morphometric analysis of microscopic rondel11As per the International Code for Phytolith Nomenclature 2.0 the names of recognized phytolith morphotypes are written in small caps in this report (Neumann et al., 2019). phytoliths (plant opal microfossils) produced in the cobs of 24 historic Southwestern North American landraces of maize (Zea mays L.) after all were grown in a well-documented agronomic field study. We also present an in situ study of the location of rondel phytolith production within the maize cob and provide a detailed review of previous maize phytolith studies. We found that glumes contained abundant rondel phytoliths throughout the tissue; however, lemma/palea tissue contained no phytoliths. In contrast, cupule tissue had some areas with abundant phytoliths, some with fewer scattered phytoliths, and vast areas that contained no rondel phytoliths. The rondel-rich areas appear to be where the glumes had once attached to the cupule and may be remnants of glume tissue adhering to the cupule. From the morphometric study, we found there were significant differences in the size morphometries of glume rondels depending on their cob location (top, middle, base) but no significant differences in shape morphometries. Using shape morphometries, we could not discriminate reliably among maize cob rondel phytoliths produced by the diverse landraces considered. The inclusion of morphometrics from areas in addition to or in combination with the outer periclinal surface may allow for some discrimination of maize landraces and is an avenue that should be explored further. Although our approach was not successful at identifying differences between essentially modern landraces, there may be significant rondel phytolith morphometric differences between wild, progenitor, and domesticated Zea.},
	urldate = {2024-03-22},
	journal = {Journal of Archaeological Science: Reports},
	author = {Yost, Chad L. and Michas, McCaela and Adams, Karen R. and Swarts, Kelly and Puseman, Kathryn and Ball, Terry},
	month = feb,
	year = {2021},
	keywords = {Glumes, Landrace, Maize, Morphometrics, Phytoliths},
	pages = {102732},
}

We present the first comprehensive computer-assisted morphometric analysis of microscopic rondel11As per the International Code for Phytolith Nomenclature 2.0 the names of recognized phytolith morphotypes are written in small caps in this report (Neumann et al., 2019). phytoliths (plant opal microfossils) produced in the cobs of 24 historic Southwestern North American landraces of maize (Zea mays L.) after all were grown in a well-documented agronomic field study. We also present an in situ study of the location of rondel phytolith production within the maize cob and provide a detailed review of previous maize phytolith studies. We found that glumes contained abundant rondel phytoliths throughout the tissue; however, lemma/palea tissue contained no phytoliths. In contrast, cupule tissue had some areas with abundant phytoliths, some with fewer scattered phytoliths, and vast areas that contained no rondel phytoliths. The rondel-rich areas appear to be where the glumes had once attached to the cupule and may be remnants of glume tissue adhering to the cupule. From the morphometric study, we found there were significant differences in the size morphometries of glume rondels depending on their cob location (top, middle, base) but no significant differences in shape morphometries. Using shape morphometries, we could not discriminate reliably among maize cob rondel phytoliths produced by the diverse landraces considered. The inclusion of morphometrics from areas in addition to or in combination with the outer periclinal surface may allow for some discrimination of maize landraces and is an avenue that should be explored further. Although our approach was not successful at identifying differences between essentially modern landraces, there may be significant rondel phytolith morphometric differences between wild, progenitor, and domesticated Zea.

@article{swarts_joint_2021,
	title = {Joint analysis of days to flowering reveals independent temperate adaptations in maize},
	volume = {126},
	copyright = {2021 The Author(s), under exclusive licence to The Genetics Society},
	issn = {1365-2540},
	url = {https://www.nature.com/articles/s41437-021-00422-z},
	doi = {10.1038/s41437-021-00422-z},
	abstract = {Domesticates are an excellent model for understanding biological consequences of rapid climate change. Maize (Zea mays ssp. mays) was domesticated from a tropical grass yet is widespread across temperate regions today. We investigate the biological basis of temperate adaptation in diverse structured nested association mapping (NAM) populations from China, Europe (Dent and Flint) and the United States as well as in the Ames inbred diversity panel, using days to flowering as a proxy. Using cross-population prediction, where high prediction accuracy derives from overall genomic relatedness, shared genetic architecture, and sufficient diversity in the training population, we identify patterns in predictive ability across the five populations. To identify the source of temperate adapted alleles in these populations, we predict top associated genome-wide association study (GWAS) identified loci in a Random Forest Classifier using independent temperate–tropical North American populations based on lines selected from Hapmap3 as predictors. We find that North American populations are well predicted (AUC equals 0.89 and 0.85 for Ames and USNAM, respectively), European populations somewhat well predicted (AUC equals 0.59 and 0.67 for the Dent and Flint panels, respectively) and that the Chinese population is not predicted well at all (AUC is 0.47), suggesting an independent adaptation process for early flowering in China. Multiple adaptations for the complex trait days to flowering in maize provide hope for similar natural systems under climate change.},
	language = {en},
	number = {6},
	urldate = {2024-03-22},
	journal = {Heredity},
	author = {Swarts, Kelly and Bauer, Eva and Glaubitz, Jeffrey C. and Ho, Tiffany and Johnson, Lynn and Li, Yongxiang and Li, Yu and Miller, Zachary and Romay, Cinta and Schön, Chris-Carolin and Wang, Tianyu and Zhang, Zhiwu and Buckler, Edward S. and Bradbury, Peter},
	month = jun,
	year = {2021},
	note = {Publisher: Nature Publishing Group},
	keywords = {Evolutionary genetics, Quantitative trait},
	pages = {929--941},
}

Domesticates are an excellent model for understanding biological consequences of rapid climate change. Maize (Zea mays ssp. mays) was domesticated from a tropical grass yet is widespread across temperate regions today. We investigate the biological basis of temperate adaptation in diverse structured nested association mapping (NAM) populations from China, Europe (Dent and Flint) and the United States as well as in the Ames inbred diversity panel, using days to flowering as a proxy. Using cross-population prediction, where high prediction accuracy derives from overall genomic relatedness, shared genetic architecture, and sufficient diversity in the training population, we identify patterns in predictive ability across the five populations. To identify the source of temperate adapted alleles in these populations, we predict top associated genome-wide association study (GWAS) identified loci in a Random Forest Classifier using independent temperate–tropical North American populations based on lines selected from Hapmap3 as predictors. We find that North American populations are well predicted (AUC equals 0.89 and 0.85 for Ames and USNAM, respectively), European populations somewhat well predicted (AUC equals 0.59 and 0.67 for the Dent and Flint panels, respectively) and that the Chinese population is not predicted well at all (AUC is 0.47), suggesting an independent adaptation process for early flowering in China. Multiple adaptations for the complex trait days to flowering in maize provide hope for similar natural systems under climate change.

@article{marhavy_histochemical_2021,
	title = {Histochemical {Staining} of {Suberin} in {Plant} {Roots}},
	volume = {11},
	issn = {2331-8325},
	url = {https://bio-protocol.org/e3904},
	doi = {10/gkcvgh},
	language = {en},
	number = {3},
	urldate = {2021-06-03},
	journal = {BIO-PROTOCOL},
	author = {Marhavý, Peter and Siddique, Shahid},
	year = {2021},
}

@article{marhavy_peter_histochemical_2021,
	title = {Histochemical {Staining} of {Suberin} in {Plant} {Roots}},
	volume = {11},
	url = {https://bio-protocol.org/en/bpdetail?id=3904&type=0},
	doi = {10.21769/BioProtoc.3904},
	abstract = {Histological stains are useful tools for characterizing cell shape, arrangement and the material they are made from. Stains can be used individually or simultaneously to mark different cell structures or polymers within the same cells, and to visualize them in different colors. Histological stains can be combined with genetically-encoded fluorescent proteins, which are useful for understanding of plant development. To visualize suberin lamellae by fluorescent microscopy, we improved a histological staining procedure with the dyes Fluorol Yellow 088 and aniline blue. In the complex plant organs such as roots, suberin lamellae are deposited deep within the root on the endodermal cell wall. Our procedure yields reliable and detailed images that can be used to determine the suberin pattern in root cells. The main advantage of this protocol is its efficiency, the detailed visualization of suberin localization it generates in the root, and the possibility of returning to the confocal images to analyze and re-evaluate data if necessary.},
	language = {en},
	number = {2},
	urldate = {2024-02-08},
	journal = {Bio-protocol},
	author = {{Marhavý, Peter} and {Siddique, Shahid}},
	month = feb,
	year = {2021},
	pages = {e3904},
}

Histological stains are useful tools for characterizing cell shape, arrangement and the material they are made from. Stains can be used individually or simultaneously to mark different cell structures or polymers within the same cells, and to visualize them in different colors. Histological stains can be combined with genetically-encoded fluorescent proteins, which are useful for understanding of plant development. To visualize suberin lamellae by fluorescent microscopy, we improved a histological staining procedure with the dyes Fluorol Yellow 088 and aniline blue. In the complex plant organs such as roots, suberin lamellae are deposited deep within the root on the endodermal cell wall. Our procedure yields reliable and detailed images that can be used to determine the suberin pattern in root cells. The main advantage of this protocol is its efficiency, the detailed visualization of suberin localization it generates in the root, and the possibility of returning to the confocal images to analyze and re-evaluate data if necessary.

@article{jeon_recent_2021,
	title = {Recent advances in peptide signaling during {Arabidopsis} root development},
	volume = {72},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erab050},
	doi = {10.1093/jxb/erab050},
	abstract = {Roots provide the plant with water and nutrients and anchor it in a substrate. Root development is controlled by plant hormones and various sets of transcription factors. Recently, various small peptides and their cognate receptors have been identified as controlling root development. Small peptides bind to membrane-localized receptor-like kinases, inducing their dimerization with co-receptor proteins for signaling activation and giving rise to cellular signaling outputs. Small peptides function as local and long-distance signaling molecules involved in cell-to-cell communication networks, coordinating root development. In this review, we survey recent advances in the peptide ligand-mediated signaling pathways involved in the control of root development in Arabidopsis. We describe the interconnection between peptide signaling and conventional phytohormone signaling. Additionally, we discuss the diversity of identified peptide–receptor interactions during plant root development.},
	number = {8},
	urldate = {2023-11-14},
	journal = {Journal of Experimental Botany},
	author = {Jeon, Byeong Wook and Kim, Min-Jung and Pandey, Shashank K and Oh, Eunkyoo and Seo, Pil Joon and Kim, Jungmook},
	month = apr,
	year = {2021},
	pages = {2889--2902},
}

Roots provide the plant with water and nutrients and anchor it in a substrate. Root development is controlled by plant hormones and various sets of transcription factors. Recently, various small peptides and their cognate receptors have been identified as controlling root development. Small peptides bind to membrane-localized receptor-like kinases, inducing their dimerization with co-receptor proteins for signaling activation and giving rise to cellular signaling outputs. Small peptides function as local and long-distance signaling molecules involved in cell-to-cell communication networks, coordinating root development. In this review, we survey recent advances in the peptide ligand-mediated signaling pathways involved in the control of root development in Arabidopsis. We describe the interconnection between peptide signaling and conventional phytohormone signaling. Additionally, we discuss the diversity of identified peptide–receptor interactions during plant root development.

@article{guo_low_2021,
	title = {Low genetic diversity and population connectivity fuel vulnerability to climate change for the {Tertiary} relict pine {Pinus} bungeana},
	volume = {61},
	issn = {1759-6831},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/jse.12821},
	doi = {10.1111/jse.12821},
	abstract = {Endemic species are important components of regional biodiversity and hold the key to understanding local adaptation and evolutionary processes that shape species distributions. This study investigated the biogeographic history of a relict conifer Pinus bungeana Zucc. ex Endl. confined to central China. We examined genetic diversity in P. bungeana using genotyping-by-sequencing and chloroplast and mitochondrial DNA markers. We performed spatial and temporal inference of recent genetic and demographic changes, and dissected the impacts of geography and environmental gradients on population differentiation. We then projected P. bungeana's risk of decline under future climates. We found extremely low nucleotide diversity (average π 0.0014), and strong population structure (global FST 0.234) even at regional scales, reflecting long-term isolation in small populations. The species experienced severe bottlenecks in the early Pliocene and continued to decline in the Pleistocene in the western distribution, whereas the east expanded recently. Local adaptation played a small (8\%) but significant role in population diversity. Low genetic diversity in fragmented populations makes the species highly vulnerable to climate change, particularly in marginal and relict populations. We suggest that conservation efforts should focus on enhancing gene pool and population growth through assisted migration within each genetic cluster to reduce the risk of further genetic drift and extinction.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Journal of Systematics and Evolution},
	author = {Guo, Jing-Fang and Wang, Baosheng and Liu, Zhan-Lin and Mao, Jian-Feng and Wang, Xiao-Ru and Zhao, Wei},
	month = dec,
	year = {2021},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/jse.12821},
	keywords = {Pinus bungeana, climate relict, genetic diversity, genomic offset, migration barrier, population bottleneck},
	pages = {143--156},
}

Endemic species are important components of regional biodiversity and hold the key to understanding local adaptation and evolutionary processes that shape species distributions. This study investigated the biogeographic history of a relict conifer Pinus bungeana Zucc. ex Endl. confined to central China. We examined genetic diversity in P. bungeana using genotyping-by-sequencing and chloroplast and mitochondrial DNA markers. We performed spatial and temporal inference of recent genetic and demographic changes, and dissected the impacts of geography and environmental gradients on population differentiation. We then projected P. bungeana's risk of decline under future climates. We found extremely low nucleotide diversity (average π 0.0014), and strong population structure (global FST 0.234) even at regional scales, reflecting long-term isolation in small populations. The species experienced severe bottlenecks in the early Pliocene and continued to decline in the Pleistocene in the western distribution, whereas the east expanded recently. Local adaptation played a small (8%) but significant role in population diversity. Low genetic diversity in fragmented populations makes the species highly vulnerable to climate change, particularly in marginal and relict populations. We suggest that conservation efforts should focus on enhancing gene pool and population growth through assisted migration within each genetic cluster to reduce the risk of further genetic drift and extinction.

@article{shen_chromosome-scale_2021,
	title = {Chromosome-{Scale} {Genome} {Assembly} for {Chinese} {Sour} {Jujube} and {Insights} {Into} {Its} {Genome} {Evolution} and {Domestication} {Signature}},
	volume = {12},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2021.773090},
	doi = {10.3389/fpls.2021.773090},
	abstract = {Sour or wild jujube fruits and dried seeds are popular food all over the world. In this study, we reported a high-quality genome assembly of sour jujube (Ziziphus jujuba Mill. var. spinosa), with a size of 406 Mbp and scaffold N50 of 30.3 Mbp, which experienced only γ hexaploidization event, without recent genome duplication. Population structure analysis identified four jujube subgroups (two domesticated ones, i.e., D1 in West China and D2 in East/SouthEast China, semi-wild, and wild), which underwent an evolutionary history of a significant decline of effective population size during the Last Glacial Period. The respective selection signatures of three subgroups were discovered, such as strong peaks on chromosomes \#3 in D1, \#1 in D2, and \#4 in wild. Genes under the most significant selection on chromosomes \#4 in wild were confirmed to be involved in fruit variations among jujube accessions, in transcriptomic analysis. Our study offered novel insights into the jujube population structure and domestication and provided valuable genomic resources for jujube improvement in stress response and fruit flavor in the future.},
	urldate = {2023-04-27},
	journal = {Frontiers in Plant Science},
	author = {Shen, Lian-Ying and Luo, Hang and Wang, Xiao-Ling and Wang, Xue-Meng and Qiu, Xiao-Jing and Liu, Hui and Zhou, Shan-Shan and Jia, Kai-Hua and Nie, Shuai and Bao, Yu-Tao and Zhang, Ren-Gang and Yun, Quan-Zheng and Chai, Ying-Hui and Lu, Jin-Ying and Li, Yu and Zhao, Shu-Wei and Mao, Jian-Feng and Jia, Shan-Gang and Mao, Yong-Min},
	year = {2021},
}

Sour or wild jujube fruits and dried seeds are popular food all over the world. In this study, we reported a high-quality genome assembly of sour jujube (Ziziphus jujuba Mill. var. spinosa), with a size of 406 Mbp and scaffold N50 of 30.3 Mbp, which experienced only γ hexaploidization event, without recent genome duplication. Population structure analysis identified four jujube subgroups (two domesticated ones, i.e., D1 in West China and D2 in East/SouthEast China, semi-wild, and wild), which underwent an evolutionary history of a significant decline of effective population size during the Last Glacial Period. The respective selection signatures of three subgroups were discovered, such as strong peaks on chromosomes #3 in D1, #1 in D2, and #4 in wild. Genes under the most significant selection on chromosomes #4 in wild were confirmed to be involved in fruit variations among jujube accessions, in transcriptomic analysis. Our study offered novel insights into the jujube population structure and domestication and provided valuable genomic resources for jujube improvement in stress response and fruit flavor in the future.

@article{zhou_comprehensive_2021,
	title = {A comprehensive annotation dataset of intact {LTR} retrotransposons of 300 plant genomes},
	volume = {8},
	copyright = {2021 The Author(s)},
	issn = {2052-4463},
	url = {https://www.nature.com/articles/s41597-021-00968-x},
	doi = {10.1038/s41597-021-00968-x},
	abstract = {LTR retrotransposons (LTR-RTs) are ubiquitous and represent the dominant repeat element in plant genomes, playing important roles in functional variation, genome plasticity and evolution. With the advent of new sequencing technologies, a growing number of whole-genome sequences have been made publicly available, making it possible to carry out systematic analyses of LTR-RTs. However, a comprehensive and unified annotation of LTR-RTs in plant groups is still lacking. Here, we constructed a plant intact LTR-RTs dataset, which is designed to classify and annotate intact LTR-RTs with a standardized procedure. The dataset currently comprises a total of 2,593,685 intact LTR-RTs from genomes of 300 plant species representing 93 families of 46 orders. The dataset is accompanied by sequence, diverse structural and functional annotation, age determination and classification information associated with the LTR-RTs. This dataset will contribute valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.},
	language = {en},
	number = {1},
	urldate = {2023-04-27},
	journal = {Scientific Data},
	author = {Zhou, Shan-Shan and Yan, Xue-Mei and Zhang, Kai-Fu and Liu, Hui and Xu, Jie and Nie, Shuai and Jia, Kai-Hua and Jiao, Si-Qian and Zhao, Wei and Zhao, You-Jie and Porth, Ilga and El Kassaby, Yousry A. and Wang, Tongli and Mao, Jian-Feng},
	month = jul,
	year = {2021},
	note = {Number: 1
Publisher: Nature Publishing Group},
	keywords = {Data mining, Mobile elements},
	pages = {174},
}

LTR retrotransposons (LTR-RTs) are ubiquitous and represent the dominant repeat element in plant genomes, playing important roles in functional variation, genome plasticity and evolution. With the advent of new sequencing technologies, a growing number of whole-genome sequences have been made publicly available, making it possible to carry out systematic analyses of LTR-RTs. However, a comprehensive and unified annotation of LTR-RTs in plant groups is still lacking. Here, we constructed a plant intact LTR-RTs dataset, which is designed to classify and annotate intact LTR-RTs with a standardized procedure. The dataset currently comprises a total of 2,593,685 intact LTR-RTs from genomes of 300 plant species representing 93 families of 46 orders. The dataset is accompanied by sequence, diverse structural and functional annotation, age determination and classification information associated with the LTR-RTs. This dataset will contribute valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.

@article{jiao_variation_2021,
	title = {Variation in {Platycladus} orientalis ({Cupressaceae}) {Reproductive} {Output} and {Its} {Effect} on {Seed} {Orchard} {Crops}’ {Genetic} {Diversity}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	issn = {1999-4907},
	url = {https://www.mdpi.com/1999-4907/12/11/1429},
	doi = {10.3390/f12111429},
	abstract = {The genetic efficiency of seed orchards is crucial for determining seed crops’ genetic gain and diversity. Platycladus orientalis is a conifer tree of important ecological value in China. Here, we assessed the reproductive output (fertility) variation for 166 clones in a first-generation P. orientalis seed orchard over five years and across three years for each gender (female: 2017, 2018, and 2020 and male: 2017, 2019, and 2021). Fertility variation and genetic diversity parameters were estimated for each gender-year combination. The reproductive output (fertility) variation differed among years, provinces, clones nested within provinces, and ramets within clones. We observed asymmetry in the gender reproductive output and parental imbalance and determined their profound effects on the genetic diversity of these seed crops. The maleness index revealed the existence of female-biased or male-biased clones. When seeds from multiple individuals and years were blended, we found an increase in the effective number of parents (Np) and in genetic diversity (GD), and a reduced fertility variation (Ψ) in the seed orchard. When we set the effective number of parents (Np) to 30, the GD of the seed orchard could be maintained at more than 95\%. Thus, achieving genetic diversity balance in seed production can be accomplished through monitoring the fertility variation of orchards and through the utilization of the thereby generated information for the advanced generation of seed orchards.},
	language = {en},
	number = {11},
	urldate = {2023-04-27},
	journal = {Forests},
	author = {Jiao, Si-Qian and Li, Meiyu and Zhu, Yuan-Jiao and Zhou, Shan-Shan and Zhao, Shi-Wei and Li, Zhi-Chao and Bao, Yu-Tao and Shi, Tian-Le and Zhang, Hui-Jin and Yang, Xiao-Lei and Zhu, Ji-Jun and Porth, Ilga and El-Kassaby, Yousry A. and Cheng, Shi-Ping and Li, Yue and Mao, Jian-Feng},
	month = nov,
	year = {2021},
	note = {Number: 11
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {\textit{Platycladus orientalis}, effective parent number, fertility variation, parental balance, reproductive strobili production},
	pages = {1429},
}

The genetic efficiency of seed orchards is crucial for determining seed crops’ genetic gain and diversity. Platycladus orientalis is a conifer tree of important ecological value in China. Here, we assessed the reproductive output (fertility) variation for 166 clones in a first-generation P. orientalis seed orchard over five years and across three years for each gender (female: 2017, 2018, and 2020 and male: 2017, 2019, and 2021). Fertility variation and genetic diversity parameters were estimated for each gender-year combination. The reproductive output (fertility) variation differed among years, provinces, clones nested within provinces, and ramets within clones. We observed asymmetry in the gender reproductive output and parental imbalance and determined their profound effects on the genetic diversity of these seed crops. The maleness index revealed the existence of female-biased or male-biased clones. When seeds from multiple individuals and years were blended, we found an increase in the effective number of parents (Np) and in genetic diversity (GD), and a reduced fertility variation (Ψ) in the seed orchard. When we set the effective number of parents (Np) to 30, the GD of the seed orchard could be maintained at more than 95%. Thus, achieving genetic diversity balance in seed production can be accomplished through monitoring the fertility variation of orchards and through the utilization of the thereby generated information for the advanced generation of seed orchards.

@article{he_chromosome-scale_2021,
	title = {Chromosome-scale assembly of the genome of {Salix} dunnii reveals a male-heterogametic sex determination system on chromosome 7},
	volume = {21},
	issn = {1755-0998},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.13362},
	doi = {10.1111/1755-0998.13362},
	abstract = {Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads and Hi-C reads to assemble the first chromosome-scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328 Mb in total was assembled in 29 scaffolds, and includes 31,501 predicted genes. Analyses of short-read sequence data that included female and male plants suggested a male heterogametic sex-determining factor on chromosome 7, implying that, unlike the female heterogamety of most species in the genus Salix, male heterogamety evolved in the subgenus Salix. The S. dunnii sex-linked region occupies about 3.21 Mb of chromosome 7 in females (representing its position in the X chromosome), probably within a pericentromeric region. Our data suggest that this region is enriched for transposable element insertions, and about one-third of its 124 protein-coding genes were gained via duplications from other genome regions. We detect purifying selection on the genes that were ancestrally present in the region, though some have been lost. Transcriptome data from female and male individuals show more male- than female-biased genes in catkin and leaf tissues, and indicate enrichment for male-biased genes in the pseudo-autosomal regions. Our study provides valuable genomic resources for further studies of sex-determining regions in the family Salicaceae, and sex chromosome evolution.},
	language = {en},
	number = {6},
	urldate = {2023-04-27},
	journal = {Molecular Ecology Resources},
	author = {He, Li and Jia, Kai-Hua and Zhang, Ren-Gang and Wang, Yuan and Shi, Tian-Le and Li, Zhi-Chao and Zeng, Si-Wen and Cai, Xin-Jie and Wagner, Natascha Dorothea and Hörandl, Elvira and Muyle, Aline and Yang, Ke and Charlesworth, Deborah and Mao, Jian-Feng},
	year = {2021},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.13362},
	keywords = {XX/XY, gene expression, genome-wide association, long terminal repeat-retrotransposons, sex-linked region},
	pages = {1966--1982},
}

Sex determination systems in plants can involve either female or male heterogamety (ZW or XY, respectively). Here we used Illumina short reads, Oxford Nanopore Technologies (ONT) long reads and Hi-C reads to assemble the first chromosome-scale genome of a female willow tree (Salix dunnii), and to predict genes using transcriptome sequences and available databases. The final genome sequence of 328 Mb in total was assembled in 29 scaffolds, and includes 31,501 predicted genes. Analyses of short-read sequence data that included female and male plants suggested a male heterogametic sex-determining factor on chromosome 7, implying that, unlike the female heterogamety of most species in the genus Salix, male heterogamety evolved in the subgenus Salix. The S. dunnii sex-linked region occupies about 3.21 Mb of chromosome 7 in females (representing its position in the X chromosome), probably within a pericentromeric region. Our data suggest that this region is enriched for transposable element insertions, and about one-third of its 124 protein-coding genes were gained via duplications from other genome regions. We detect purifying selection on the genes that were ancestrally present in the region, though some have been lost. Transcriptome data from female and male individuals show more male- than female-biased genes in catkin and leaf tissues, and indicate enrichment for male-biased genes in the pseudo-autosomal regions. Our study provides valuable genomic resources for further studies of sex-determining regions in the family Salicaceae, and sex chromosome evolution.

@article{molina_arabidopsis_2021,
	title = {Arabidopsis cell wall composition determines disease resistance specificity and fitness},
	volume = {118},
	url = {https://www.pnas.org/doi/abs/10.1073/pnas.2010243118},
	doi = {10.1073/pnas.2010243118},
	abstract = {Plant cell walls are complex structures subject to dynamic remodeling in response to developmental and environmental cues and play essential functions in disease resistance responses. We tested the specific contribution of plant cell walls to immunity by determining the susceptibility of a set of Arabidopsis cell wall mutants (cwm) to pathogens with different parasitic styles: a vascular bacterium, a necrotrophic fungus, and a biotrophic oomycete. Remarkably, most cwm mutants tested (29/34; 85.3\%) showed alterations in their resistance responses to at least one of these pathogens in comparison to wild-type plants, illustrating the relevance of wall composition in determining disease-resistance phenotypes. We found that the enhanced resistance of cwm plants to the necrotrophic and vascular pathogens negatively impacted cwm fitness traits, such as biomass and seed yield. Enhanced resistance of cwm plants is not only mediated by canonical immune pathways, like those modulated by phytohormones or microbe-associated molecular patterns, which are not deregulated in the cwm tested. Pectin-enriched wall fractions isolated from cwm plants triggered immune responses in wild-type plants, suggesting that wall-mediated defensive pathways might contribute to cwm resistance. Cell walls of cwm plants show a high diversity of composition alterations as revealed by glycome profiling that detect specific wall carbohydrate moieties. Mathematical analysis of glycome profiling data identified correlations between the amounts of specific wall carbohydrate moieties and disease resistance phenotypes of cwm plants. These data support the relevant and specific function of plant wall composition in plant immune response modulation and in balancing disease resistance/development trade-offs.},
	number = {5},
	urldate = {2023-03-10},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Molina, Antonio and Miedes, Eva and Bacete, Laura and Rodríguez, Tinguaro and Mélida, Hugo and Denancé, Nicolas and Sánchez-Vallet, Andrea and Rivière, Marie-Pierre and López, Gemma and Freydier, Amandine and Barlet, Xavier and Pattathil, Sivakumar and Hahn, Michael and Goffner, Deborah},
	month = feb,
	year = {2021},
	note = {Publisher: Proceedings of the National Academy of Sciences},
	pages = {e2010243118},
}

Plant cell walls are complex structures subject to dynamic remodeling in response to developmental and environmental cues and play essential functions in disease resistance responses. We tested the specific contribution of plant cell walls to immunity by determining the susceptibility of a set of Arabidopsis cell wall mutants (cwm) to pathogens with different parasitic styles: a vascular bacterium, a necrotrophic fungus, and a biotrophic oomycete. Remarkably, most cwm mutants tested (29/34; 85.3%) showed alterations in their resistance responses to at least one of these pathogens in comparison to wild-type plants, illustrating the relevance of wall composition in determining disease-resistance phenotypes. We found that the enhanced resistance of cwm plants to the necrotrophic and vascular pathogens negatively impacted cwm fitness traits, such as biomass and seed yield. Enhanced resistance of cwm plants is not only mediated by canonical immune pathways, like those modulated by phytohormones or microbe-associated molecular patterns, which are not deregulated in the cwm tested. Pectin-enriched wall fractions isolated from cwm plants triggered immune responses in wild-type plants, suggesting that wall-mediated defensive pathways might contribute to cwm resistance. Cell walls of cwm plants show a high diversity of composition alterations as revealed by glycome profiling that detect specific wall carbohydrate moieties. Mathematical analysis of glycome profiling data identified correlations between the amounts of specific wall carbohydrate moieties and disease resistance phenotypes of cwm plants. These data support the relevant and specific function of plant wall composition in plant immune response modulation and in balancing disease resistance/development trade-offs.

@article{rebaque_cell_2021,
	title = {Cell wall-derived mixed-linked β-1,3/1,4-glucans trigger immune responses and disease resistance in plants},
	volume = {106},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15185},
	doi = {10.1111/tpj.15185},
	abstract = {Pattern-triggered immunity (PTI) is activated in plants upon recognition by pattern recognition receptors (PRRs) of damage- and microbe-associated molecular patterns (DAMPs and MAMPs) derived from plants or microorganisms, respectively. To understand better the plant mechanisms involved in the perception of carbohydrate-based structures recognized as DAMPs/MAMPs, we have studied the ability of mixed-linked β-1,3/1,4-glucans (MLGs), present in some plant and microbial cell walls, to trigger immune responses and disease resistance in plants. A range of MLG structures were tested for their capacity to induce PTI hallmarks, such as cytoplasmic Ca2+ elevations, reactive oxygen species production, phosphorylation of mitogen-activated protein kinases and gene transcriptional reprogramming. These analyses revealed that MLG oligosaccharides are perceived by Arabidopsis thaliana and identified a trisaccharide, β-d-cellobiosyl-(1,3)-β-d-glucose (MLG43), as the smallest MLG structure triggering strong PTI responses. These MLG43-mediated PTI responses are partially dependent on LysM PRRs CERK1, LYK4 and LYK5, as they were weaker in cerk1 and lyk4 lyk5 mutants than in wild-type plants. Cross-elicitation experiments between MLG43 and the carbohydrate MAMP chitohexaose [β-1,4-d-(GlcNAc)6], which is also perceived by these LysM PRRs, indicated that the mechanism of MLG43 recognition could differ from that of chitohexaose, which is fully impaired in cerk1 and lyk4 lyk5 plants. MLG43 treatment confers enhanced disease resistance in A. thaliana to the oomycete Hyaloperonospora arabidopsidis and in tomato and pepper to different bacterial and fungal pathogens. Our data support the classification of MLGs as a group of carbohydrate-based molecular patterns that are perceived by plants and trigger immune responses and disease resistance.},
	language = {en},
	number = {3},
	urldate = {2023-03-10},
	journal = {The Plant Journal},
	author = {Rebaque, Diego and del Hierro, Irene and López, Gemma and Bacete, Laura and Vilaplana, Francisco and Dallabernardina, Pietro and Pfrengle, Fabian and Jordá, Lucía and Sánchez-Vallet, Andrea and Pérez, Rosa and Brunner, Frédéric and Molina, Antonio and Mélida, Hugo},
	year = {2021},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.15185},
	keywords = {Arabidopsis thaliana, Capsicum annuum, Hyaloperonospora arabidopsidis, Solanum lycopersicum, cell wall, disease resistance, mixed-linked glucan, pattern triggered immunity, plant immunity},
	pages = {601--615},
}

Pattern-triggered immunity (PTI) is activated in plants upon recognition by pattern recognition receptors (PRRs) of damage- and microbe-associated molecular patterns (DAMPs and MAMPs) derived from plants or microorganisms, respectively. To understand better the plant mechanisms involved in the perception of carbohydrate-based structures recognized as DAMPs/MAMPs, we have studied the ability of mixed-linked β-1,3/1,4-glucans (MLGs), present in some plant and microbial cell walls, to trigger immune responses and disease resistance in plants. A range of MLG structures were tested for their capacity to induce PTI hallmarks, such as cytoplasmic Ca2+ elevations, reactive oxygen species production, phosphorylation of mitogen-activated protein kinases and gene transcriptional reprogramming. These analyses revealed that MLG oligosaccharides are perceived by Arabidopsis thaliana and identified a trisaccharide, β-d-cellobiosyl-(1,3)-β-d-glucose (MLG43), as the smallest MLG structure triggering strong PTI responses. These MLG43-mediated PTI responses are partially dependent on LysM PRRs CERK1, LYK4 and LYK5, as they were weaker in cerk1 and lyk4 lyk5 mutants than in wild-type plants. Cross-elicitation experiments between MLG43 and the carbohydrate MAMP chitohexaose [β-1,4-d-(GlcNAc)6], which is also perceived by these LysM PRRs, indicated that the mechanism of MLG43 recognition could differ from that of chitohexaose, which is fully impaired in cerk1 and lyk4 lyk5 plants. MLG43 treatment confers enhanced disease resistance in A. thaliana to the oomycete Hyaloperonospora arabidopsidis and in tomato and pepper to different bacterial and fungal pathogens. Our data support the classification of MLGs as a group of carbohydrate-based molecular patterns that are perceived by plants and trigger immune responses and disease resistance.

@article{bag_solubilization_2021,
	title = {Solubilization {Method} for {Isolation} of {Photosynthetic} {Mega}- and {Super}-complexes from {Conifer} {Thylakoids}},
	volume = {11},
	url = {https://bio-protocol.org/e4144},
	abstract = {Photosynthesis is the main process by which sunlight is harvested and converted into chemical energy and has been a focal point of fundamental research in plant biology for decades. In higher plants, the process takes place in the thylakoid membranes where the two photosystems (PSI and PSII) are located. In the past few decades, the evolution of biophysical and biochemical techniques allowed detailed studies of the thylakoid organization and the interaction between protein complexes and cofactors. These studies have mainly focused on model plants, such as Arabidopsis, pea, spinach, and tobacco, which are grown in climate chambers even though significant differences between indoor and outdoor growth conditions are present. In this manuscript, we present a new mild-solubilization procedure for use with \“fragile\” samples such as thylakoids from conifers growing outdoors. Here, the solubilization protocol is optimized with two detergents in two species, namely Norway spruce (Picea abies) and Scots pine (Pinus sylvestris). We have optimized the isolation and characterization of PSI and PSII multimeric mega- and super-complexes in a close-to-native condition by Blue-Native gel electrophoresis. Eventually, our protocol will not only help in the characterization of photosynthetic complexes from conifers but also in understanding winter adaptation.},
	number = {17},
	urldate = {2021-10-05},
	journal = {Bio-protocol},
	author = {Bag, Pushan and Schröder, Wolfgang P. and Jansson, Stefan and Farci, Domenica},
	month = sep,
	year = {2021},
	pages = {e4144--e4144},
}

Photosynthesis is the main process by which sunlight is harvested and converted into chemical energy and has been a focal point of fundamental research in plant biology for decades. In higher plants, the process takes place in the thylakoid membranes where the two photosystems (PSI and PSII) are located. In the past few decades, the evolution of biophysical and biochemical techniques allowed detailed studies of the thylakoid organization and the interaction between protein complexes and cofactors. These studies have mainly focused on model plants, such as Arabidopsis, pea, spinach, and tobacco, which are grown in climate chambers even though significant differences between indoor and outdoor growth conditions are present. In this manuscript, we present a new mild-solubilization procedure for use with “fragile” samples such as thylakoids from conifers growing outdoors. Here, the solubilization protocol is optimized with two detergents in two species, namely Norway spruce (Picea abies) and Scots pine (Pinus sylvestris). We have optimized the isolation and characterization of PSI and PSII multimeric mega- and super-complexes in a close-to-native condition by Blue-Native gel electrophoresis. Eventually, our protocol will not only help in the characterization of photosynthetic complexes from conifers but also in understanding winter adaptation.

@article{bhati_microproteins_2021,
	title = {{MicroProteins}: {Expanding} functions and novel modes of regulation},
	volume = {14},
	issn = {1674-2052},
	shorttitle = {{MicroProteins}},
	url = {https://www.cell.com/molecular-plant/abstract/S1674-2052(21)00006-X},
	doi = {10.1016/j.molp.2021.01.006},
	language = {English},
	number = {5},
	urldate = {2022-11-30},
	journal = {Molecular Plant},
	author = {Bhati, Kaushal Kumar and Dolde, Ulla and Wenkel, Stephan},
	month = may,
	year = {2021},
	pages = {705--707},
}

@article{rodrigues_microprotein_2021,
	title = {A {microProtein} repressor complex in the shoot meristem controls the transition to flowering},
	volume = {187},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab235},
	doi = {10.1093/plphys/kiab235},
	abstract = {MicroProteins are potent post-translational regulators. In Arabidopsis (Arabidopsis thaliana), the miP1a/b microProteins delay floral transition by forming a complex with CONSTANS (CO) and the co-repressor protein TOPLESS. To better understand the function of the miP1a microProtein in floral repression, we performed a genetic suppressor screen to identify suppressors of miP1a (sum) function. One mutant, sum1, exhibited strong suppression of the miP1a-induced late-flowering phenotype. Mapping of sum1 identified another allele of the gene encoding the histone H3K4 demethylase JUMONJI14 (JMJ14), which is required for miP1a function. Plants carrying mutations in JMJ14 exhibit an early flowering phenotype that is largely dependent on CO activity, supporting an additional role for CO in the repressive complex. We further investigated whether miP1a function involves chromatin modification, performed whole-genome methylome sequencing studies with plants ectopically expressing miP1a, and identified differentially methylated regions (DMRs). Among these DMRs is the promoter of FLOWERING LOCUS T (FT), the prime target of miP1a that is ectopically methylated in a JMJ14-dependent manner. Moreover, when aberrantly expressed at the shoot apex, CO induces early flowering, but only when JMJ14 is mutated. Detailed analysis of the genetic interaction among CO, JMJ14, miP1a/b, and TPL revealed a potential role for CO as a repressor of flowering in the shoot apical meristem (SAM). Altogether, our results suggest that a repressor complex operates in the SAM, likely to maintain it in an undifferentiated state until leaf-derived florigen signals induce SAM conversion into a floral meristem.},
	number = {1},
	urldate = {2022-11-30},
	journal = {Plant Physiology},
	author = {Rodrigues, Vandasue L. and Dolde, Ulla and Sun, Bin and Blaakmeer, Anko and Straub, Daniel and Eguen, Tenai and Botterweg-Paredes, Esther and Hong, Shinyoung and Graeff, Moritz and Li, Man-Wah and Gendron, Joshua M. and Wenkel, Stephan},
	month = sep,
	year = {2021},
	pages = {187--202},
}

MicroProteins are potent post-translational regulators. In Arabidopsis (Arabidopsis thaliana), the miP1a/b microProteins delay floral transition by forming a complex with CONSTANS (CO) and the co-repressor protein TOPLESS. To better understand the function of the miP1a microProtein in floral repression, we performed a genetic suppressor screen to identify suppressors of miP1a (sum) function. One mutant, sum1, exhibited strong suppression of the miP1a-induced late-flowering phenotype. Mapping of sum1 identified another allele of the gene encoding the histone H3K4 demethylase JUMONJI14 (JMJ14), which is required for miP1a function. Plants carrying mutations in JMJ14 exhibit an early flowering phenotype that is largely dependent on CO activity, supporting an additional role for CO in the repressive complex. We further investigated whether miP1a function involves chromatin modification, performed whole-genome methylome sequencing studies with plants ectopically expressing miP1a, and identified differentially methylated regions (DMRs). Among these DMRs is the promoter of FLOWERING LOCUS T (FT), the prime target of miP1a that is ectopically methylated in a JMJ14-dependent manner. Moreover, when aberrantly expressed at the shoot apex, CO induces early flowering, but only when JMJ14 is mutated. Detailed analysis of the genetic interaction among CO, JMJ14, miP1a/b, and TPL revealed a potential role for CO as a repressor of flowering in the shoot apical meristem (SAM). Altogether, our results suggest that a repressor complex operates in the SAM, likely to maintain it in an undifferentiated state until leaf-derived florigen signals induce SAM conversion into a floral meristem.

@article{castro_effects_2021,
	title = {Effects of {Early}, {Small}-{Scale} {Nitrogen} {Addition} on {Germination} and {Early} {Growth} of {Scots} {Pine} ({Pinus} sylvestris) {Seedlings} and on the {Recruitment} of the {Root}-{Associated} {Fungal} {Community}},
	volume = {12},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/1999-4907/12/11/1589},
	doi = {10/gnr3sf},
	abstract = {Scots pine (Pinus sylvestris L.) is one of the most economically important species to the Swedish forest industry, and cost-efficient planting methods are needed to ensure successful reestablishment after harvesting forest stands. While the majority of clear-cuts are replanted with pre-grown seedlings, direct seeding can be a viable option on poorer sites. Organic fertilizer has been shown to improve planted seedling establishment, but the effect on direct seeding is less well known. Therefore, at a scarified (disc trencher harrowed) clear-cut site in northern Sweden, we evaluated the effect of early, small-scale nitrogen addition on establishment and early recruitment of fungi from the disturbed soil community by site-planted Scots pine seeds. Individual seeds were planted using a moisture retaining germination matrix containing 10 mg nitrogen in the form of either arginine phosphate or ammonium nitrate. After one growing season, we collected seedlings and assessed the fungal community of seedling roots and the surrounding soil. Our results demonstrate that early, small-scale N addition increases seedling survival and needle carbon content, that there is rapid recruitment of ectomycorrhizal fungi to the roots and rhizosphere of the young seedlings and that this rapid recruitment was modified but not prevented by N addition.},
	language = {en},
	number = {11},
	urldate = {2021-12-16},
	journal = {Forests},
	author = {Castro, David and Schneider, Andreas N. and Holmlund, Mattias and Näsholm, Torgny and Street, Nathaniel R. and Hurry, Vaughan},
	month = nov,
	year = {2021},
	keywords = {Scots pine, boreal forest, clear-cut, ectomycorrhiza, fungal community composition, mycobiome, nitrogen addition},
	pages = {1589},
}

Scots pine (Pinus sylvestris L.) is one of the most economically important species to the Swedish forest industry, and cost-efficient planting methods are needed to ensure successful reestablishment after harvesting forest stands. While the majority of clear-cuts are replanted with pre-grown seedlings, direct seeding can be a viable option on poorer sites. Organic fertilizer has been shown to improve planted seedling establishment, but the effect on direct seeding is less well known. Therefore, at a scarified (disc trencher harrowed) clear-cut site in northern Sweden, we evaluated the effect of early, small-scale nitrogen addition on establishment and early recruitment of fungi from the disturbed soil community by site-planted Scots pine seeds. Individual seeds were planted using a moisture retaining germination matrix containing 10 mg nitrogen in the form of either arginine phosphate or ammonium nitrate. After one growing season, we collected seedlings and assessed the fungal community of seedling roots and the surrounding soil. Our results demonstrate that early, small-scale N addition increases seedling survival and needle carbon content, that there is rapid recruitment of ectomycorrhizal fungi to the roots and rhizosphere of the young seedlings and that this rapid recruitment was modified but not prevented by N addition.

@article{parker_biohybrid_2021,
	title = {Biohybrid plants with electronic roots via in vivo polymerization of conjugated oligomers},
	volume = {8},
	issn = {2051-6355},
	url = {https://pubs.rsc.org/en/content/articlelanding/2021/mh/d1mh01423d},
	doi = {10/gnh3cp},
	abstract = {Plant processes, ranging from photosynthesis through production of biomaterials to environmental sensing and adaptation, can be used in technology via integration of functional materials and devices. Previously, plants with integrated organic electronic devices and circuits distributed in their vascular tissue and organs have been demonstrated. To circumvent biological barriers, and thereby access the internal tissue, plant cuttings were used, which resulted in biohybrids with limited lifetime and use. Here, we report intact plants with electronic functionality that continue to grow and develop enabling plant-biohybrid systems that fully maintain their biological processes. The biocatalytic machinery of the plant cell wall was leveraged to seamlessly integrate conductors with mixed ionic–electronic conductivity along the root system of the plants. Cell wall peroxidases catalyzed ETE-S polymerization while the plant tissue served as the template, organizing the polymer in a favorable manner. The conductivity of the resulting p(ETE-S) roots reached the order of 10 S cm−1 and remained stable over the course of 4 weeks while the roots continued to grow. The p(ETE-S) roots were used to build supercapacitors that outperform previous plant-biohybrid charge storage demonstrations. Plants were not affected by the electronic functionalization but adapted to this new hybrid state by developing a more complex root system. Biohybrid plants with electronic roots pave the way for autonomous systems with potential applications in energy, sensing and robotics.},
	language = {en},
	number = {12},
	urldate = {2021-11-18},
	journal = {Materials Horizons},
	author = {Parker, Daniela and Daguerre, Yohann and Dufil, Gwennaël and Mantione, Daniele and Solano, Eduardo and Cloutet, Eric and Hadziioannou, Georges and Näsholm, Torgny and Berggren, Magnus and Pavlopoulou, Eleni and Stavrinidou, Eleni},
	month = nov,
	year = {2021},
	pages = {3295--3305},
}

Plant processes, ranging from photosynthesis through production of biomaterials to environmental sensing and adaptation, can be used in technology via integration of functional materials and devices. Previously, plants with integrated organic electronic devices and circuits distributed in their vascular tissue and organs have been demonstrated. To circumvent biological barriers, and thereby access the internal tissue, plant cuttings were used, which resulted in biohybrids with limited lifetime and use. Here, we report intact plants with electronic functionality that continue to grow and develop enabling plant-biohybrid systems that fully maintain their biological processes. The biocatalytic machinery of the plant cell wall was leveraged to seamlessly integrate conductors with mixed ionic–electronic conductivity along the root system of the plants. Cell wall peroxidases catalyzed ETE-S polymerization while the plant tissue served as the template, organizing the polymer in a favorable manner. The conductivity of the resulting p(ETE-S) roots reached the order of 10 S cm−1 and remained stable over the course of 4 weeks while the roots continued to grow. The p(ETE-S) roots were used to build supercapacitors that outperform previous plant-biohybrid charge storage demonstrations. Plants were not affected by the electronic functionalization but adapted to this new hybrid state by developing a more complex root system. Biohybrid plants with electronic roots pave the way for autonomous systems with potential applications in energy, sensing and robotics.

@article{malivert_feronia_2021,
	title = {{FERONIA} and microtubules independently contribute to mechanical integrity in the {Arabidopsis} shoot},
	volume = {19},
	issn = {1545-7885},
	url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001454},
	doi = {10/gpkx26},
	abstract = {To survive, cells must constantly resist mechanical stress. In plants, this involves the reinforcement of cell walls, notably through microtubule-dependent cellulose deposition. How wall sensing might contribute to this response is unknown. Here, we tested whether the microtubule response to stress acts downstream of known wall sensors. Using a multistep screen with 11 mutant lines, we identify FERONIA (FER) as the primary candidate for the cell’s response to stress in the shoot. However, this does not imply that FER acts upstream of the microtubule response to stress. In fact, when performing mechanical perturbations, we instead show that the expected microtubule response to stress does not require FER. We reveal that the feronia phenotype can be partially rescued by reducing tensile stress levels. Conversely, in the absence of both microtubules and FER, cells appear to swell and burst. Altogether, this shows that the microtubule response to stress acts as an independent pathway to resist stress, in parallel to FER. We propose that both pathways are required to maintain the mechanical integrity of plant cells.},
	language = {en},
	number = {11},
	urldate = {2022-02-25},
	journal = {PLOS Biology},
	author = {Malivert, Alice and Erguvan, Özer and Chevallier, Antoine and Dehem, Antoine and Friaud, Rodrigue and Liu, Mengying and Martin, Marjolaine and Peyraud, Théophile and Hamant, Olivier and Verger, Stéphane},
	month = nov,
	year = {2021},
	keywords = {Anisotropy, Cellulose, Hypocotyl, Mechanical stress, Microtubules, Pavement cells, Plant cotyledon, Seedlings},
	pages = {e3001454},
}

To survive, cells must constantly resist mechanical stress. In plants, this involves the reinforcement of cell walls, notably through microtubule-dependent cellulose deposition. How wall sensing might contribute to this response is unknown. Here, we tested whether the microtubule response to stress acts downstream of known wall sensors. Using a multistep screen with 11 mutant lines, we identify FERONIA (FER) as the primary candidate for the cell’s response to stress in the shoot. However, this does not imply that FER acts upstream of the microtubule response to stress. In fact, when performing mechanical perturbations, we instead show that the expected microtubule response to stress does not require FER. We reveal that the feronia phenotype can be partially rescued by reducing tensile stress levels. Conversely, in the absence of both microtubules and FER, cells appear to swell and burst. Altogether, this shows that the microtubule response to stress acts as an independent pathway to resist stress, in parallel to FER. We propose that both pathways are required to maintain the mechanical integrity of plant cells.

@article{lutter_climate_2021,
	title = {Climate {Benefit} of {Different} {Tree} {Species} on {Former} {Agricultural} {Land} in {Northern} {Europe}},
	volume = {12},
	url = {https://www.mdpi.com/1999-4907/12/12/1810},
	doi = {10/gn64qp},
	abstract = {The new European Union Forest Strategy for 2030 aims to plant an additional 3 billion trees on non-forest land to mitigate climate change. However, the choice of tree species for afforestation to achieve the maximum climate benefit is unclear. We compared the climate benefit of six different species in terms of carbon (C) sequestration in biomass and the harvested wood substitution in products to avoid carbon dioxide (CO2) emissions from fossil-based materials over the 100-year period by afforesting about \¼ of the available area in northern Europe. The highest climate benefit was observed for larch, both at a stand scale (1626 Mg CO2 eqv. ha\−1) and at the landscape level for the studied scenario (579 million Mg CO2 eqv.). Larch was followed by Norway spruce, poplar, hybrid aspen and birch, showing a climate benefit about 40\–50\% lower than that for larch. The climate benefit of willow was about 70\% lower than larch. Willow showed 6\–14-fold lower C stocks at the landscape level after 100 years than other tree species. The major climate benefit over the 100-year period comes from wood substitution and avoided emissions, but C stock buildup at the landscape level also removes significant amounts of CO2 already present in the atmosphere. The choice of tree species is important to maximize climate change mitigation.},
	language = {en},
	number = {12},
	urldate = {2022-01-17},
	journal = {Forests},
	author = {Lutter, Reimo and Stål, Gustav and Arnesson Ceder, Lina and Lim, Hyungwoo and Padari, Allar and Tullus, Hardi and Nordin, Annika and Lundmark, Tomas},
	month = dec,
	year = {2021},
	keywords = {Norway spruce, carbon substitution, climate change, forest carbon, hybrid aspen, larch, poplar, silver birch, willow},
	pages = {1810},
}

The new European Union Forest Strategy for 2030 aims to plant an additional 3 billion trees on non-forest land to mitigate climate change. However, the choice of tree species for afforestation to achieve the maximum climate benefit is unclear. We compared the climate benefit of six different species in terms of carbon (C) sequestration in biomass and the harvested wood substitution in products to avoid carbon dioxide (CO2) emissions from fossil-based materials over the 100-year period by afforesting about ¼ of the available area in northern Europe. The highest climate benefit was observed for larch, both at a stand scale (1626 Mg CO2 eqv. ha−1) and at the landscape level for the studied scenario (579 million Mg CO2 eqv.). Larch was followed by Norway spruce, poplar, hybrid aspen and birch, showing a climate benefit about 40–50% lower than that for larch. The climate benefit of willow was about 70% lower than larch. Willow showed 6–14-fold lower C stocks at the landscape level after 100 years than other tree species. The major climate benefit over the 100-year period comes from wood substitution and avoided emissions, but C stock buildup at the landscape level also removes significant amounts of CO2 already present in the atmosphere. The choice of tree species is important to maximize climate change mitigation.

@article{escamez_fluorescence_2021,
	title = {Fluorescence {Lifetime} {Imaging} as an {In} {Situ} and {Label}-{Free} {Readout} for the {Chemical} {Composition} of {Lignin}},
	volume = {9},
	url = {https://doi.org/10.1021/acssuschemeng.1c06780},
	doi = {10/gnr3sb},
	abstract = {Naturally fluorescent polymeric molecules such as collagen, resilin, cutin, suberin, or lignin can serve as renewable sources of bioproducts. Theoretical physics predicts that the fluorescence lifetime of these polymers is related to their chemical composition. We verified this prediction for lignin, a major structural element in plant cell walls that form woody biomass. Lignin is composed of different phenylpropanoid units, and its composition affects its properties, biological functions, and the utilization of wood biomass. We carried out fluorescence lifetime imaging microscopy (FLIM) measurements of wood cell wall lignin in a population of 90 hybrid aspen trees genetically engineered to display differences in cell wall chemistry and structure. We also measured the wood cell wall composition by classical analytical methods in these trees. Using statistical modeling and machine learning algorithms, we identified parameters of fluorescence lifetime that predict the content of S-type and G-type lignin units, the two main types of units in the lignin of angiosperm (flowering) plants. In a first step toward tailoring lignin biosynthesis toward improvement of woody biomass feedstocks, we show how FLIM can reveal the dynamics of lignin biosynthesis in two different biological contexts, including in vivo while lignin is being synthesized in the walls of living cells.},
	number = {51},
	urldate = {2021-12-14},
	journal = {ACS Sustainable Chemistry \& Engineering},
	author = {Escamez, Sacha and Terryn, Christine and Gandla, Madhavi Latha and Yassin, Zakiya and Scheepers, Gerhard and Näsholm, Torgny and Sundman, Ola and Jönsson, Leif J. and Lundberg-Felten, Judith and Tuominen, Hannele and Niittylä, Totte and Paës, Gabriel},
	month = dec,
	year = {2021},
	pages = {17381--17392},
}

Naturally fluorescent polymeric molecules such as collagen, resilin, cutin, suberin, or lignin can serve as renewable sources of bioproducts. Theoretical physics predicts that the fluorescence lifetime of these polymers is related to their chemical composition. We verified this prediction for lignin, a major structural element in plant cell walls that form woody biomass. Lignin is composed of different phenylpropanoid units, and its composition affects its properties, biological functions, and the utilization of wood biomass. We carried out fluorescence lifetime imaging microscopy (FLIM) measurements of wood cell wall lignin in a population of 90 hybrid aspen trees genetically engineered to display differences in cell wall chemistry and structure. We also measured the wood cell wall composition by classical analytical methods in these trees. Using statistical modeling and machine learning algorithms, we identified parameters of fluorescence lifetime that predict the content of S-type and G-type lignin units, the two main types of units in the lignin of angiosperm (flowering) plants. In a first step toward tailoring lignin biosynthesis toward improvement of woody biomass feedstocks, we show how FLIM can reveal the dynamics of lignin biosynthesis in two different biological contexts, including in vivo while lignin is being synthesized in the walls of living cells.

@article{dufil_plant_2021,
	title = {Plant {Bioelectronics} and {Biohybrids}: {The} {Growing} {Contribution} of {Organic} {Electronic} and {Carbon}-{Based} {Materials}},
	issn = {0009-2665},
	shorttitle = {Plant {Bioelectronics} and {Biohybrids}},
	url = {https://doi.org/10.1021/acs.chemrev.1c00525},
	doi = {10/gnx7vd},
	abstract = {Life in our planet is highly dependent on plants as they are the primary source of food, regulators of the atmosphere, and providers of a variety of materials. In this work, we review the progress on bioelectronic devices for plants and biohybrid systems based on plants, therefore discussing advancements that view plants either from a biological or a technological perspective, respectively. We give an overview on wearable and implantable bioelectronic devices for monitoring and modulating plant physiology that can be used as tools in basic plant science or find application in agriculture. Furthermore, we discuss plant-wearable devices for monitoring a plant’s microenvironment that will enable optimization of growth conditions. The review then covers plant biohybrid systems where plants are an integral part of devices or are converted to devices upon functionalization with smart materials, including self-organized electronics, plant nanobionics, and energy applications. The review focuses on advancements based on organic electronic and carbon-based materials and discusses opportunities, challenges, as well as future steps.},
	urldate = {2021-12-29},
	journal = {Chemical Reviews},
	author = {Dufil, Gwennaël and Bernacka-Wojcik, Iwona and Armada-Moreira, Adam and Stavrinidou, Eleni},
	month = dec,
	year = {2021},
}

Life in our planet is highly dependent on plants as they are the primary source of food, regulators of the atmosphere, and providers of a variety of materials. In this work, we review the progress on bioelectronic devices for plants and biohybrid systems based on plants, therefore discussing advancements that view plants either from a biological or a technological perspective, respectively. We give an overview on wearable and implantable bioelectronic devices for monitoring and modulating plant physiology that can be used as tools in basic plant science or find application in agriculture. Furthermore, we discuss plant-wearable devices for monitoring a plant’s microenvironment that will enable optimization of growth conditions. The review then covers plant biohybrid systems where plants are an integral part of devices or are converted to devices upon functionalization with smart materials, including self-organized electronics, plant nanobionics, and energy applications. The review focuses on advancements based on organic electronic and carbon-based materials and discusses opportunities, challenges, as well as future steps.

@article{koh_mapping_2021,
	title = {Mapping and engineering of auxin-induced plasma membrane dissociation in {BRX} family proteins},
	volume = {33},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koab076},
	doi = {10.1093/plcell/koab076},
	abstract = {Angiosperms have evolved the phloem for the long-distance transport of metabolites. The complex process of phloem development involves genes that only occur in vascular plant lineages. For example, in Arabidopsis thaliana, the BREVIS RADIX (BRX) gene is required for continuous root protophloem differentiation, together with PROTEIN KINASE ASSOCIATED WITH BRX (PAX). BRX and its BRX-LIKE (BRXL) homologs are composed of four highly conserved domains including the signature tandem BRX domains that are separated by variable spacers. Nevertheless, BRX family proteins have functionally diverged. For instance, BRXL2 can only partially replace BRX in the root protophloem. This divergence is reflected in physiologically relevant differences in protein behavior, such as auxin-induced plasma membrane dissociation of BRX, which is not observed for BRXL2. Here we dissected the differential functions of BRX family proteins using a set of amino acid substitutions and domain swaps. Our data suggest that the plasma membrane-associated tandem BRX domains are both necessary and sufficient to convey the biological outputs of BRX function and therefore constitute an important regulatory entity. Moreover, PAX target phosphosites in the linker between the two BRX domains mediate the auxin-induced plasma membrane dissociation. Engineering these sites into BRXL2 renders this modified protein auxin-responsive and thereby increases its biological activity in the root protophloem context.},
	number = {6},
	urldate = {2022-05-02},
	journal = {The Plant Cell},
	author = {Koh, Samuel W H and Marhava, Petra and Rana, Surbhi and Graf, Alina and Moret, Bernard and Bassukas, Alkistis E L and Zourelidou, Melina and Kolb, Martina and Hammes, Ulrich Z and Schwechheimer, Claus and Hardtke, Christian S},
	month = jun,
	year = {2021},
	pages = {1945--1960},
}

Angiosperms have evolved the phloem for the long-distance transport of metabolites. The complex process of phloem development involves genes that only occur in vascular plant lineages. For example, in Arabidopsis thaliana, the BREVIS RADIX (BRX) gene is required for continuous root protophloem differentiation, together with PROTEIN KINASE ASSOCIATED WITH BRX (PAX). BRX and its BRX-LIKE (BRXL) homologs are composed of four highly conserved domains including the signature tandem BRX domains that are separated by variable spacers. Nevertheless, BRX family proteins have functionally diverged. For instance, BRXL2 can only partially replace BRX in the root protophloem. This divergence is reflected in physiologically relevant differences in protein behavior, such as auxin-induced plasma membrane dissociation of BRX, which is not observed for BRXL2. Here we dissected the differential functions of BRX family proteins using a set of amino acid substitutions and domain swaps. Our data suggest that the plasma membrane-associated tandem BRX domains are both necessary and sufficient to convey the biological outputs of BRX function and therefore constitute an important regulatory entity. Moreover, PAX target phosphosites in the linker between the two BRX domains mediate the auxin-induced plasma membrane dissociation. Engineering these sites into BRXL2 renders this modified protein auxin-responsive and thereby increases its biological activity in the root protophloem context.

@article{sjogren_branched-chain_2021,
	title = {Branched-chain amino acid metabolism is regulated by {ERRα} in primary human myotubes and is further impaired by glucose loading in type 2 diabetes},
	volume = {64},
	issn = {1432-0428},
	url = {https://doi.org/10.1007/s00125-021-05481-9},
	doi = {10.1007/s00125-021-05481-9},
	abstract = {Increased levels of branched-chain amino acids (BCAAs) are associated with type 2 diabetes pathogenesis. However, most metabolomic studies are limited to an analysis of plasma metabolites under fasting conditions, rather than the dynamic shift in response to a metabolic challenge. Moreover, metabolomic profiles of peripheral tissues involved in glucose homeostasis are scarce and the transcriptomic regulation of genes involved in BCAA catabolism is partially unknown. This study aimed to identify differences in circulating and skeletal muscle BCAA levels in response to an OGTT in individuals with normal glucose tolerance (NGT) or type 2 diabetes. Additionally, transcription factors involved in the regulation of the BCAA gene set were identified.},
	language = {en},
	number = {9},
	urldate = {2022-04-08},
	journal = {Diabetologia},
	author = {Sjögren, Rasmus J. O. and Rizo-Roca, David and Chibalin, Alexander V. and Chorell, Elin and Furrer, Regula and Katayama, Shintaro and Harada, Jun and Karlsson, Håkan K. R. and Handschin, Christoph and Moritz, Thomas and Krook, Anna and Näslund, Erik and Zierath, Juleen R.},
	month = sep,
	year = {2021},
	pages = {2077--2091},
}

Increased levels of branched-chain amino acids (BCAAs) are associated with type 2 diabetes pathogenesis. However, most metabolomic studies are limited to an analysis of plasma metabolites under fasting conditions, rather than the dynamic shift in response to a metabolic challenge. Moreover, metabolomic profiles of peripheral tissues involved in glucose homeostasis are scarce and the transcriptomic regulation of genes involved in BCAA catabolism is partially unknown. This study aimed to identify differences in circulating and skeletal muscle BCAA levels in response to an OGTT in individuals with normal glucose tolerance (NGT) or type 2 diabetes. Additionally, transcription factors involved in the regulation of the BCAA gene set were identified.

@article{zimmermann_phosphorylated_2021,
	title = {The phosphorylated pathway of serine biosynthesis links plant growth with nitrogen metabolism},
	volume = {186},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab167},
	doi = {10/gmrwxt},
	abstract = {Because it is the precursor for various essential cellular components, the amino acid serine is indispensable for every living organism. In plants, serine is synthesized by two major pathways: photorespiration and the phosphorylated pathway of serine biosynthesis (PPSB). However, the importance of these pathways in providing serine for plant development is not fully understood. In this study, we examine the relative contributions of photorespiration and PPSB to providing serine for growth and metabolism in the C3 model plant Arabidopsis thaliana. Our analyses of cell proliferation and elongation reveal that PPSB-derived serine is indispensable for plant growth and its loss cannot be compensated by photorespiratory serine biosynthesis. Using isotope labeling, we show that PPSB-deficiency impairs the synthesis of proteins and purine nucleotides in plants. Furthermore, deficiency in PPSB-mediated serine biosynthesis leads to a strong accumulation of metabolites related to nitrogen metabolism. This result corroborates 15N-isotope labeling in which we observed an increased enrichment in labeled amino acids in PPSB-deficient plants. Expression studies indicate that elevated ammonium uptake and higher glutamine synthetase/glutamine oxoglutarate aminotransferase (GS/GOGAT) activity causes this phenotype. Metabolic analyses further show that elevated nitrogen assimilation and reduced amino acid turnover into proteins and nucleotides are the most likely driving forces for changes in respiratory metabolism and amino acid catabolism in PPSB-deficient plants. Accordingly, we conclude that even though photorespiration generates high amounts of serine in plants, PPSB-derived serine is more important for plant growth and its deficiency triggers the induction of nitrogen assimilation, most likely as an amino acid starvation response.},
	number = {3},
	urldate = {2022-02-25},
	journal = {Plant Physiology},
	author = {Zimmermann, Sandra E and Benstein, Ruben M and Flores-Tornero, María and Blau, Samira and Anoman, Armand D and Rosa-Téllez, Sara and Gerlich, Silke C and Salem, Mohamed A and Alseekh, Saleh and Kopriva, Stanislav and Wewer, Vera and Flügge, Ulf-Ingo and Jacoby, Richard P and Fernie, Alisdair R and Giavalisco, Patrick and Ros, Roc and Krueger, Stephan},
	month = jul,
	year = {2021},
	pages = {1487--1506},
}

Because it is the precursor for various essential cellular components, the amino acid serine is indispensable for every living organism. In plants, serine is synthesized by two major pathways: photorespiration and the phosphorylated pathway of serine biosynthesis (PPSB). However, the importance of these pathways in providing serine for plant development is not fully understood. In this study, we examine the relative contributions of photorespiration and PPSB to providing serine for growth and metabolism in the C3 model plant Arabidopsis thaliana. Our analyses of cell proliferation and elongation reveal that PPSB-derived serine is indispensable for plant growth and its loss cannot be compensated by photorespiratory serine biosynthesis. Using isotope labeling, we show that PPSB-deficiency impairs the synthesis of proteins and purine nucleotides in plants. Furthermore, deficiency in PPSB-mediated serine biosynthesis leads to a strong accumulation of metabolites related to nitrogen metabolism. This result corroborates 15N-isotope labeling in which we observed an increased enrichment in labeled amino acids in PPSB-deficient plants. Expression studies indicate that elevated ammonium uptake and higher glutamine synthetase/glutamine oxoglutarate aminotransferase (GS/GOGAT) activity causes this phenotype. Metabolic analyses further show that elevated nitrogen assimilation and reduced amino acid turnover into proteins and nucleotides are the most likely driving forces for changes in respiratory metabolism and amino acid catabolism in PPSB-deficient plants. Accordingly, we conclude that even though photorespiration generates high amounts of serine in plants, PPSB-derived serine is more important for plant growth and its deficiency triggers the induction of nitrogen assimilation, most likely as an amino acid starvation response.

@article{bag_atlas_2021,
	title = {An atlas of the {Norway} spruce needle seasonal transcriptome},
	volume = {108},
	issn = {1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/tpj.15530},
	doi = {10.1111/tpj.15530},
	abstract = {Boreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce (Picea abies) needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 until June 30), cell walls, organelles, etc., were formed, and this developmental program heavily influenced the transcriptome, explained by over-represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July–August), autumn (September–October), winter (November–February), and spring (March–April), where over-represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools.},
	language = {en},
	number = {6},
	urldate = {2021-11-04},
	journal = {The Plant Journal},
	author = {Bag, Pushan and Lihavainen, Jenna and Delhomme, Nicolas and Riquelme, Thomas and Robinson, Kathryn M and Jansson, Stefan},
	month = oct,
	year = {2021},
	keywords = {Conifers, Norway spruce, Seasonal adaptation, Transcriptomics, conifers, resource, seasonal adaptation, transcriptomics},
}

Boreal conifers possess a tremendous ability to survive and remain evergreen during harsh winter conditions and resume growth during summer. This is enabled by coordinated regulation of major cellular functions at the level of gene expression, metabolism, and physiology. Here we present a comprehensive characterization of the annual changes in the global transcriptome of Norway spruce (Picea abies) needles as a resource to understand needle development and acclimation processes throughout the year. In young, growing needles (May 15 until June 30), cell walls, organelles, etc., were formed, and this developmental program heavily influenced the transcriptome, explained by over-represented Gene Ontology (GO) categories. Later changes in gene expression were smaller but four phases were recognized: summer (July–August), autumn (September–October), winter (November–February), and spring (March–April), where over-represented GO categories demonstrated how the needles acclimated to the various seasons. Changes in the seasonal global transcriptome profile were accompanied by differential expression of members of the major transcription factor families. We present a tentative model of how cellular activities are regulated over the year in needles of Norway spruce, which demonstrates the value of mining this dataset, accessible in ConGenIE together with advanced visualization tools.

@article{dikaya_insights_2021,
	title = {Insights into the role of alternative splicing in plant temperature response},
	volume = {72},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erab234},
	doi = {10/gkhp7j},
	abstract = {Alternative splicing occurs in all eukaryotic organisms. Since the first description of multiexon genes and the splicing machinery, the field has expanded rapidly, especially in animals and yeast. However, our knowledge about splicing in plants is still quite fragmented. Though eukaryotes show some similarity in the composition and dynamics of their splicing machinery, observations of unique plant traits are only starting to emerge. For instance, plant alternative splicing is closely linked to their ability to perceive various environmental stimuli. Due to their sessile lifestyle, temperature is a central source of information, allowing plants to adjust their development to match current growth conditions. Hence, seasonal temperature fluctuations and day–night cycles can strongly influence plant morphology across developmental stages. Here we discuss available data on temperature-dependent alternative splicing in plants. Given its fragmented state, it is not always possible to fit specific observations into a coherent picture, yet it is sufficient to estimate the complexity of this field and the need for further research. Better understanding of alternative splicing as a part of plant temperature response and adaptation may also prove to be a powerful tool for both fundamental and applied sciences.},
	number = {21},
	urldate = {2022-02-04},
	journal = {Journal of Experimental Botany},
	author = {Dikaya, Varvara and El Arbi, Nabila and Rojas-Murcia, Nelson and Nardeli, Sarah Muniz and Goretti, Daniela and Schmid, Markus},
	month = nov,
	year = {2021},
	pages = {7384--7403},
}

Alternative splicing occurs in all eukaryotic organisms. Since the first description of multiexon genes and the splicing machinery, the field has expanded rapidly, especially in animals and yeast. However, our knowledge about splicing in plants is still quite fragmented. Though eukaryotes show some similarity in the composition and dynamics of their splicing machinery, observations of unique plant traits are only starting to emerge. For instance, plant alternative splicing is closely linked to their ability to perceive various environmental stimuli. Due to their sessile lifestyle, temperature is a central source of information, allowing plants to adjust their development to match current growth conditions. Hence, seasonal temperature fluctuations and day–night cycles can strongly influence plant morphology across developmental stages. Here we discuss available data on temperature-dependent alternative splicing in plants. Given its fragmented state, it is not always possible to fit specific observations into a coherent picture, yet it is sufficient to estimate the complexity of this field and the need for further research. Better understanding of alternative splicing as a part of plant temperature response and adaptation may also prove to be a powerful tool for both fundamental and applied sciences.

@article{papaioannou_sex_2021,
	title = {Sex without crossing over in the yeast {Saccharomycodes} ludwigii},
	volume = {22},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/s13059-021-02521-w},
	doi = {10.1186/s13059-021-02521-w},
	abstract = {Intermixing of genomes through meiotic reassortment and recombination of homologous chromosomes is a unifying theme of sexual reproduction in eukaryotic organisms and is considered crucial for their adaptive evolution. Previous studies of the budding yeast species Saccharomycodes ludwigii suggested that meiotic crossing over might be absent from its sexual life cycle, which is predominated by fertilization within the meiotic tetrad.},
	number = {1},
	urldate = {2021-11-12},
	journal = {Genome Biology},
	author = {Papaioannou, Ioannis A. and Dutreux, Fabien and Peltier, France A. and Maekawa, Hiromi and Delhomme, Nicolas and Bardhan, Amit and Friedrich, Anne and Schacherer, Joseph and Knop, Michael},
	month = nov,
	year = {2021},
	keywords = {Achiasmate meiosis, Automixis, Crossing over, Intratetrad mating, Linkage disequilibrium, Meiotic recombination, Mutation accumulation, Mutation rate, Saccharomycodes ludwigii},
	pages = {303},
}

Intermixing of genomes through meiotic reassortment and recombination of homologous chromosomes is a unifying theme of sexual reproduction in eukaryotic organisms and is considered crucial for their adaptive evolution. Previous studies of the budding yeast species Saccharomycodes ludwigii suggested that meiotic crossing over might be absent from its sexual life cycle, which is predominated by fertilization within the meiotic tetrad.

@article{pandey_epigenetic_2021,
	title = {Epigenetic {Regulation} of {Temperature} {Responses} – {Past} {Successes} and {Future} {Challenges}},
	volume = {72},
	issn = {0022-0957, 1460-2431},
	url = {https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erab248/6288481},
	doi = {10.1093/jxb/erab248},
	abstract = {Abstract
            In contrast to animals, plants cannot avoid unfavorable temperature conditions. Instead, plants have evolved intricate signaling pathways that enable them to perceive and respond to temperature. General acclimation processes that prepare the plant to respond to stressful heat and cold, usually occur throughout the whole plant. More specific temperature responses, however, are limited to certain tissues or cell types. While global responses are amenable to epigenomic analyses, responses which are highly localized are more problematic as the chromatin in question is not easily accessible. Here we review the current knowledge of the epigenetic regulation of FLOWERING LOCUS C and FLOWERING LOCUS T as examples of temperature-responsive flowering time regulators that are expressed broadly throughout the plants and in specific cell types, respectively. While undoubtably extremely successful, we reason that future analyses would benefit from higher spatiotemporal resolution. We conclude by reviewing methods and successful applications of tissue- and cell type-specific epigenomic analyses and provide a brief outlook into the future, single-cell epigenomics.},
	language = {en},
	number = {21},
	urldate = {2021-06-03},
	journal = {Journal of Experimental Botany},
	author = {Pandey, Saurabh Prakash and Benstein, Ruben M and Wang, Yanwei and Schmid, Markus},
	month = may,
	year = {2021},
	pages = {7482--7497},
}

Abstract In contrast to animals, plants cannot avoid unfavorable temperature conditions. Instead, plants have evolved intricate signaling pathways that enable them to perceive and respond to temperature. General acclimation processes that prepare the plant to respond to stressful heat and cold, usually occur throughout the whole plant. More specific temperature responses, however, are limited to certain tissues or cell types. While global responses are amenable to epigenomic analyses, responses which are highly localized are more problematic as the chromatin in question is not easily accessible. Here we review the current knowledge of the epigenetic regulation of FLOWERING LOCUS C and FLOWERING LOCUS T as examples of temperature-responsive flowering time regulators that are expressed broadly throughout the plants and in specific cell types, respectively. While undoubtably extremely successful, we reason that future analyses would benefit from higher spatiotemporal resolution. We conclude by reviewing methods and successful applications of tissue- and cell type-specific epigenomic analyses and provide a brief outlook into the future, single-cell epigenomics.

@article{tarvainen_limited_2021,
	title = {Limited vertical {CO2} transport in stems of mature boreal {Pinus} sylvestris trees},
	volume = {41},
	issn = {1758-4469},
	url = {https://academic.oup.com/treephys/article/41/1/63/5898915},
	doi = {10.1093/treephys/tpaa113},
	abstract = {Abstract
            Several studies have suggested that CO2 transport in the transpiration stream can considerably bias estimates of root and stem respiration in ring-porous and diffuse-porous tree species. Whether this also happens in species with tracheid xylem anatomy and lower sap flow rates, such as conifers, is currently unclear. We infused 13C-labelled solution into the xylem near the base of two 90-year-old Pinus sylvestris L. trees. A custom-built gas exchange system and an online isotopic analyser were used to sample the CO2 efflux and its isotopic composition continuously from four positions along the bole and one upper canopy shoot in each tree. Phloem and needle tissue 13C enrichment was also evaluated at these positions. Most of the 13C label was lost by diffusion within a few metres of the infusion point indicating rapid CO2 loss during vertical xylem transport. No 13C enrichment was detected in the upper bole needle tissues. Furthermore, mass balance calculations showed that c. 97\% of the locally respired CO2 diffused radially to the atmosphere. Our results support the notion that xylem CO2 transport is of limited magnitude in conifers. This implies that the concerns that stem transport of CO2 derived from root respiration biases chamber-based estimates of forest carbon cycling may be unwarranted for mature conifer stands.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Tree Physiology},
	author = {Tarvainen, Lasse and Wallin, Göran and Linder, Sune and Näsholm, Torgny and Oren, Ram and Ottosson Löfvenius, Mikaell and Räntfors, Mats and Tor-Ngern, Pantana and Marshall, John D},
	editor = {Steppe, Kathy},
	month = jan,
	year = {2021},
	pages = {63--75},
}

Abstract Several studies have suggested that CO2 transport in the transpiration stream can considerably bias estimates of root and stem respiration in ring-porous and diffuse-porous tree species. Whether this also happens in species with tracheid xylem anatomy and lower sap flow rates, such as conifers, is currently unclear. We infused 13C-labelled solution into the xylem near the base of two 90-year-old Pinus sylvestris L. trees. A custom-built gas exchange system and an online isotopic analyser were used to sample the CO2 efflux and its isotopic composition continuously from four positions along the bole and one upper canopy shoot in each tree. Phloem and needle tissue 13C enrichment was also evaluated at these positions. Most of the 13C label was lost by diffusion within a few metres of the infusion point indicating rapid CO2 loss during vertical xylem transport. No 13C enrichment was detected in the upper bole needle tissues. Furthermore, mass balance calculations showed that c. 97% of the locally respired CO2 diffused radially to the atmosphere. Our results support the notion that xylem CO2 transport is of limited magnitude in conifers. This implies that the concerns that stem transport of CO2 derived from root respiration biases chamber-based estimates of forest carbon cycling may be unwarranted for mature conifer stands.

@article{shen_boptype_2021,
	title = {The {BOP}‐type co‐transcriptional regulator {NODULE} {ROOT1} promotes stem secondary growth of the tropical {Cannabaceae} tree {Parasponia} andersonii},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.15242},
	doi = {10/gjs436},
	language = {en},
	urldate = {2021-06-03},
	journal = {The Plant Journal},
	author = {Shen, Defeng and Holmer, Rens and Kulikova, Olga and Mannapperuma, Chanaka and Street, Nathaniel R. and Yan, Zhichun and Maden, Thomas and Bu, Fengjiao and Zhang, Yuanyuan and Geurts, Rene and Magne, Kévin},
	month = apr,
	year = {2021},
	pages = {tpj.15242},
}

@article{jonsson_mechanochemical_2021,
	title = {Mechanochemical feedback mediates tissue bending required for seedling emergence},
	volume = {31},
	issn = {0960-9822},
	url = {https://www.cell.com/current-biology/abstract/S0960-9822(20)31836-4},
	doi = {10.1016/j.cub.2020.12.016},
	language = {en},
	number = {6},
	urldate = {2021-06-03},
	journal = {Current Biology},
	author = {Jonsson, Kristoffer and Lathe, Rahul S. and Kierzkowski, Daniel and Routier-Kierzkowska, Anne-Lise and Hamant, Olivier and Bhalerao, Rishikesh P.},
	month = mar,
	year = {2021},
	keywords = {Arabidopsis, PIN proteins, PMEI, apical hook, auxin, cell wall, development, differential growth, pectin methylesterification},
	pages = {1154--1164.e3},
}

@article{ding_phytochrome_2021,
	title = {Phytochrome {B} and {PHYTOCHROME} {INTERACTING} {FACTOR8} modulate seasonal growth in trees},
	volume = {232},
	copyright = {© 2021 The Authors. New Phytologist © 2021 New Phytologist Foundation},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.17350},
	doi = {10.1111/nph.17350},
	abstract = {The seasonally synchronized annual growth cycle that is regulated mainly by photoperiod and temperature cues is a crucial adaptive strategy for perennial plants in boreal and temperate ecosystems. Phytochrome B (phyB), as a light and thermal sensor, has been extensively studied in Arabidopsis. However, the specific mechanisms for how the phytochrome photoreceptors control the phenology in tree species remain poorly understood. We characterized the functions of PHYB genes and their downstream PHYTOCHROME INTERACTING FACTOR (PIF) targets in the regulation of shade avoidance and seasonal growth in hybrid aspen trees. We show that while phyB1 and phyB2, as phyB in other plants, act as suppressors of shoot elongation during vegetative growth, they act as promoters of tree seasonal growth. Furthermore, while the Populus homologs of both PIF4 and PIF8 are involved in the shade avoidance syndrome (SAS), only PIF8 plays a major role as a suppressor of seasonal growth. Our data suggest that the PHYB-PIF8 regulon controls seasonal growth through the regulation of FT and CENL1 expression while a genome-wide transcriptome analysis suggests how, in Populus trees, phyB coordinately regulates SAS responses and seasonal growth cessation.},
	language = {en},
	number = {6},
	urldate = {2021-06-21},
	journal = {New Phytologist},
	author = {Ding, Jihua and Zhang, Bo and Li, Yue and André, Domenique and Nilsson, Ove},
	month = mar,
	year = {2021},
	keywords = {PHYTOCHROME B, PHYTOCHROME INTERACTING FACTOR8, Populus, bud break, growth cessation, shade avoidance},
	pages = {2339--2352},
}

The seasonally synchronized annual growth cycle that is regulated mainly by photoperiod and temperature cues is a crucial adaptive strategy for perennial plants in boreal and temperate ecosystems. Phytochrome B (phyB), as a light and thermal sensor, has been extensively studied in Arabidopsis. However, the specific mechanisms for how the phytochrome photoreceptors control the phenology in tree species remain poorly understood. We characterized the functions of PHYB genes and their downstream PHYTOCHROME INTERACTING FACTOR (PIF) targets in the regulation of shade avoidance and seasonal growth in hybrid aspen trees. We show that while phyB1 and phyB2, as phyB in other plants, act as suppressors of shoot elongation during vegetative growth, they act as promoters of tree seasonal growth. Furthermore, while the Populus homologs of both PIF4 and PIF8 are involved in the shade avoidance syndrome (SAS), only PIF8 plays a major role as a suppressor of seasonal growth. Our data suggest that the PHYB-PIF8 regulon controls seasonal growth through the regulation of FT and CENL1 expression while a genome-wide transcriptome analysis suggests how, in Populus trees, phyB coordinately regulates SAS responses and seasonal growth cessation.

@article{casanova-saez_auxin_2021,
	title = {Auxin {Metabolism} in {Plants}},
	volume = {13},
	issn = {1943-0264},
	url = {http://cshperspectives.cshlp.org/lookup/doi/10.1101/cshperspect.a039867},
	doi = {10/gkcr6m},
	abstract = {The major natural auxin in plants, indole-3-acetic acid (IAA), orchestrates a plethora of developmental responses that largely depend on the formation of auxin concentration gradients within plant tissues. Together with inter- and intracellular transport, IAA metabolism—which comprises biosynthesis, conjugation, and degradation—modulates auxin gradients and is therefore critical for plant growth. It is now very well established that IAA is mainly produced from Trp and that the IPyA pathway is a major and universally conserved biosynthetic route in plants, while other redundant pathways operate in parallel. Recent findings have shown that metabolic inactivation of IAA is also redundantly performed by oxidation and conjugation processes. An exquisite spatiotemporal expression of the genes for auxin synthesis and inactivation have been shown to drive several plant developmental processes. Moreover, a group of transcription factors and epigenetic regulators controlling the expression of auxin metabolic genes have been identified in past years, which are illuminating the road to understanding the molecular mechanisms behind the coordinated responses of local auxin metabolism to specific cues. Besides transcriptional regulation, subcellular compartmentalization of the IAA metabolism and posttranslational modifications of the metabolic enzymes are emerging as important contributors to IAA homeostasis. In this review, we summarize the current knowledge on (1) the pathways for IAA biosynthesis and inactivation in plants, (2) the influence of spatiotemporally regulated IAA metabolism on auxin-mediated responses, and (3) the regulatory mechanisms that modulate IAA levels in response to external and internal cues during plant development.},
	language = {en},
	number = {3},
	urldate = {2021-06-03},
	journal = {Cold Spring Harbor Perspectives in Biology},
	author = {Casanova-Sáez, Rubén and Mateo-Bonmatí, Eduardo and Ljung, Karin},
	month = mar,
	year = {2021},
	pages = {a039867},
}

The major natural auxin in plants, indole-3-acetic acid (IAA), orchestrates a plethora of developmental responses that largely depend on the formation of auxin concentration gradients within plant tissues. Together with inter- and intracellular transport, IAA metabolism—which comprises biosynthesis, conjugation, and degradation—modulates auxin gradients and is therefore critical for plant growth. It is now very well established that IAA is mainly produced from Trp and that the IPyA pathway is a major and universally conserved biosynthetic route in plants, while other redundant pathways operate in parallel. Recent findings have shown that metabolic inactivation of IAA is also redundantly performed by oxidation and conjugation processes. An exquisite spatiotemporal expression of the genes for auxin synthesis and inactivation have been shown to drive several plant developmental processes. Moreover, a group of transcription factors and epigenetic regulators controlling the expression of auxin metabolic genes have been identified in past years, which are illuminating the road to understanding the molecular mechanisms behind the coordinated responses of local auxin metabolism to specific cues. Besides transcriptional regulation, subcellular compartmentalization of the IAA metabolism and posttranslational modifications of the metabolic enzymes are emerging as important contributors to IAA homeostasis. In this review, we summarize the current knowledge on (1) the pathways for IAA biosynthesis and inactivation in plants, (2) the influence of spatiotemporally regulated IAA metabolism on auxin-mediated responses, and (3) the regulatory mechanisms that modulate IAA levels in response to external and internal cues during plant development.

@article{le_scale-up_2021,
	title = {Scale-up of {Somatic} {Embryogenesis} {Plant} {Production} of {Hybrid} {Larch} ({Larix} x eurolepis) {Using} {Temporary} {Immersion} {Bioreactors}},
	volume = {57},
	issn = {1071-2690},
	language = {English},
	number = {SUPPL 1},
	journal = {In Vitro Cellular \& Developmental Biology-Animal},
	author = {Le, K.-C. and Egertsdotter, U.},
	month = jun,
	year = {2021},
	keywords = {⛔ No DOI found},
	pages = {S38--S39},
}

@article{kloth_sli1_2021,
	title = {{SLI1} confers broad-spectrum resistance to phloem-feeding insects},
	volume = {44},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14064},
	doi = {10/gjzng9},
	abstract = {Resistance (R) genes usually compete in a coevolutionary arms race with reciprocal effectors to confer strain-specific resistance to pathogens or herbivorous insects. Here, we investigate the specificity of SLI1, a recently identified R gene in Arabidopsis that encodes a small heat shock-like protein involved in resistance to Myzus persicae aphids. In a panel with several aphid and whitefly species, SLI1 compromised reproductive rates of three species: the tobacco aphid M. persicae nicotianae, the cabbage aphid Brevicoryne brassicae and the cabbage whitefly Aleyrodes proletella. Electrical penetration graph recording of aphid behaviour, revealed shorter salivations and a 3-to-5-fold increase in phloem feeding on sli1 loss-of-function plants. The mustard aphid Lipaphis erysimi and Bemisia tabaci whitefly were not affected by SLI1. Unlike the other two aphid species, L. erysimi exhibited repetitive salivations preceding successful phloem feeding, indicating a role of salivary effectors in overcoming SLI1-mediated resistance. Microscopic characterization showed that SLI1 proteins localize in the sieve tubes of virtually all above- and below-ground tissues and co-localize with the aphid stylet tip after penetration of the sieve element plasma membrane. These observations reveal an unconventional R gene that escapes the paradigm of strain specificity and confers broad-spectrum quantitative resistance to phloem-feeding insects.},
	language = {en},
	number = {8},
	urldate = {2021-12-16},
	journal = {Plant, Cell \& Environment},
	author = {Kloth, Karen J. and Shah, Parth and Broekgaarden, Colette and Ström, Cecilia and Albrectsen, Benedicte R. and Dicke, Marcel},
	year = {2021},
	keywords = {R genes, aphids, phloem, plant resistance, whiteflies},
	pages = {2765--2776},
}

Resistance (R) genes usually compete in a coevolutionary arms race with reciprocal effectors to confer strain-specific resistance to pathogens or herbivorous insects. Here, we investigate the specificity of SLI1, a recently identified R gene in Arabidopsis that encodes a small heat shock-like protein involved in resistance to Myzus persicae aphids. In a panel with several aphid and whitefly species, SLI1 compromised reproductive rates of three species: the tobacco aphid M. persicae nicotianae, the cabbage aphid Brevicoryne brassicae and the cabbage whitefly Aleyrodes proletella. Electrical penetration graph recording of aphid behaviour, revealed shorter salivations and a 3-to-5-fold increase in phloem feeding on sli1 loss-of-function plants. The mustard aphid Lipaphis erysimi and Bemisia tabaci whitefly were not affected by SLI1. Unlike the other two aphid species, L. erysimi exhibited repetitive salivations preceding successful phloem feeding, indicating a role of salivary effectors in overcoming SLI1-mediated resistance. Microscopic characterization showed that SLI1 proteins localize in the sieve tubes of virtually all above- and below-ground tissues and co-localize with the aphid stylet tip after penetration of the sieve element plasma membrane. These observations reveal an unconventional R gene that escapes the paradigm of strain specificity and confers broad-spectrum quantitative resistance to phloem-feeding insects.

@article{martinez-hidalgo_medicago_2021,
	title = {Medicago root nodule microbiomes: insights into a complex ecosystem with potential candidates for plant growth promotion},
	issn = {1573-5036},
	shorttitle = {Medicago root nodule microbiomes},
	url = {https://doi.org/10.1007/s11104-021-05247-7},
	doi = {10/gn2mjd},
	abstract = {Studying the legume nodule microbiome is important for understanding the development and nutrition of the plants inhabited by the various microbes within and upon them. We analyzed the microbiomes of these underground organs from both an important crop plant (Medicago sativa) and a related legume (M. polymorpha) using metagenomic and culture-based techniques to identify the main cultivatable contributors to plant growth enhancement.},
	language = {en},
	urldate = {2022-01-07},
	journal = {Plant and Soil},
	author = {Martínez-Hidalgo, Pilar and Humm, Ethan A. and Still, David W. and Shi, Baochen and Pellegrini, Matteo and de la Roca, Gabriela and Veliz, Esteban and Maymon, Maskit and Bru, Pierrick and Huntemann, Marcel and Clum, Alicia and Palaniappan, Krishnaveni and Varghese, Neha and Mukherjee, Supratim and Reddy, T. B. K. and Daum, Chris and Ivanova, Natalia N. and Kyrpides, Nikos C. and Shapiro, Nicole and Eloe-Fadrosh, Emiley A. and Hirsch, Ann M.},
	month = dec,
	year = {2021},
}

Studying the legume nodule microbiome is important for understanding the development and nutrition of the plants inhabited by the various microbes within and upon them. We analyzed the microbiomes of these underground organs from both an important crop plant (Medicago sativa) and a related legume (M. polymorpha) using metagenomic and culture-based techniques to identify the main cultivatable contributors to plant growth enhancement.

@article{liu_centromere-specific_2021,
	title = {Centromere-{Specific} {Retrotransposons} and {Very}-{Long}-{Chain} {Fatty} {Acid} {Biosynthesis} in the {Genome} of {Yellowhorn} ({Xanthoceras} sorbifolium, {Sapindaceae}), an {Oil}-{Producing} {Tree} {With} {Significant} {Drought} {Resistance}},
	volume = {12},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2021.766389},
	doi = {10/gnsqvv},
	abstract = {In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95\% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7\% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30\% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.},
	urldate = {2021-12-16},
	journal = {Frontiers in Plant Science},
	author = {Liu, Hui and Yan, Xue-Mei and Wang, Xin-rui and Zhang, Dong-Xu and Zhou, Qingyuan and Shi, Tian-Le and Jia, Kai-Hua and Tian, Xue-Chan and Zhou, Shan-Shan and Zhang, Ren-Gang and Yun, Quan-Zheng and Wang, Qing and Xiang, Qiuhong and Mannapperuma, Chanaka and Van Zalen, Elena and Street, Nathaniel R. and Porth, Ilga and El-Kassaby, Yousry A. and Zhao, Wei and Wang, Xiao-Ru and Guan, Wenbin and Mao, Jian-Feng},
	year = {2021},
	pages = {2546},
}

In-depth genome characterization is still lacking for most of biofuel crops, especially for centromeres, which play a fundamental role during nuclear division and in the maintenance of genome stability. This study applied long-read sequencing technologies to assemble a highly contiguous genome for yellowhorn (Xanthoceras sorbifolium), an oil-producing tree, and conducted extensive comparative analyses to understand centromere structure and evolution, and fatty acid biosynthesis. We produced a reference-level genome of yellowhorn, ∼470 Mb in length with ∼95% of contigs anchored onto 15 chromosomes. Genome annotation identified 22,049 protein-coding genes and 65.7% of the genome sequence as repetitive elements. Long terminal repeat retrotransposons (LTR-RTs) account for ∼30% of the yellowhorn genome, which is maintained by a moderate birth rate and a low removal rate. We identified the centromeric regions on each chromosome and found enrichment of centromere-specific retrotransposons of LINE1 and Gypsy in these regions, which have evolved recently (∼0.7 MYA). We compared the genomes of three cultivars and found frequent inversions. We analyzed the transcriptomes from different tissues and identified the candidate genes involved in very-long-chain fatty acid biosynthesis and their expression profiles. Collinear block analysis showed that yellowhorn shared the gamma (γ) hexaploidy event with Vitis vinifera but did not undergo any further whole-genome duplication. This study provides excellent genomic resources for understanding centromere structure and evolution and for functional studies in this important oil-producing plant.

@article{muralidhara_perturbations_2021,
	title = {Perturbations in plant energy homeostasis prime lateral root initiation via {SnRK1}-{bZIP63}-{ARF19} signaling},
	volume = {118},
	copyright = {© 2021 . https://www.pnas.org/site/aboutpnas/licenses.xhtmlPublished under the PNAS license.},
	issn = {0027-8424, 1091-6490},
	url = {https://www.pnas.org/content/118/37/e2106961118},
	doi = {10/gmvnsg},
	abstract = {Plants adjust their energy metabolism to continuous environmental fluctuations, resulting in a tremendous plasticity in their architecture. The regulatory circuits involved, however, remain largely unresolved. In Arabidopsis, moderate perturbations in photosynthetic activity, administered by short-term low light exposure or unexpected darkness, lead to increased lateral root (LR) initiation. Consistent with expression of low-energy markers, these treatments alter energy homeostasis and reduce sugar availability in roots. Here, we demonstrate that the LR response requires the metabolic stress sensor kinase Snf1-RELATED-KINASE1 (SnRK1), which phosphorylates the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) that directly binds and activates the promoter of AUXIN RESPONSE FACTOR19 (ARF19), a key regulator of LR initiation. Consistently, starvation-induced ARF19 transcription is impaired in bzip63 mutants. This study highlights a positive developmental function of SnRK1. During energy limitation, LRs are initiated and primed for outgrowth upon recovery. Hence, this study provides mechanistic insights into how energy shapes the agronomically important root system.},
	language = {en},
	number = {37},
	urldate = {2021-11-12},
	journal = {Proceedings of the National Academy of Sciences},
	author = {Muralidhara, Prathibha and Weiste, Christoph and Collani, Silvio and Krischke, Markus and Kreisz, Philipp and Draken, Jan and Feil, Regina and Mair, Andrea and Teige, Markus and Müller, Martin J. and Schmid, Markus and Becker, Dirk and Lunn, John E. and Rolland, Filip and Hanson, Johannes and Dröge-Laser, Wolfgang},
	month = sep,
	year = {2021},
	keywords = {ARF19, SnRK1, bZIP63, lateral root, metabolic homeostasis},
}

Plants adjust their energy metabolism to continuous environmental fluctuations, resulting in a tremendous plasticity in their architecture. The regulatory circuits involved, however, remain largely unresolved. In Arabidopsis, moderate perturbations in photosynthetic activity, administered by short-term low light exposure or unexpected darkness, lead to increased lateral root (LR) initiation. Consistent with expression of low-energy markers, these treatments alter energy homeostasis and reduce sugar availability in roots. Here, we demonstrate that the LR response requires the metabolic stress sensor kinase Snf1-RELATED-KINASE1 (SnRK1), which phosphorylates the transcription factor BASIC LEUCINE ZIPPER63 (bZIP63) that directly binds and activates the promoter of AUXIN RESPONSE FACTOR19 (ARF19), a key regulator of LR initiation. Consistently, starvation-induced ARF19 transcription is impaired in bzip63 mutants. This study highlights a positive developmental function of SnRK1. During energy limitation, LRs are initiated and primed for outgrowth upon recovery. Hence, this study provides mechanistic insights into how energy shapes the agronomically important root system.

@article{fataftah_gigantea_2021,
	title = {{GIGANTEA} influences leaf senescence in trees in two different ways},
	volume = {187},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab439},
	doi = {10/gnxfqw},
	abstract = {GIGANTEA (GI) genes have a central role in plant development and influence several processes. Hybrid aspen T89 (Populus tremula x tremuloides) trees with low GI expression engineered through RNAi show severely compromised growth. To study the effect of reduced GI expression on leaf traits with special emphasis on leaf senescence, we grafted GI-RNAi scions onto wild-type rootstocks and successfully restored growth of the scions. The RNAi line had a distorted leaf shape and reduced photosynthesis, probably caused by modulation of phloem or stomatal function, increased starch accumulation, a higher carbon-to-nitrogen ratio, and reduced capacity to withstand moderate light stress. GI-RNAi also induced senescence under long day (LD) and moderate light conditions. Furthermore, the GI-RNAi lines were affected in their capacity to respond to “autumn environmental cues” inducing senescence, a type of leaf senescence that has physiological and biochemical characteristics that differ from those of senescence induced directly by stress under LD conditions. Overexpression of GI delayed senescence under simulated autumn conditions. The two different effects on leaf senescence under LD or simulated autumn conditions were not affected by the expression of FLOWERING LOCUS T. GI expression regulated leaf senescence locally—the phenotype followed the genotype of the branch, independent of its position on the tree—and trees with modified gene expression were affected in a similar way when grown in the field as under controlled conditions. Taken together, GI plays a central role in sensing environmental changes during autumn and determining the appropriate timing for leaf senescence in Populus.},
	number = {4},
	urldate = {2021-10-15},
	journal = {Plant Physiology},
	author = {Fataftah, Nazeer and Bag, Pushan and André, Domenique and Lihavainen, Jenna and Zhang, Bo and Ingvarsson, Pär K and Nilsson, Ove and Jansson, Stefan},
	month = sep,
	year = {2021},
	pages = {2435--2450},
}

GIGANTEA (GI) genes have a central role in plant development and influence several processes. Hybrid aspen T89 (Populus tremula x tremuloides) trees with low GI expression engineered through RNAi show severely compromised growth. To study the effect of reduced GI expression on leaf traits with special emphasis on leaf senescence, we grafted GI-RNAi scions onto wild-type rootstocks and successfully restored growth of the scions. The RNAi line had a distorted leaf shape and reduced photosynthesis, probably caused by modulation of phloem or stomatal function, increased starch accumulation, a higher carbon-to-nitrogen ratio, and reduced capacity to withstand moderate light stress. GI-RNAi also induced senescence under long day (LD) and moderate light conditions. Furthermore, the GI-RNAi lines were affected in their capacity to respond to “autumn environmental cues” inducing senescence, a type of leaf senescence that has physiological and biochemical characteristics that differ from those of senescence induced directly by stress under LD conditions. Overexpression of GI delayed senescence under simulated autumn conditions. The two different effects on leaf senescence under LD or simulated autumn conditions were not affected by the expression of FLOWERING LOCUS T. GI expression regulated leaf senescence locally—the phenotype followed the genotype of the branch, independent of its position on the tree—and trees with modified gene expression were affected in a similar way when grown in the field as under controlled conditions. Taken together, GI plays a central role in sensing environmental changes during autumn and determining the appropriate timing for leaf senescence in Populus.

@article{nguyen_effect_2021,
	title = {Effect of additive, dominant and epistatic variances on breeding and deployment strategy in {Norway} spruce},
	issn = {0015-752X},
	url = {https://doi.org/10.1093/forestry/cpab052},
	doi = {10/gnzpmt},
	abstract = {Genetic variances are important parameters and have a great impact on the determination of optimal breeding strategies of tree species. A large clonal testing program was conducted to estimate additive, dominant and epistatic variances for the development of breeding and deployment strategies in Norway spruce (Picea abies (L.) Karst.). The analysis results of genetic variation for growth and wood properties in two clonal trials in central Sweden indicated that the important sources of total genetic variation were both additive and non-additive genetic variances. Additive genetic variation accounted for the majority of total genetic variation for diameter at breast height (DBH) and wood quality traits, whereas non-additive genetic variation was significant only for tree height at an early age. Predicted genetic gain was the highest for clonal deployment based on best tested (replicated) clones (4.7–65.3 per cent), followed by clonal deployment of the best individual trees from a full-sib family trial (3.5–57.7 per cent), and the deployment of seedlings generated by open-pollination (1.9–48.3 per cent).},
	urldate = {2022-01-05},
	journal = {Forestry: An International Journal of Forest Research},
	author = {Nguyen, Hong T H and Chen, Zhi-Qiang and Fries, Anders and Berlin, Mats and Hallingbäck, Henrik R and Wu, Harry X},
	month = dec,
	year = {2021},
	pages = {cpab052},
}

Genetic variances are important parameters and have a great impact on the determination of optimal breeding strategies of tree species. A large clonal testing program was conducted to estimate additive, dominant and epistatic variances for the development of breeding and deployment strategies in Norway spruce (Picea abies (L.) Karst.). The analysis results of genetic variation for growth and wood properties in two clonal trials in central Sweden indicated that the important sources of total genetic variation were both additive and non-additive genetic variances. Additive genetic variation accounted for the majority of total genetic variation for diameter at breast height (DBH) and wood quality traits, whereas non-additive genetic variation was significant only for tree height at an early age. Predicted genetic gain was the highest for clonal deployment based on best tested (replicated) clones (4.7–65.3 per cent), followed by clonal deployment of the best individual trees from a full-sib family trial (3.5–57.7 per cent), and the deployment of seedlings generated by open-pollination (1.9–48.3 per cent).

@article{christie_qtlxplorer_2021,
	title = {{qtlXplorer}: an online systems genetics browser in the {Eucalyptus} {Genome} {Integrative} {Explorer} ({EucGenIE})},
	volume = {22},
	issn = {1471-2105},
	shorttitle = {{qtlXplorer}},
	url = {https://doi.org/10.1186/s12859-021-04514-9},
	doi = {10/gnxfq5},
	abstract = {Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking.},
	number = {1},
	urldate = {2021-12-29},
	journal = {BMC Bioinformatics},
	author = {Christie, Nanette and Mannapperuma, Chanaka and Ployet, Raphael and van der Merwe, Karen and Mähler, Niklas and Delhomme, Nicolas and Naidoo, Sanushka and Mizrachi, Eshchar and Street, Nathaniel R. and Myburg, Alexander A.},
	month = dec,
	year = {2021},
	keywords = {Co-expression, Database, EucGenIE, Eucalyptus, Genome browser, Online resource, Systems genetics, eQTL, qtlXplorer, ‘Omics integration},
	pages = {595},
}

Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking.

@article{sgobba_unravel_2021,
	title = {Unravel the {Local} {Complexity} of {Biological} {Environments} by {MALDI} {Mass} {Spectrometry} {Imaging}},
	volume = {22},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/1422-0067/22/22/12393},
	doi = {10/gnp9hb},
	abstract = {Classic metabolomic methods have proven to be very useful to study functional biology and variation in the chemical composition of different tissues. However, they do not provide any information in terms of spatial localization within fine structures. Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) does and reaches at best a spatial resolution of 0.25 μm depending on the laser setup, making it a very powerful tool to analyze the local complexity of biological samples at the cellular level. Here, we intend to give an overview of the diversity of the molecules and localizations analyzed using this method as well as to update on the latest adaptations made to circumvent the complexity of samples. MALDI MSI has been widely used in medical sciences and is now developing in research areas as diverse as entomology, microbiology, plant biology, and plant–microbe interactions, the rhizobia symbiosis being the most exhaustively described so far. Those are the fields of interest on which we will focus to demonstrate MALDI MSI strengths in characterizing the spatial distributions of metabolites, lipids, and peptides in relation to biological questions.},
	language = {en},
	number = {22},
	urldate = {2021-12-02},
	journal = {International Journal of Molecular Sciences},
	author = {Sgobba, Elvira and Daguerre, Yohann and Giampà, Marco},
	month = jan,
	year = {2021},
	note = {Number: 22
Publisher: Multidisciplinary Digital Publishing Institute},
	keywords = {MALDI MSI, imaging, lipidomics, metabolomics, microbiology, plants},
	pages = {12393},
}

Classic metabolomic methods have proven to be very useful to study functional biology and variation in the chemical composition of different tissues. However, they do not provide any information in terms of spatial localization within fine structures. Matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) does and reaches at best a spatial resolution of 0.25 μm depending on the laser setup, making it a very powerful tool to analyze the local complexity of biological samples at the cellular level. Here, we intend to give an overview of the diversity of the molecules and localizations analyzed using this method as well as to update on the latest adaptations made to circumvent the complexity of samples. MALDI MSI has been widely used in medical sciences and is now developing in research areas as diverse as entomology, microbiology, plant biology, and plant–microbe interactions, the rhizobia symbiosis being the most exhaustively described so far. Those are the fields of interest on which we will focus to demonstrate MALDI MSI strengths in characterizing the spatial distributions of metabolites, lipids, and peptides in relation to biological questions.

@article{rendon-anaya_adaptive_2021,
	title = {Adaptive introgression facilitate adaptation to high latitudes in {European} aspen ({Populus} tremula {L}.)},
	volume = {38},
	issn = {1537-1719},
	url = {https://doi.org/10.1093/molbev/msab229},
	doi = {10.1093/molbev/msab229},
	abstract = {Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole genome re-sequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum (LGM), we detected an adaptive introgression event in a genome region of ∼500kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin - probably Russian - of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results therefore emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits.},
	language = {eng},
	number = {11},
	journal = {Molecular Biology and Evolution},
	author = {Rendón-Anaya, Martha and Wilson, Jonathan and Sveinsson, Sæmundur and Fedorkov, Aleksey and Cottrell, Joan and Bailey, Mark E. S. and Ruņģis, Dainis and Lexer, Christian and Jansson, Stefan and Robinson, Kathryn M. and Street, Nathaniel R. and Ingvarsson, Pär K.},
	month = jul,
	year = {2021},
	pages = {5034--5050},
}

Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole genome re-sequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum (LGM), we detected an adaptive introgression event in a genome region of ∼500kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin - probably Russian - of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results therefore emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits.

@article{dob_jasmonate_2021,
	title = {Jasmonate inhibits adventitious root initiation through repression of {CKX1} and activation of {RAP2}.{6L} transcription factor in {Arabidopsis}},
	volume = {72},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/erab358},
	doi = {10.1093/jxb/erab358},
	abstract = {Adventitious rooting is a de novo organogenesis process that enables plants to propagate clonally and cope with environmental stresses. Adventitious root initiation (ARI) is controlled by interconnected transcriptional and hormonal networks, but there is little knowledge of the genetic and molecular programs orchestrating these networks. Thus, we have applied genome-wide transcriptome profiling to elucidate the profound transcriptional reprogramming events preceding ARI. These reprogramming events are associated with the downregulation of cytokinin (CK) signaling and response genes, which could be triggers for ARI. Interestingly, we found that CK free-base (iP, tZ, cZ and DHZ) content declined during ARI, due to downregulation of de novo CK biosynthesis and upregulation of CK inactivation pathways. We also found that MYC2-dependent jasmonate (JA) signaling inhibits ARI by downregulating the expression of the CYTOKININ OXIDASE/DEHYDROGENASE1 (CKX1) gene. We also demonstrated that JA and CK synergistically activate expression of RELATED to APETALA2.6 LIKE (RAP2.6L) transcription factor, and constitutive expression of this transcription factor strongly inhibits ARI. Collectively, our findings reveal that previously unknown genetic interactions between JA and CK play key roles in ARI},
	number = {20},
	urldate = {2021-08-18},
	journal = {Journal of Experimental Botany},
	author = {Dob, Asma and Lakehal, Abdellah and Novak, Ondrej and Bellini, Catherine},
	month = jul,
	year = {2021},
	keywords = {Adventitious roots, Arabidopsis, Arabidopsis Proteins, CKX1, Cyclopentanes, Gene Expression Regulation, Plant, MYC2, Oxylipins, Plant Roots, RAP2.6L, Transcription Factors, cytokinins, jasmonate, light, vegetative propagation},
	pages = {7107--7118},
}

Adventitious rooting is a de novo organogenesis process that enables plants to propagate clonally and cope with environmental stresses. Adventitious root initiation (ARI) is controlled by interconnected transcriptional and hormonal networks, but there is little knowledge of the genetic and molecular programs orchestrating these networks. Thus, we have applied genome-wide transcriptome profiling to elucidate the profound transcriptional reprogramming events preceding ARI. These reprogramming events are associated with the downregulation of cytokinin (CK) signaling and response genes, which could be triggers for ARI. Interestingly, we found that CK free-base (iP, tZ, cZ and DHZ) content declined during ARI, due to downregulation of de novo CK biosynthesis and upregulation of CK inactivation pathways. We also found that MYC2-dependent jasmonate (JA) signaling inhibits ARI by downregulating the expression of the CYTOKININ OXIDASE/DEHYDROGENASE1 (CKX1) gene. We also demonstrated that JA and CK synergistically activate expression of RELATED to APETALA2.6 LIKE (RAP2.6L) transcription factor, and constitutive expression of this transcription factor strongly inhibits ARI. Collectively, our findings reveal that previously unknown genetic interactions between JA and CK play key roles in ARI

@article{igamberdiev_pyrophosphate_2021,
	title = {Pyrophosphate as an alternative energy currency in plants},
	volume = {478},
	issn = {0264-6021},
	url = {https://doi.org/10.1042/BCJ20200940},
	doi = {10.1042/BCJ20200940},
	abstract = {In the conditions of [Mg2+] elevation that occur, in particular, under low oxygen stress and are the consequence of the decrease in [ATP] and increase in [ADP] and [AMP], pyrophosphate (PPi) can function as an alternative energy currency in plant cells. In addition to its production by various metabolic pathways, PPi can be synthesized in the combined reactions of pyruvate, phosphate dikinase (PPDK) and pyruvate kinase (PK) by so-called PK/PPDK substrate cycle, and in the reverse reaction of membrane-bound H+-pyrophosphatase, which uses the energy of electrochemical gradients generated on tonoplast and plasma membrane. The PPi can then be consumed in its active forms of MgPPi and Mg2PPi by PPi-utilizing enzymes, which require an elevated [Mg2+]. This ensures a continuous operation of glycolysis in the conditions of suppressed ATP synthesis, keeping metabolism energy efficient and less dependent on ATP.},
	language = {en},
	number = {8},
	urldate = {2021-06-03},
	journal = {Biochemical Journal},
	author = {Igamberdiev, Abir U. and Kleczkowski, Leszek A.},
	month = apr,
	year = {2021},
	pages = {1515--1524},
}

In the conditions of [Mg2+] elevation that occur, in particular, under low oxygen stress and are the consequence of the decrease in [ATP] and increase in [ADP] and [AMP], pyrophosphate (PPi) can function as an alternative energy currency in plant cells. In addition to its production by various metabolic pathways, PPi can be synthesized in the combined reactions of pyruvate, phosphate dikinase (PPDK) and pyruvate kinase (PK) by so-called PK/PPDK substrate cycle, and in the reverse reaction of membrane-bound H+-pyrophosphatase, which uses the energy of electrochemical gradients generated on tonoplast and plasma membrane. The PPi can then be consumed in its active forms of MgPPi and Mg2PPi by PPi-utilizing enzymes, which require an elevated [Mg2+]. This ensures a continuous operation of glycolysis in the conditions of suppressed ATP synthesis, keeping metabolism energy efficient and less dependent on ATP.

@article{wu_balancing_2021,
	title = {Balancing {Breeding} for {Growth} and {Fecundity} in {Radiata} {Pine} (\textit{{Pinus} radiata} {D}. {Don}) {Breeding} {Programme}},
	volume = {14},
	issn = {1752-4571, 1752-4571},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/eva.13164},
	doi = {10.1111/eva.13164},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Evolutionary Applications},
	author = {Wu, Harry X. and Ker, Richard and Chen, Zhiqiang and Ivkovic, Milos},
	month = mar,
	year = {2021},
	pages = {834--846},
}

@article{calderon_how_2021,
	series = {Cell signaling and gene regulation},
	title = {How retrograde signaling is intertwined with the evolution of photosynthetic eukaryotes},
	volume = {63},
	issn = {1369-5266},
	url = {https://www.sciencedirect.com/science/article/pii/S1369526621000935},
	doi = {10/gmkx8p},
	abstract = {Chloroplasts and mitochondria evolved from free-living prokaryotic organisms that entered the eukaryotic cell through endosymbiosis. The gradual conversion from endosymbiont to organelle during the course of evolution was accompanied by the development of a communication system between the host and the endosymbiont, referred to as retrograde signaling or organelle-to-nucleus signaling. In higher plants, plastid-to-nucleus signaling involves multiple signaling pathways necessary to coordinate plastid function and cellular responses to developmental and environmental stimuli. Phylogenetic reconstructions using sequence information from evolutionarily diverse photosynthetic eukaryotes have begun to provide information about how retrograde signaling pathways were adopted and modified in different lineages over time. A tight communication system was likely a major facilitator of plants conquest of the land because it would have enabled the algal ancestors of land plants to better allocate their cellular resources in response to high light and desiccation, the major stressor for streptophyte algae in a terrestrial habitat. In this review, we aim to give an evolutionary perspective on plastid-to-nucleus signaling.},
	language = {en},
	urldate = {2021-11-12},
	journal = {Current Opinion in Plant Biology},
	author = {Calderon, Robert H. and Strand, Åsa},
	month = oct,
	year = {2021},
	keywords = {Cyanobacteria, Endosymbiosis event, Mitochondria, Plastids, Retrograde signals, Stress, lncRNA.},
	pages = {102093},
}

Chloroplasts and mitochondria evolved from free-living prokaryotic organisms that entered the eukaryotic cell through endosymbiosis. The gradual conversion from endosymbiont to organelle during the course of evolution was accompanied by the development of a communication system between the host and the endosymbiont, referred to as retrograde signaling or organelle-to-nucleus signaling. In higher plants, plastid-to-nucleus signaling involves multiple signaling pathways necessary to coordinate plastid function and cellular responses to developmental and environmental stimuli. Phylogenetic reconstructions using sequence information from evolutionarily diverse photosynthetic eukaryotes have begun to provide information about how retrograde signaling pathways were adopted and modified in different lineages over time. A tight communication system was likely a major facilitator of plants conquest of the land because it would have enabled the algal ancestors of land plants to better allocate their cellular resources in response to high light and desiccation, the major stressor for streptophyte algae in a terrestrial habitat. In this review, we aim to give an evolutionary perspective on plastid-to-nucleus signaling.

@article{le_temporary_2021,
	title = {Temporary immersion bioreactor system for propagation by somatic embryogenesis of hybrid larch ({Larix} × eurolepis {Henry})},
	volume = {32},
	issn = {2215-017X},
	url = {https://www.sciencedirect.com/science/article/pii/S2215017X21001004},
	doi = {10/gnj3pm},
	abstract = {Somatic embryogenesis (SE) has high potential for large-scale clonal propagation of conifers. Different types of bioreactor cultures have been tested for the conifer SE process where the temporary immersion bioreactors (TIBs) have proved to be useful across the different developmental steps of the SE process. In the present study the use of TIBs was tested for hybrid larch (Larix × eurolepis Henry). The results showed two-fold increases in both fresh weight (FW) of pro-embryogenic masses (PEMs) and yield of cotyledonary embryos in the TIBs compared to solid medium in plates. For the germination phase, the highest number of roots per plant, the root length and height of plants were also obtained in the TIBs. The results show that the TIB system can be successfully used to support scale up of plant production in all steps of the SE process from proliferation to germination of hybrid larch (Larix × eurolepis Henry).},
	language = {en},
	urldate = {2021-11-12},
	journal = {Biotechnology Reports},
	author = {Le, Kim-Cuong and Dedicova, Beata and Johansson, Sofie and Lelu-Walter, Marie-Anne and Egertsdotter, Ulrika},
	month = dec,
	year = {2021},
	keywords = {Germination, Horizontal TIB, Larix × eurolepis, Scale up, Somatic embryogenesis, Vertical TIB, ×},
	pages = {e00684},
}

Somatic embryogenesis (SE) has high potential for large-scale clonal propagation of conifers. Different types of bioreactor cultures have been tested for the conifer SE process where the temporary immersion bioreactors (TIBs) have proved to be useful across the different developmental steps of the SE process. In the present study the use of TIBs was tested for hybrid larch (Larix × eurolepis Henry). The results showed two-fold increases in both fresh weight (FW) of pro-embryogenic masses (PEMs) and yield of cotyledonary embryos in the TIBs compared to solid medium in plates. For the germination phase, the highest number of roots per plant, the root length and height of plants were also obtained in the TIBs. The results show that the TIB system can be successfully used to support scale up of plant production in all steps of the SE process from proliferation to germination of hybrid larch (Larix × eurolepis Henry).

@article{chen_determination_2021,
	title = {Determination of conifer age biomarker {DAL1} interactome using {Y2H}-seq},
	volume = {1},
	copyright = {2021 The Author(s)},
	issn = {2767-3812},
	url = {http://www.maxapress.com/rticle/doi/10.48130/FR-2021-0012},
	doi = {10/gnj3pg},
	abstract = {Age is a sophisticated physiological signal that ensures the sequence of different developmental stages in organisms. The regulation of ageing pathways appears to differ between gymnosperms and angiosperms. We previously identified \textit{DAL1} as a conserved conifer age biomarker that plays a crucial role in the transition from vegetative to reproductive life-history phases in pines. Therefore, elucidating the specific interaction events related to DAL1 is key to understanding how age drives conifer development. Large-scale yeast two-hybrid (Y2H) analysis followed by next-generation high-throughput sequencing (Y2H-seq) allowed us to identify 135 PtDAL1 interacting proteins in \textit{Pinus tabuliformis}. Our study found that PtDAL1 interacting proteins showed an ageing-related module, with sophisticated interacting networks composed of transcription factors (TFs), transcriptional regulators (TRs), and kinases. These interacting proteins are produced in response to a variety of phytohormones and environmental signals, and are likely involved in wood formation, needle development, oleoresin terpenoids biosynthesis, and reproductive development. In this study, we propose a novel regulation model of conifer ageing pathways whereby PtDAL1 coordinates different environmental stimuli and interacts with corresponding proteins to regulate appropriate development.},
	language = {en},
	number = {1},
	urldate = {2021-11-22},
	journal = {Forestry Research},
	author = {Chen, Xi and Zhu, Qianya and Nie, Yumeng and Han, Fangxu and Li, Yue and Wu, Harry X. and Niu, Shihui},
	month = jul,
	year = {2021},
	pages = {1--12},
}

Age is a sophisticated physiological signal that ensures the sequence of different developmental stages in organisms. The regulation of ageing pathways appears to differ between gymnosperms and angiosperms. We previously identified DAL1 as a conserved conifer age biomarker that plays a crucial role in the transition from vegetative to reproductive life-history phases in pines. Therefore, elucidating the specific interaction events related to DAL1 is key to understanding how age drives conifer development. Large-scale yeast two-hybrid (Y2H) analysis followed by next-generation high-throughput sequencing (Y2H-seq) allowed us to identify 135 PtDAL1 interacting proteins in Pinus tabuliformis. Our study found that PtDAL1 interacting proteins showed an ageing-related module, with sophisticated interacting networks composed of transcription factors (TFs), transcriptional regulators (TRs), and kinases. These interacting proteins are produced in response to a variety of phytohormones and environmental signals, and are likely involved in wood formation, needle development, oleoresin terpenoids biosynthesis, and reproductive development. In this study, we propose a novel regulation model of conifer ageing pathways whereby PtDAL1 coordinates different environmental stimuli and interacts with corresponding proteins to regulate appropriate development.

@article{seyfferth_populuspterf85_2021,
	title = {{PopulusPtERF85} {Balances} {Xylem} {Cell} {Expansion} and {Secondary} {Cell} {Wall} {Formation} in {Hybrid} {Aspen}},
	volume = {10},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/2073-4409/10/8/1971},
	doi = {10.3390/cells10081971},
	abstract = {Secondary growth relies on precise and specialized transcriptional networks that determine cell division, differentiation, and maturation of xylem cells. We identified a novel role for the ethylene-induced Populus Ethylene Response Factor PtERF85 (Potri.015G023200) in balancing xylem cell expansion and secondary cell wall (SCW) formation in hybrid aspen (Populus tremula x tremuloides). Expression of PtERF85 is high in phloem and cambium cells and during the expansion of xylem cells, while it is low in maturing xylem tissue. Extending PtERF85 expression into SCW forming zones of woody tissues through ectopic expression reduced wood density and SCW thickness of xylem fibers but increased fiber diameter. Xylem transcriptomes from the transgenic trees revealed transcriptional induction of genes involved in cell expansion, translation, and growth. The expression of genes associated with plant vascular development and the biosynthesis of SCW chemical components such as xylan and lignin, was down-regulated in the transgenic trees. Our results suggest that PtERF85 activates genes related to xylem cell expansion, while preventing transcriptional activation of genes related to SCW formation. The importance of precise spatial expression of PtERF85 during wood development together with the observed phenotypes in response to ectopic PtERF85 expression suggests that PtERF85 contributes to the transition of fiber cells from elongation to secondary cell wall deposition.},
	language = {en},
	number = {8},
	urldate = {2021-09-02},
	journal = {Cells},
	author = {Seyfferth, Carolin and Wessels, Bernard A. and Vahala, Jorma and Kangasjärvi, Jaakko and Delhomme, Nicolas and Hvidsten, Torgeir R. and Tuominen, Hannele and Lundberg-Felten, Judith},
	month = aug,
	year = {2021},
	keywords = {ERF85 (CRF4), cell wall thickness, lignin, ribosome biogenesis, wood development, xylem expansion},
	pages = {1971},
}

Secondary growth relies on precise and specialized transcriptional networks that determine cell division, differentiation, and maturation of xylem cells. We identified a novel role for the ethylene-induced Populus Ethylene Response Factor PtERF85 (Potri.015G023200) in balancing xylem cell expansion and secondary cell wall (SCW) formation in hybrid aspen (Populus tremula x tremuloides). Expression of PtERF85 is high in phloem and cambium cells and during the expansion of xylem cells, while it is low in maturing xylem tissue. Extending PtERF85 expression into SCW forming zones of woody tissues through ectopic expression reduced wood density and SCW thickness of xylem fibers but increased fiber diameter. Xylem transcriptomes from the transgenic trees revealed transcriptional induction of genes involved in cell expansion, translation, and growth. The expression of genes associated with plant vascular development and the biosynthesis of SCW chemical components such as xylan and lignin, was down-regulated in the transgenic trees. Our results suggest that PtERF85 activates genes related to xylem cell expansion, while preventing transcriptional activation of genes related to SCW formation. The importance of precise spatial expression of PtERF85 during wood development together with the observed phenotypes in response to ectopic PtERF85 expression suggests that PtERF85 contributes to the transition of fiber cells from elongation to secondary cell wall deposition.

@article{ahlinder_life_2021,
	title = {Life stage-specific inbreeding depression in long-lived {Pinaceae} species depends on population connectivity},
	volume = {11},
	issn = {2045-2322},
	url = {http://www.nature.com/articles/s41598-021-88128-4},
	doi = {10.1038/s41598-021-88128-4},
	abstract = {Inbreeding depression (ID) is a fundamental selective pressure that shapes mating systems and population genetic structures in plants. Although it has been shown that ID varies over the life stages of shorter-lived plants, less is known about how the fitness effects of inbreeding vary across life stages in long-lived species. We conducted a literature survey in the Pinaceae, a tree family known to harbour some of the highest mutational loads ever reported. Using a meta-regression model, we investigated distributions of inbreeding depression over life stages, adjusting for effects of inbreeding levels and the genetic differentiation of populations within species. The final dataset contained 147 estimates of ID across life stages from 41 studies. 44 Fst estimates were collected from 40 peer-reviewed studies for the 18 species to aid genetic differentiation modelling. Partitioning species into fragmented and well-connected groups using Fst resulted in the best way (i.e. trade-off between high goodness-of-fit of the model to the data and reduced model complexity) to incorporate genetic connectivity in the meta-regression analysis. Inclusion of a life stage term and its interaction with the inbreeding coefficient (F) dramatically increased model precision. We observed that the correlation between ID and F was significant at the earliest life stage. Although partitioning of species populations into fragmented and well-connected groups explained little of the between-study heterogeneity, the inclusion of an interaction between life stage and population differentiation revealed that populations with fragmented distributions suffered lower inbreeding depression at early embryonic stages than species with well-connected populations. There was no evidence for increased ID in late life stages in well-connected populations, although ID tended to increase across life stages in the fragmented group. These findings suggest that life stage data should be included in inbreeding depression studies and that inbreeding needs to be managed over life stages in commercial populations of long-lived plants.},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {Scientific Reports},
	author = {Ahlinder, Jon and Giles, Barbara E. and García-Gil, M. Rosario},
	month = apr,
	year = {2021},
	pages = {8834},
}

Inbreeding depression (ID) is a fundamental selective pressure that shapes mating systems and population genetic structures in plants. Although it has been shown that ID varies over the life stages of shorter-lived plants, less is known about how the fitness effects of inbreeding vary across life stages in long-lived species. We conducted a literature survey in the Pinaceae, a tree family known to harbour some of the highest mutational loads ever reported. Using a meta-regression model, we investigated distributions of inbreeding depression over life stages, adjusting for effects of inbreeding levels and the genetic differentiation of populations within species. The final dataset contained 147 estimates of ID across life stages from 41 studies. 44 Fst estimates were collected from 40 peer-reviewed studies for the 18 species to aid genetic differentiation modelling. Partitioning species into fragmented and well-connected groups using Fst resulted in the best way (i.e. trade-off between high goodness-of-fit of the model to the data and reduced model complexity) to incorporate genetic connectivity in the meta-regression analysis. Inclusion of a life stage term and its interaction with the inbreeding coefficient (F) dramatically increased model precision. We observed that the correlation between ID and F was significant at the earliest life stage. Although partitioning of species populations into fragmented and well-connected groups explained little of the between-study heterogeneity, the inclusion of an interaction between life stage and population differentiation revealed that populations with fragmented distributions suffered lower inbreeding depression at early embryonic stages than species with well-connected populations. There was no evidence for increased ID in late life stages in well-connected populations, although ID tended to increase across life stages in the fragmented group. These findings suggest that life stage data should be included in inbreeding depression studies and that inbreeding needs to be managed over life stages in commercial populations of long-lived plants.

@article{bag_light_2021,
	title = {Light {Harvesting} in {Fluctuating} {Environments}: {Evolution} and {Function} of {Antenna} {Proteins} across {Photosynthetic} {Lineage}},
	volume = {10},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	shorttitle = {Light {Harvesting} in {Fluctuating} {Environments}},
	url = {https://www.mdpi.com/2223-7747/10/6/1184},
	doi = {10/gkhz4d},
	abstract = {Photosynthesis is the major natural process that can harvest and harness solar energy into chemical energy. Photosynthesis is performed by a vast number of organisms from single cellular bacteria to higher plants and to make the process efficient, all photosynthetic organisms possess a special type of pigment protein complex(es) that is (are) capable of trapping light energy, known as photosynthetic light-harvesting antennae. From an evolutionary point of view, simpler (unicellular) organisms typically have a simple antenna, whereas higher plants possess complex antenna systems. The higher complexity of the antenna systems provides efficient fine tuning of photosynthesis. This relationship between the complexity of the antenna and the increasing complexity of the organism is mainly related to the remarkable acclimation capability of complex organisms under fluctuating environmental conditions. These antenna complexes not only harvest light, but also provide photoprotection under fluctuating light conditions. In this review, the evolution, structure, and function of different antenna complexes, from single cellular organisms to higher plants, are discussed in the context of the ability to acclimate and adapt to cope under fluctuating environmental conditions.},
	language = {en},
	number = {6},
	urldate = {2021-06-15},
	journal = {Plants},
	author = {Bag, Pushan},
	month = jun,
	year = {2021},
	keywords = {angiosperms, cyanobacteria, evolution, gymnosperms, light-harvesting complexes, photoprotection, photosynthesis, phycobilisomes},
	pages = {1184},
}

Photosynthesis is the major natural process that can harvest and harness solar energy into chemical energy. Photosynthesis is performed by a vast number of organisms from single cellular bacteria to higher plants and to make the process efficient, all photosynthetic organisms possess a special type of pigment protein complex(es) that is (are) capable of trapping light energy, known as photosynthetic light-harvesting antennae. From an evolutionary point of view, simpler (unicellular) organisms typically have a simple antenna, whereas higher plants possess complex antenna systems. The higher complexity of the antenna systems provides efficient fine tuning of photosynthesis. This relationship between the complexity of the antenna and the increasing complexity of the organism is mainly related to the remarkable acclimation capability of complex organisms under fluctuating environmental conditions. These antenna complexes not only harvest light, but also provide photoprotection under fluctuating light conditions. In this review, the evolution, structure, and function of different antenna complexes, from single cellular organisms to higher plants, are discussed in the context of the ability to acclimate and adapt to cope under fluctuating environmental conditions.

@article{calleja-rodriguez_genomic_2021,
	title = {Genomic {Predictions} {With} {Nonadditive} {Effects} {Improved} {Estimates} of {Additive} {Effects} and {Predictions} of {Total} {Genetic} {Values} in {Pinus} sylvestris},
	volume = {12},
	issn = {1664-462X},
	doi = {10/gmhq7h},
	abstract = {Genomic selection study (GS) focusing on nonadditive genetic effects of dominance and the first order of epistatic effects, in a full-sib family population of 695 Scots pine (Pinus sylvestris L.) trees, was undertaken for growth and wood quality traits, using 6,344 single nucleotide polymorphism markers (SNPs) generated by genotyping-by-sequencing (GBS). Genomic marker-based relationship matrices offer more effective modeling of nonadditive genetic effects than pedigree-based models, thus increasing the knowledge on the relevance of dominance and epistatic variation in forest tree breeding. Genomic marker-based models were compared with pedigree-based models showing a considerable dominance and epistatic variation for growth traits. Nonadditive genetic variation of epistatic nature (additive × additive) was detected for growth traits, wood density (DEN), and modulus of elasticity (MOEd) representing between 2.27 and 34.5\% of the total phenotypic variance. Including dominance variance in pedigree-based Best Linear Unbiased Prediction (PBLUP) and epistatic variance in genomic-based Best Linear Unbiased Prediction (GBLUP) resulted in decreased narrow-sense heritability and increased broad-sense heritability for growth traits, DEN and MOEd. Higher genetic gains were reached with early GS based on total genetic values, than with conventional pedigree selection for a selection intensity of 1\%. This study indicates that nonadditive genetic variance may have a significant role in the variation of selection traits of Scots pine, thus clonal deployment could be an attractive alternative for the species. Additionally, confidence in the role of nonadditive genetic effects in this breeding program should be pursued in the future, using GS.},
	language = {eng},
	journal = {Frontiers in Plant Science},
	author = {Calleja-Rodriguez, Ainhoa and Chen, ZhiQiang and Suontama, Mari and Pan, Jin and Wu, Harry X.},
	year = {2021},
	keywords = {dominance, epistasis, genetic gain, genomic prediction, nonadditive effects, response to selection, scots pine (Pinus sylvestris L)},
	pages = {666820},
}

Genomic selection study (GS) focusing on nonadditive genetic effects of dominance and the first order of epistatic effects, in a full-sib family population of 695 Scots pine (Pinus sylvestris L.) trees, was undertaken for growth and wood quality traits, using 6,344 single nucleotide polymorphism markers (SNPs) generated by genotyping-by-sequencing (GBS). Genomic marker-based relationship matrices offer more effective modeling of nonadditive genetic effects than pedigree-based models, thus increasing the knowledge on the relevance of dominance and epistatic variation in forest tree breeding. Genomic marker-based models were compared with pedigree-based models showing a considerable dominance and epistatic variation for growth traits. Nonadditive genetic variation of epistatic nature (additive × additive) was detected for growth traits, wood density (DEN), and modulus of elasticity (MOEd) representing between 2.27 and 34.5% of the total phenotypic variance. Including dominance variance in pedigree-based Best Linear Unbiased Prediction (PBLUP) and epistatic variance in genomic-based Best Linear Unbiased Prediction (GBLUP) resulted in decreased narrow-sense heritability and increased broad-sense heritability for growth traits, DEN and MOEd. Higher genetic gains were reached with early GS based on total genetic values, than with conventional pedigree selection for a selection intensity of 1%. This study indicates that nonadditive genetic variance may have a significant role in the variation of selection traits of Scots pine, thus clonal deployment could be an attractive alternative for the species. Additionally, confidence in the role of nonadditive genetic effects in this breeding program should be pursued in the future, using GS.

@article{capador-barreto_killing_2021,
	title = {Killing two enemies with one stone? {Genomics} of resistance to two sympatric pathogens in {Norway} spruce},
	volume = {30},
	issn = {1365-294X},
	shorttitle = {Killing two enemies with one stone?},
	doi = {10.1111/mec.16058},
	abstract = {Trees must cope with the attack of multiple pathogens, often simultaneously during their long lifespan. Ironically, the genetic and molecular mechanisms controlling this process are poorly understood. The objective of this study was to compare the genetic component of resistance in Norway spruce to Heterobasidion annosum s.s. and its sympatric congener Heterobasidion parviporum. Heterobasidion root- and stem-rot is a major disease of Norway spruce caused by members of the Heterobasidion annosum species complex. Resistance to both pathogens was measured using artificial inoculations in half-sib families of Norway spruce trees originating from central to northern Europe. The genetic component of resistance was analysed using 63,760 genome-wide exome-capture sequenced SNPs and multitrait genome-wide associations. No correlation was found for resistance to the two pathogens; however, associations were found between genomic variants and resistance traits with synergic or antagonist pleiotropic effects to both pathogens. Additionally, a latitudinal cline in resistance in the bark to H. annosum s.s. was found; trees from southern latitudes, with a later bud-set and thicker stem diameter, allowed longer lesions, but this was not the case for H. parviporum. In summary, this study detects genomic variants with pleiotropic effects which explain multiple disease resistance from a genic level and could be useful for selection of resistant trees to both pathogens. Furthermore, it highlights the need for additional research to understand the evolution of resistance traits to multiple pathogens in trees.},
	language = {eng},
	number = {18},
	journal = {Molecular Ecology},
	author = {Capador-Barreto, Hernán D. and Bernhardsson, Carolina and Milesi, Pascal and Vos, Ingrid and Lundén, Karl and Wu, Harry X. and Karlsson, Bo and Ingvarsson, Pär K. and Stenlid, Jan and Elfstrand, Malin},
	month = sep,
	year = {2021},
	keywords = {Basidiomycota, Genome wide association study (GWAS), Genomics, Homicide, Norway, Picea, Picea abies, Plant Diseases, cline, disease resistance, genome-wide association study, pleiotropy, root-rot},
	pages = {4433--4447},
}

Trees must cope with the attack of multiple pathogens, often simultaneously during their long lifespan. Ironically, the genetic and molecular mechanisms controlling this process are poorly understood. The objective of this study was to compare the genetic component of resistance in Norway spruce to Heterobasidion annosum s.s. and its sympatric congener Heterobasidion parviporum. Heterobasidion root- and stem-rot is a major disease of Norway spruce caused by members of the Heterobasidion annosum species complex. Resistance to both pathogens was measured using artificial inoculations in half-sib families of Norway spruce trees originating from central to northern Europe. The genetic component of resistance was analysed using 63,760 genome-wide exome-capture sequenced SNPs and multitrait genome-wide associations. No correlation was found for resistance to the two pathogens; however, associations were found between genomic variants and resistance traits with synergic or antagonist pleiotropic effects to both pathogens. Additionally, a latitudinal cline in resistance in the bark to H. annosum s.s. was found; trees from southern latitudes, with a later bud-set and thicker stem diameter, allowed longer lesions, but this was not the case for H. parviporum. In summary, this study detects genomic variants with pleiotropic effects which explain multiple disease resistance from a genic level and could be useful for selection of resistant trees to both pathogens. Furthermore, it highlights the need for additional research to understand the evolution of resistance traits to multiple pathogens in trees.

@article{cheng_haplotype-resolved_2021,
	title = {Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger},
	volume = {8},
	issn = {2662-6810},
	doi = {10/gmhq7d},
	abstract = {Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.},
	language = {eng},
	number = {1},
	journal = {Horticulture Research},
	author = {Cheng, Shi-Ping and Jia, Kai-Hua and Liu, Hui and Zhang, Ren-Gang and Li, Zhi-Chao and Zhou, Shan-Shan and Shi, Tian-Le and Ma, Ai-Chu and Yu, Cong-Wen and Gao, Chan and Cao, Guang-Lei and Zhao, Wei and Nie, Shuai and Guo, Jing-Fang and Jiao, Si-Qian and Tian, Xue-Chan and Yan, Xue-Mei and Bao, Yu-Tao and Yun, Quan-Zheng and Wang, Xin-Zhu and Porth, Ilga and El-Kassaby, Yousry A. and Wang, Xiao-Ru and Li, Zhen and Van de Peer, Yves and Mao, Jian-Feng},
	month = aug,
	year = {2021},
	pages = {188},
}

Ginger (Zingiber officinale) is one of the most valued spice plants worldwide; it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance. Here, we present a haplotype-resolved, chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb. Remarkable structural variation was identified between haplotypes, and two inversions larger than 15 Mb on chromosome 4 may be associated with ginger infertility. We performed a comprehensive, spatiotemporal, genome-wide analysis of allelic expression patterns, revealing that most alleles are coordinately expressed. The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements, greater coding sequence divergence, more relaxed selection pressure, and more transcription factor binding site differences. We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis. Our allele-aware assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in ginger.

@article{graca_high-resolution_2021,
	title = {High-resolution model of {Arabidopsis} {Photosystem} {II} reveals the structural consequences of digitonin-extraction},
	volume = {11},
	copyright = {2021 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-021-94914-x},
	doi = {10/gmgjvj},
	abstract = {In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the status of a model organism; nonetheless, a high-resolution structure of its Photosystem II is missing. We present the first Cryo-EM high-resolution structure of Arabidopsis PSII supercomplex with average resolution of 2.79 Å, an important model for future PSII studies. The digitonin extracted PSII complexes demonstrate the importance of: the LHG2630-lipid-headgroup in the trimerization of the light-harvesting complex II; the stabilization of the PsbJ subunit and the CP43-loop E by DGD520-lipid; the choice of detergent for the integrity of membrane protein complexes. Furthermore, our data shows at the anticipated Mn4CaO5-site a single metal ion density as a reminiscent early stage of Photosystem II photoactivation.},
	language = {en},
	number = {1},
	urldate = {2021-08-26},
	journal = {Scientific Reports},
	author = {Graça, André T. and Hall, Michael and Persson, Karina and Schröder, Wolfgang P.},
	month = jul,
	year = {2021},
	pages = {15534},
}

In higher plants, the photosynthetic process is performed and regulated by Photosystem II (PSII). Arabidopsis thaliana was the first higher plant with a fully sequenced genome, conferring it the status of a model organism; nonetheless, a high-resolution structure of its Photosystem II is missing. We present the first Cryo-EM high-resolution structure of Arabidopsis PSII supercomplex with average resolution of 2.79 Å, an important model for future PSII studies. The digitonin extracted PSII complexes demonstrate the importance of: the LHG2630-lipid-headgroup in the trimerization of the light-harvesting complex II; the stabilization of the PsbJ subunit and the CP43-loop E by DGD520-lipid; the choice of detergent for the integrity of membrane protein complexes. Furthermore, our data shows at the anticipated Mn4CaO5-site a single metal ion density as a reminiscent early stage of Photosystem II photoactivation.

@article{gratz_organic_2021,
	title = {Organic nitrogen nutrition: {LHT1}.2 protein from hybrid aspen ({Populus} tremula {L}. x tremuloides {Michx}) is a functional amino acid transporter and a homolog of {Arabidopsis} {LHT1}},
	volume = {41},
	issn = {1758-4469},
	shorttitle = {Organic nitrogen nutrition},
	doi = {10.1093/treephys/tpab029},
	abstract = {The contribution of amino acids (AAs) to soil nitrogen (N) fluxes is higher than previously thought. The fact that AA uptake is pivotal for N nutrition in boreal ecosystems highlights plant AA transporters as key components of the N cycle. At the same time, very little is known about AA transport and respective transporters in trees. Tree genomes may contain 13 or more genes encoding the lysine histidine transporter (LHT) family proteins, and this complicates the study of their significance for tree N-use efficiency. With the strategy of obtaining a tool to study N-use efficiency, our aim was to identify and characterize a relevant AA transporter in hybrid aspen (Populus tremula L. x tremuloides Michx.). We identified PtrLHT1.2, the closest homolog of Arabidopsis thaliana (L.) Heynh AtLHT1, which is expressed in leaves, stems and roots. Complementation of a yeast AA uptake mutant verified the function of PtrLHT1.2 as an AA transporter. Furthermore, PtrLHT1.2 was able to fully complement the phenotypes of the Arabidopsis AA uptake mutant lht1 aap5, including early leaf senescence-like phenotype, reduced growth, decreased plant N levels and reduced root AA uptake. Amino acid uptake studies finally showed that PtrLHT1.2 is a high affinity transporter for neutral and acidic AAs. Thus, we identified a functional AtLHT1 homolog in hybrid aspen, which harbors the potential to enhance overall plant N levels and hence increase biomass production. This finding provides a valuable tool for N nutrition studies in trees and opens new avenues to optimizing tree N-use efficiency.},
	language = {eng},
	number = {8},
	journal = {Tree Physiology},
	author = {Gratz, Regina and Ahmad, Iftikhar and Svennerstam, Henrik and Jämtgård, Sandra and Love, Jonathan and Holmlund, Mattias and Ivanov, Rumen and Ganeteg, Ulrika},
	month = aug,
	year = {2021},
	keywords = {Amino Acid Transport Systems, Arabidopsis, Ecosystem, Nitrogen, Populus, Populus tremula L. x tremuloides Michx, amino acid transport, amino acid uptake, early senescence-like phenotype, hybrid aspen, lysine histidine transporter (LHT), nitrogen nutrition, organic nitrogen},
	pages = {1479--1496},
}

The contribution of amino acids (AAs) to soil nitrogen (N) fluxes is higher than previously thought. The fact that AA uptake is pivotal for N nutrition in boreal ecosystems highlights plant AA transporters as key components of the N cycle. At the same time, very little is known about AA transport and respective transporters in trees. Tree genomes may contain 13 or more genes encoding the lysine histidine transporter (LHT) family proteins, and this complicates the study of their significance for tree N-use efficiency. With the strategy of obtaining a tool to study N-use efficiency, our aim was to identify and characterize a relevant AA transporter in hybrid aspen (Populus tremula L. x tremuloides Michx.). We identified PtrLHT1.2, the closest homolog of Arabidopsis thaliana (L.) Heynh AtLHT1, which is expressed in leaves, stems and roots. Complementation of a yeast AA uptake mutant verified the function of PtrLHT1.2 as an AA transporter. Furthermore, PtrLHT1.2 was able to fully complement the phenotypes of the Arabidopsis AA uptake mutant lht1 aap5, including early leaf senescence-like phenotype, reduced growth, decreased plant N levels and reduced root AA uptake. Amino acid uptake studies finally showed that PtrLHT1.2 is a high affinity transporter for neutral and acidic AAs. Thus, we identified a functional AtLHT1 homolog in hybrid aspen, which harbors the potential to enhance overall plant N levels and hence increase biomass production. This finding provides a valuable tool for N nutrition studies in trees and opens new avenues to optimizing tree N-use efficiency.

@article{haggstrom_survival_2021,
	title = {Survival and growth of {Scots} pine ({Pinus} sylvestris) seedlings in north {Sweden}: effects of planting position and arginine phosphate addition},
	volume = {0},
	issn = {0282-7581},
	shorttitle = {Survival and growth of {Scots} pine ({Pinus} sylvestris) seedlings in north {Sweden}},
	url = {https://doi.org/10.1080/02827581.2021.1957999},
	doi = {10/gmhq68},
	abstract = {Forest regeneration by tree planting on harvested sites in the boreal forests of northern Europe is frequently preceded by site preparation to increase survival and growth of the seedlings. We studied whether a small addition of arginine phosphate (AP treatment) at the time of planting would further enhance the seedlings’ early performance. Following two growth seasons, we investigated survival and growth of Scots pine (Pinus sylvestris) seedlings on 11 locations between latitudes 61.1°N and 67.1°N in the boreal forest of northern Sweden. The planting positions of seedlings were on capped mounds and bare mineral soil following mechanical site preparation, and in non-prepared soil. We found that seedling survival following site preparation increased with AP treatment. On capped mounds, seedling survival was more variable and appeared more dependent on precipitation during the first month after planting than seedlings positioned in the mineral soil. The positive effect of AP treatment on seedling growth differed between sites and was more pronounced on sites with longer growing seasons. AP treatment had no significant effect on survival of seedlings planted in non-prepared soil, while the positive effect on growth was more pronounced at sites with higher fertility using this planting position.},
	number = {0},
	urldate = {2021-08-18},
	journal = {Scandinavian Journal of Forest Research},
	author = {Häggström, Bodil and Domevscik, Matej and Öhlund, Jonas and Nordin, Annika},
	month = jul,
	year = {2021},
	keywords = {Pinus sylvestris, arginine phosphate, conifer plantations, cultivation, damage, establishment, fertilization, forest regeneration, norway spruce, organic nitrogen, performance, picea-abies, planting positions, seedling   growth, seedling growth, seedling survival, site preparation},
	pages = {1--11},
}

Forest regeneration by tree planting on harvested sites in the boreal forests of northern Europe is frequently preceded by site preparation to increase survival and growth of the seedlings. We studied whether a small addition of arginine phosphate (AP treatment) at the time of planting would further enhance the seedlings’ early performance. Following two growth seasons, we investigated survival and growth of Scots pine (Pinus sylvestris) seedlings on 11 locations between latitudes 61.1°N and 67.1°N in the boreal forest of northern Sweden. The planting positions of seedlings were on capped mounds and bare mineral soil following mechanical site preparation, and in non-prepared soil. We found that seedling survival following site preparation increased with AP treatment. On capped mounds, seedling survival was more variable and appeared more dependent on precipitation during the first month after planting than seedlings positioned in the mineral soil. The positive effect of AP treatment on seedling growth differed between sites and was more pronounced on sites with longer growing seasons. AP treatment had no significant effect on survival of seedlings planted in non-prepared soil, while the positive effect on growth was more pronounced at sites with higher fertility using this planting position.

@article{mateo-bonmati_broadening_2021,
	title = {Broadening the roles of {UDP}-glycosyltransferases in auxin homeostasis and plant development},
	issn = {1469-8137},
	doi = {10/gmhq7j},
	abstract = {The levels of the important plant growth regulator indole-3-acetic acid (IAA) are tightly controlled within plant tissues to spatiotemporally orchestrate concentration gradients that drive plant growth and development. Metabolic inactivation of bioactive IAA is known to participate in the modulation of IAA maxima and minima. IAA can be irreversibly inactivated by oxidation and conjugation to aspartate and glutamate. Usually overlooked because of its reversible nature, the most abundant inactive IAA form is the IAA-glucose (IAA-glc) conjugate. Glycosylation of IAA in Arabidopsis thaliana is reported to be carried out by UDP-glycosyltransferase 84B1 (UGT84B1), while UGT74D1 has been implicated in the glycosylation of the irreversibly formed IAA catabolite oxIAA. Here we demonstrated that both UGT84B1 and UGT74D1 modulate IAA levels throughout plant development by dual IAA and oxIAA glycosylation. Moreover, we identified a novel UGT subfamily whose members redundantly mediate the glycosylation of oxIAA and modulate skotomorphogenic growth.},
	language = {eng},
	journal = {The New Phytologist},
	author = {Mateo-Bonmatí, Eduardo and Casanova-Sáez, Rubén and Šimura, Jan and Ljung, Karin},
	month = jul,
	year = {2021},
	keywords = {Arabidopsis, IAA-glucose, UDP-glycosyltransferases (UGT), auxin, indole-3-acetic acid (IAA), oxIAA-glucose},
}

The levels of the important plant growth regulator indole-3-acetic acid (IAA) are tightly controlled within plant tissues to spatiotemporally orchestrate concentration gradients that drive plant growth and development. Metabolic inactivation of bioactive IAA is known to participate in the modulation of IAA maxima and minima. IAA can be irreversibly inactivated by oxidation and conjugation to aspartate and glutamate. Usually overlooked because of its reversible nature, the most abundant inactive IAA form is the IAA-glucose (IAA-glc) conjugate. Glycosylation of IAA in Arabidopsis thaliana is reported to be carried out by UDP-glycosyltransferase 84B1 (UGT84B1), while UGT74D1 has been implicated in the glycosylation of the irreversibly formed IAA catabolite oxIAA. Here we demonstrated that both UGT84B1 and UGT74D1 modulate IAA levels throughout plant development by dual IAA and oxIAA glycosylation. Moreover, we identified a novel UGT subfamily whose members redundantly mediate the glycosylation of oxIAA and modulate skotomorphogenic growth.

@article{mishra_plastid-localized_2021,
	title = {The {Plastid}-{Localized} {AtFtsHi3} {Pseudo}-{Protease} of {Arabidopsis} thaliana {Has} an {Impact} on {Plant} {Growth} and {Drought} {Tolerance}},
	volume = {12},
	issn = {1664-462X},
	doi = {10/gk3wn7},
	abstract = {While drought severely affects plant growth and crop production, the molecular mechanisms of the drought response of plants remain unclear. In this study, we demonstrated for the first time the effect of the pseudo-protease AtFtsHi3 of Arabidopsis thaliana on overall plant growth and in drought tolerance. An AtFTSHi3 knock-down mutant [ftshi3-1(kd)] displayed a pale-green phenotype with lower photosynthetic efficiency and Darwinian fitness compared to wild type (Wt). An observed delay in seed germination of ftshi3-1(kd) was attributed to overaccumulation of abscisic acid (ABA); ftshi3-1(kd) seedlings showed partial sensitivity to exogenous ABA. Being exposed to similar severity of soil drying, ftshi3-1(kd) was drought-tolerant up to 20 days after the last irrigation, while wild type plants wilted after 12 days. Leaves of ftshi3-1(kd) contained reduced stomata size, density, and a smaller stomatic aperture. During drought stress, ftshi3-1(kd) showed lowered stomatal conductance, increased intrinsic water-use efficiency (WUEi), and slower stress acclimation. Expression levels of ABA-responsive genes were higher in leaves of ftshi3-1(kd) than Wt; DREB1A, but not DREB2A, was significantly upregulated during drought. However, although ftshi3-1(kd) displayed a drought-tolerant phenotype in aboveground tissue, the root-associated bacterial community responded to drought.},
	language = {eng},
	journal = {Frontiers in Plant Science},
	author = {Mishra, Laxmi S. and Mishra, Sanatkumar and Caddell, Daniel F. and Coleman-Derr, Devin and Funk, Christiane},
	year = {2021},
	keywords = {Arabidopis thaliana, abscisic acid, chloroplast, drought, filamentation temperature-sensitive H protease, root microbiome},
	pages = {694727},
}

While drought severely affects plant growth and crop production, the molecular mechanisms of the drought response of plants remain unclear. In this study, we demonstrated for the first time the effect of the pseudo-protease AtFtsHi3 of Arabidopsis thaliana on overall plant growth and in drought tolerance. An AtFTSHi3 knock-down mutant [ftshi3-1(kd)] displayed a pale-green phenotype with lower photosynthetic efficiency and Darwinian fitness compared to wild type (Wt). An observed delay in seed germination of ftshi3-1(kd) was attributed to overaccumulation of abscisic acid (ABA); ftshi3-1(kd) seedlings showed partial sensitivity to exogenous ABA. Being exposed to similar severity of soil drying, ftshi3-1(kd) was drought-tolerant up to 20 days after the last irrigation, while wild type plants wilted after 12 days. Leaves of ftshi3-1(kd) contained reduced stomata size, density, and a smaller stomatic aperture. During drought stress, ftshi3-1(kd) showed lowered stomatal conductance, increased intrinsic water-use efficiency (WUEi), and slower stress acclimation. Expression levels of ABA-responsive genes were higher in leaves of ftshi3-1(kd) than Wt; DREB1A, but not DREB2A, was significantly upregulated during drought. However, although ftshi3-1(kd) displayed a drought-tolerant phenotype in aboveground tissue, the root-associated bacterial community responded to drought.

@article{otvos_pickle_2021,
	title = {Pickle {Recruits} {Retinoblastoma} {Related} 1 to {Control} {Lateral} {Root} {Formation} in {Arabidopsis}},
	volume = {22},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/1422-0067/22/8/3862},
	doi = {10.3390/ijms22083862},
	abstract = {Lateral root (LR) formation is an example of a plant post-embryonic organogenesis event. LRs are issued from non-dividing cells entering consecutive steps of formative divisions, proliferation and elongation. The chromatin remodeling protein PICKLE (PKL) negatively regulates auxin-mediated LR formation through a mechanism that is not yet known. Here we show that PKL interacts with RETINOBLASTOMA-RELATED 1 (RBR1) to repress the LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) promoter activity. Since LBD16 function is required for the formative division of LR founder cells, repression mediated by the PKL–RBR1 complex negatively regulates formative division and LR formation. Inhibition of LR formation by PKL–RBR1 is counteracted by auxin, indicating that, in addition to auxin-mediated transcriptional responses, the fine-tuned process of LR formation is also controlled at the chromatin level in an auxin-signaling dependent manner.},
	language = {en},
	number = {8},
	urldate = {2021-07-01},
	journal = {International Journal of Molecular Sciences},
	author = {Ötvös, Krisztina and Miskolczi, Pál and Marhavý, Peter and Cruz-Ramírez, Alfredo and Benková, Eva and Robert, Stéphanie and Bakó, László},
	month = jan,
	year = {2021},
	keywords = {\textit{de novo} organogenesis, auxin signaling, chromatin remodeling},
	pages = {3862},
}

Lateral root (LR) formation is an example of a plant post-embryonic organogenesis event. LRs are issued from non-dividing cells entering consecutive steps of formative divisions, proliferation and elongation. The chromatin remodeling protein PICKLE (PKL) negatively regulates auxin-mediated LR formation through a mechanism that is not yet known. Here we show that PKL interacts with RETINOBLASTOMA-RELATED 1 (RBR1) to repress the LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) promoter activity. Since LBD16 function is required for the formative division of LR founder cells, repression mediated by the PKL–RBR1 complex negatively regulates formative division and LR formation. Inhibition of LR formation by PKL–RBR1 is counteracted by auxin, indicating that, in addition to auxin-mediated transcriptional responses, the fine-tuned process of LR formation is also controlled at the chromatin level in an auxin-signaling dependent manner.

@article{plett_novel_2021,
	title = {Novel {Microdialysis} {Technique} {Reveals} a {Dramatic} {Shift} in {Metabolite} {Secretion} during the {Early} {Stages} of the {Interaction} between the {Ectomycorrhizal} {Fungus} {Pisolithus} microcarpus and {Its} {Host} {Eucalyptus} grandis},
	volume = {9},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/2076-2607/9/9/1817},
	doi = {10.3390/microorganisms9091817},
	abstract = {The colonisation of tree roots by ectomycorrhizal (ECM) fungi is the result of numerous signalling exchanges between organisms, many of which occur before physical contact. However, information is lacking about these exchanges and the compounds that are secreted by each organism before contact. This is in part due to a lack of low disturbance sampling methods with sufficient temporal and spatial resolution to capture these exchanges. Using a novel in situ microdialysis approach, we sampled metabolites released from Eucalyptus grandis and Pisolithus microcarpus independently and during indirect contact over a 48-h time-course using UPLC-MS. A total of 560 and 1530 molecular features (MFs; ESI- and ESI+ respectively) were identified with significant differential abundance from control treatments. We observed that indirect contact between organisms altered the secretion of MFs to produce a distinct metabolomic profile compared to either organism independently. Many of these MFs were produced within the first hour of contact and included several phenylpropanoids, fatty acids and organic acids. These findings show that the secreted metabolome, particularly of the ECM fungus, can rapidly shift during the early stages of pre-symbiotic contact and highlight the importance of observing these early interactions in greater detail. We present microdialysis as a useful tool for examining plant–fungal signalling with high temporal resolution and with minimal experimental disturbance.},
	language = {en},
	number = {9},
	urldate = {2021-10-14},
	journal = {Microorganisms},
	author = {Plett, Krista L. and Buckley, Scott and Plett, Jonathan M. and Anderson, Ian C. and Lundberg-Felten, Judith and Jämtgård, Sandra},
	month = sep,
	year = {2021},
	pages = {1817},
}

The colonisation of tree roots by ectomycorrhizal (ECM) fungi is the result of numerous signalling exchanges between organisms, many of which occur before physical contact. However, information is lacking about these exchanges and the compounds that are secreted by each organism before contact. This is in part due to a lack of low disturbance sampling methods with sufficient temporal and spatial resolution to capture these exchanges. Using a novel in situ microdialysis approach, we sampled metabolites released from Eucalyptus grandis and Pisolithus microcarpus independently and during indirect contact over a 48-h time-course using UPLC-MS. A total of 560 and 1530 molecular features (MFs; ESI- and ESI+ respectively) were identified with significant differential abundance from control treatments. We observed that indirect contact between organisms altered the secretion of MFs to produce a distinct metabolomic profile compared to either organism independently. Many of these MFs were produced within the first hour of contact and included several phenylpropanoids, fatty acids and organic acids. These findings show that the secreted metabolome, particularly of the ECM fungus, can rapidly shift during the early stages of pre-symbiotic contact and highlight the importance of observing these early interactions in greater detail. We present microdialysis as a useful tool for examining plant–fungal signalling with high temporal resolution and with minimal experimental disturbance.

@article{prior_arabidopsis_2021,
	title = {Arabidopsis {bZIP11} {Is} a {Susceptibility} {Factor} {During} {Pseudomonas} syringae {Infection}},
	volume = {34},
	issn = {0894-0282},
	url = {https://apsjournals.apsnet.org/doi/10.1094/MPMI-11-20-0310-R},
	doi = {10/gj6p4s},
	abstract = {The induction of plant nutrient secretion systems is critical for successful pathogen infection. Some bacterial pathogens (e.g., Xanthomonas spp.) use transcription activator-like (TAL) effectors to induce transcription of SWEET sucrose efflux transporters. Pseudomonas syringae pv. tomato strain DC3000 lacks TAL effectors yet is able to induce multiple SWEETs in Arabidopsis thaliana by unknown mechanisms. Because bacteria require other nutrients in addition to sugars for efficient reproduction, we hypothesized that Pseudomonas spp. may depend on host transcription factors involved in secretory programs to increase access to essential nutrients. Bioinformatic analyses identified the Arabidopsis basic-leucine zipper transcription factor bZIP11 as a potential regulator of nutrient transporters, including SWEETs and UmamiT amino acid transporters. Inducible downregulation of bZIP11 expression in Arabidopsis resulted in reduced growth of P. syringae pv. tomato strain DC3000, whereas inducible overexpression of bZIP11 resulted in increased bacterial growth, supporting the hypothesis that bZIP11-regulated transcription programs are essential for maximal pathogen titer in leaves. Our data are consistent with a model in which a pathogen alters host transcription factor expression upstream of secretory transcription networks to promote nutrient efflux from host cells. Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.},
	number = {4},
	urldate = {2021-06-21},
	journal = {Molecular Plant-Microbe Interactions®},
	author = {Prior, Matthew J. and Selvanayagam, Jebasingh and Kim, Jung-Gun and Tomar, Monika and Jonikas, Martin and Mudgett, Mary Beth and Smeekens, Sjef and Hanson, Johannes and Frommer, Wolf B.},
	month = apr,
	year = {2021},
	pages = {439--447},
}

The induction of plant nutrient secretion systems is critical for successful pathogen infection. Some bacterial pathogens (e.g., Xanthomonas spp.) use transcription activator-like (TAL) effectors to induce transcription of SWEET sucrose efflux transporters. Pseudomonas syringae pv. tomato strain DC3000 lacks TAL effectors yet is able to induce multiple SWEETs in Arabidopsis thaliana by unknown mechanisms. Because bacteria require other nutrients in addition to sugars for efficient reproduction, we hypothesized that Pseudomonas spp. may depend on host transcription factors involved in secretory programs to increase access to essential nutrients. Bioinformatic analyses identified the Arabidopsis basic-leucine zipper transcription factor bZIP11 as a potential regulator of nutrient transporters, including SWEETs and UmamiT amino acid transporters. Inducible downregulation of bZIP11 expression in Arabidopsis resulted in reduced growth of P. syringae pv. tomato strain DC3000, whereas inducible overexpression of bZIP11 resulted in increased bacterial growth, supporting the hypothesis that bZIP11-regulated transcription programs are essential for maximal pathogen titer in leaves. Our data are consistent with a model in which a pathogen alters host transcription factor expression upstream of secretory transcription networks to promote nutrient efflux from host cells. Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

@article{takahashi_alterations_2021,
	title = {Alterations in hormonal signals spatially coordinate distinct responses to {DNA} double-strand breaks in {Arabidopsis} roots},
	volume = {7},
	issn = {2375-2548},
	doi = {10/gkzft9},
	abstract = {Plants have a high ability to cope with changing environments and grow continuously throughout life. However, the mechanisms by which plants strike a balance between stress response and organ growth remain elusive. Here, we found that DNA double-strand breaks enhance the accumulation of cytokinin hormones through the DNA damage signaling pathway in the Arabidopsis root tip. Our data showed that activation of cytokinin signaling suppresses the expression of some of the PIN-FORMED genes that encode efflux carriers of another hormone, auxin, thereby decreasing the auxin signals in the root tip and causing cell cycle arrest at G2 phase and stem cell death. Elevated cytokinin signaling also promotes an early transition from cell division to endoreplication in the basal part of the root apex. We propose that plant hormones spatially coordinate differential DNA damage responses, thereby maintaining genome integrity and minimizing cell death to ensure continuous root growth.},
	language = {eng},
	number = {25},
	journal = {Science Advances},
	author = {Takahashi, Naoki and Inagaki, Soichi and Nishimura, Kohei and Sakakibara, Hitoshi and Antoniadi, Ioanna and Karady, Michal and Ljung, Karin and Umeda, Masaaki},
	month = jun,
	year = {2021},
	pages = {eabg0993},
}

Plants have a high ability to cope with changing environments and grow continuously throughout life. However, the mechanisms by which plants strike a balance between stress response and organ growth remain elusive. Here, we found that DNA double-strand breaks enhance the accumulation of cytokinin hormones through the DNA damage signaling pathway in the Arabidopsis root tip. Our data showed that activation of cytokinin signaling suppresses the expression of some of the PIN-FORMED genes that encode efflux carriers of another hormone, auxin, thereby decreasing the auxin signals in the root tip and causing cell cycle arrest at G2 phase and stem cell death. Elevated cytokinin signaling also promotes an early transition from cell division to endoreplication in the basal part of the root apex. We propose that plant hormones spatially coordinate differential DNA damage responses, thereby maintaining genome integrity and minimizing cell death to ensure continuous root growth.

@article{pervaiz_transcriptional_2021,
	title = {The {Transcriptional} {Landscape} and {Hub} {Genes} {Associated} with {Physiological} {Responses} to {Drought} {Stress} in {Pinus} tabuliformis},
	volume = {22},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/1422-0067/22/17/9604},
	doi = {10.3390/ijms22179604},
	abstract = {Drought stress has an extensive impact on regulating various physiological, metabolic, and molecular responses. In the present study, the Pinus tabuliformis transcriptome was studied to evaluate the drought-responsive genes using RNA- Sequencing approache. The results depicted that photosynthetic rate and H2O conductance started to decline under drought but recovered 24 h after re-watering; however, the intercellular CO2 concentration (Ci) increased with the onset of drought. We identified 84 drought-responsive transcription factors, 62 protein kinases, 17 transcriptional regulators, and 10 network hub genes. Additionally, we observed the expression patterns of several important gene families, including 2192 genes positively expressed in all 48 samples, and 40 genes were commonly co-expressed in all drought and recovery stages compared with the control samples. The drought-responsive transcriptome was conserved mainly between P. tabuliformis and A. thaliana, as 70\% (6163) genes had a homologous in arabidopsis, out of which 52\% homologous (3178 genes corresponding to 2086 genes in Arabidopsis) were also drought response genes in arabidopsis. The collaborative network exhibited 10 core hub genes integrating with ABA-dependent and independent pathways closely conserved with the ABA signaling pathway in the transcription factors module. PtNCED3 from the ABA family genes had shown significantly different expression patterns under control, mild, prolonged drought, and recovery stages. We found the expression pattern was considerably increased with the prolonged drought condition. PtNCED3 highly expressed in all drought-tested samples; more interestingly, expression pattern was higher under mild and prolonged drought. PtNCED3 is reported as one of the important regulating enzymes in ABA synthesis. The continuous accumulation of ABA in leaves increased resistance against drought was due to accumulation of PtNCED3 under drought stress in the pine needles.},
	language = {en},
	number = {17},
	urldate = {2021-11-04},
	journal = {International Journal of Molecular Sciences},
	author = {Pervaiz, Tariq and Liu, Shuang-Wei and Uddin, Saleem and Amjid, Muhammad Waqas and Niu, Shi-Hui and Wu, Harry X.},
	month = jan,
	year = {2021},
	keywords = {\textit{Pinus tabuliformis}, \textit{PtNCED3}, ABA signaling, RNA-Seq, drought stress, drought-recovery},
	pages = {9604},
}

Drought stress has an extensive impact on regulating various physiological, metabolic, and molecular responses. In the present study, the Pinus tabuliformis transcriptome was studied to evaluate the drought-responsive genes using RNA- Sequencing approache. The results depicted that photosynthetic rate and H2O conductance started to decline under drought but recovered 24 h after re-watering; however, the intercellular CO2 concentration (Ci) increased with the onset of drought. We identified 84 drought-responsive transcription factors, 62 protein kinases, 17 transcriptional regulators, and 10 network hub genes. Additionally, we observed the expression patterns of several important gene families, including 2192 genes positively expressed in all 48 samples, and 40 genes were commonly co-expressed in all drought and recovery stages compared with the control samples. The drought-responsive transcriptome was conserved mainly between P. tabuliformis and A. thaliana, as 70% (6163) genes had a homologous in arabidopsis, out of which 52% homologous (3178 genes corresponding to 2086 genes in Arabidopsis) were also drought response genes in arabidopsis. The collaborative network exhibited 10 core hub genes integrating with ABA-dependent and independent pathways closely conserved with the ABA signaling pathway in the transcription factors module. PtNCED3 from the ABA family genes had shown significantly different expression patterns under control, mild, prolonged drought, and recovery stages. We found the expression pattern was considerably increased with the prolonged drought condition. PtNCED3 highly expressed in all drought-tested samples; more interestingly, expression pattern was higher under mild and prolonged drought. PtNCED3 is reported as one of the important regulating enzymes in ABA synthesis. The continuous accumulation of ABA in leaves increased resistance against drought was due to accumulation of PtNCED3 under drought stress in the pine needles.

@article{melo_metabolomic_2021,
	title = {A metabolomic study of {Gomphrena} agrestis in {Brazilian} {Cerrado} suggests drought-adaptive strategies on metabolism},
	volume = {11},
	copyright = {2021 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-021-92449-9},
	doi = {10.1038/s41598-021-92449-9},
	abstract = {Drought is the main factor that limits the distribution and productivity of plant species. In the Brazilian Cerrado, the vegetation is adapted to a seasonal climate with long- and short-term periods of drought. To analyze the metabolic strategies under such conditions, a metabolomic approach was used to characterize Gomphrena agrestis Mart. (Amaranthaceae) a native species that grows under natural conditions, in a rock-field area. Roots and leaves material from native specimens were sampled along different seasons of the year and LC–MS and GC–MS analyzed for multiple chemical constituents. The datasets derived from the different measurements were combined and evaluated using multivariate analysis. Principal component analysis was used to obtain an overview of the samples and identify outliers. Later, the data was analyzed with orthogonal projection to latent structures discriminant analysis to obtain valid models that could explain the metabolite variations in the different seasons. Two hundred and eighty metabolites were annotated, generating a unique database to characterize metabolic strategies used to cope with the effects of drought. The accumulation of fructans in the thickened roots is consistent with the storage of carbons during the rainy season to support the energy demand during a long period of drought. The accumulation of Abscisic acid, sugars and sugar alcohols, phenolics, and pigment in the leaves suggests physiological adaptations. To cope with long-term drought, the data suggests that tissue water status and storage of reserves are important to support plant survival and regrowth. However, during short-term drought, osmoregulation and oxidative protection seems to be essential, probably to support the maintenance of active photosynthesis.},
	language = {en},
	number = {1},
	urldate = {2021-11-04},
	journal = {Scientific Reports},
	author = {Melo, Geraldo Aclécio and Abreu, Ilka Nacif and de Oliveira, Maíra Baista and Budzinski, Ilara Gabriela Frasson and Silva, Lucinélia Vieira and Pimenta, Marcio Antônio Silva and Moritz, Thomas},
	month = jun,
	year = {2021},
	keywords = {Plant physiology, Plant sciences, Plant stress responses},
	pages = {12933},
}

Drought is the main factor that limits the distribution and productivity of plant species. In the Brazilian Cerrado, the vegetation is adapted to a seasonal climate with long- and short-term periods of drought. To analyze the metabolic strategies under such conditions, a metabolomic approach was used to characterize Gomphrena agrestis Mart. (Amaranthaceae) a native species that grows under natural conditions, in a rock-field area. Roots and leaves material from native specimens were sampled along different seasons of the year and LC–MS and GC–MS analyzed for multiple chemical constituents. The datasets derived from the different measurements were combined and evaluated using multivariate analysis. Principal component analysis was used to obtain an overview of the samples and identify outliers. Later, the data was analyzed with orthogonal projection to latent structures discriminant analysis to obtain valid models that could explain the metabolite variations in the different seasons. Two hundred and eighty metabolites were annotated, generating a unique database to characterize metabolic strategies used to cope with the effects of drought. The accumulation of fructans in the thickened roots is consistent with the storage of carbons during the rainy season to support the energy demand during a long period of drought. The accumulation of Abscisic acid, sugars and sugar alcohols, phenolics, and pigment in the leaves suggests physiological adaptations. To cope with long-term drought, the data suggests that tissue water status and storage of reserves are important to support plant survival and regrowth. However, during short-term drought, osmoregulation and oxidative protection seems to be essential, probably to support the maintenance of active photosynthesis.

@article{xu_uv-b-induced_2021,
	title = {{UV}-{B}-induced molecular mechanisms of stress physiology responses in the major northern {Chinese} conifer {Pinus} tabuliformis {Carr}.},
	volume = {41},
	issn = {1758-4469},
	url = {https://doi.org/10.1093/treephys/tpaa180},
	doi = {10.1093/treephys/tpaa180},
	abstract = {During their lifetimes, plants are exposed to different abiotic stress factors eliciting various physiological responses and triggering important defense processes. For UV-B radiation responses in forest trees, the genetics and molecular regulation remain to be elucidated. Here, we exposed Pinus tabuliformis Carr., a major conifer from northern China, to short-term high-intensity UV-B and employed a systems biology approach to characterize the early physiological processes and the hierarchical gene regulation, which revealed a temporal transition from primary to secondary metabolism, the buildup of enhanced antioxidant capacity and stress-signaling activation. Our findings showed that photosynthesis and biosynthesis of photosynthetic pigments were inhibited, while flavonoids and their related derivates biosynthesis, as well as glutathione and glutathione S-transferase mediated antioxidant processes, were enhanced. Likewise, stress-related phytohormones (jasmonic acid, salicylic acid and ethylene), kinase and reactive oxygen species signal transduction pathways were activated. Biological processes regulated by auxin and karrikin were, for the first time, found to be involved in plant defense against UV-B by promoting the biosynthesis of flavonoids and the improvement of antioxidant capacity in our research system. Our work evaluated the physiological and transcriptome perturbations in a conifer’s response to UV-B, and generally, highlighted the necessity of a systems biology approach in addressing plant stress biology.},
	number = {7},
	urldate = {2021-11-04},
	journal = {Tree Physiology},
	author = {Xu, Jie and Nie, Shuai and Xu, Chao-Qun and Liu, Hui and Jia, Kai-Hua and Zhou, Shan-Shan and Zhao, Wei and Zhou, Xian-Qing and El-Kassaby, Yousry A and Wang, Xiao-Ru and Porth, Ilga and Mao, Jian-Feng},
	month = jul,
	year = {2021},
	keywords = {China, Chinese red pine, Gene Expression Regulation, Plant, Pinus, RNA-seq, Stress, Physiological, Tracheophyta, Ultraviolet Rays, high energy UV-B, physiological reprogramming, time-ordered gene regulatory network},
	pages = {1247--1263},
}

During their lifetimes, plants are exposed to different abiotic stress factors eliciting various physiological responses and triggering important defense processes. For UV-B radiation responses in forest trees, the genetics and molecular regulation remain to be elucidated. Here, we exposed Pinus tabuliformis Carr., a major conifer from northern China, to short-term high-intensity UV-B and employed a systems biology approach to characterize the early physiological processes and the hierarchical gene regulation, which revealed a temporal transition from primary to secondary metabolism, the buildup of enhanced antioxidant capacity and stress-signaling activation. Our findings showed that photosynthesis and biosynthesis of photosynthetic pigments were inhibited, while flavonoids and their related derivates biosynthesis, as well as glutathione and glutathione S-transferase mediated antioxidant processes, were enhanced. Likewise, stress-related phytohormones (jasmonic acid, salicylic acid and ethylene), kinase and reactive oxygen species signal transduction pathways were activated. Biological processes regulated by auxin and karrikin were, for the first time, found to be involved in plant defense against UV-B by promoting the biosynthesis of flavonoids and the improvement of antioxidant capacity in our research system. Our work evaluated the physiological and transcriptome perturbations in a conifer’s response to UV-B, and generally, highlighted the necessity of a systems biology approach in addressing plant stress biology.

@article{haas_candidate_2021,
	title = {Candidate regulators and target genes of drought stress in needles and roots of {Norway} spruce},
	volume = {41},
	issn = {1758-4469},
	url = {https://doi.org/10.1093/treephys/tpaa178},
	doi = {10.1093/treephys/tpaa178},
	abstract = {Drought stress impacts seedling establishment, survival and whole-plant productivity. Molecular responses to drought stress have been most extensively studied in herbaceous species, mostly considering only aboveground tissues. Coniferous tree species dominate boreal forests, which are predicted to be exposed to more frequent and acute drought as a result of ongoing climate change. The associated impact at all stages of the forest tree life cycle is expected to have large-scale ecological and economic impacts. However, the molecular response to drought has not been comprehensively profiled for coniferous species. We assayed the physiological and transcriptional response of Picea abies (L.) H. Karst seedling needles and roots after exposure to mild and severe drought. Shoots and needles showed an extensive reversible plasticity for physiological measures indicative of drought-response mechanisms, including changes in stomatal conductance (gs), shoot water potential and abscisic acid (ABA). In both tissues, the most commonly observed expression profiles in response to drought were highly correlated with the ABA levels. Still, root and needle transcriptional responses contrasted, with extensive root-specific down-regulation of growth. Comparison between previously characterized Arabidopsis thaliana L. drought-response genes and P. abies revealed both conservation and divergence of transcriptional response to drought. In P. abies, transcription factors belonging to the ABA responsive element(ABRE) binding/ABRE binding factors ABA-dependent pathway had a more limited role. These results highlight the importance of profiling both above- and belowground tissues, and provide a comprehensive framework to advance the understanding of the drought response of P. abies. The results demonstrate that a short-term, severe drought induces severe physiological responses coupled to extensive transcriptome modulation and highlight the susceptibility of Norway spruce seedlings to such drought events.},
	number = {7},
	urldate = {2021-11-04},
	journal = {Tree Physiology},
	author = {Haas, Julia C and Vergara, Alexander and Serrano, Alonso R and Mishra, Sanatkumar and Hurry, Vaughan and Street, Nathaniel R},
	month = jul,
	year = {2021},
	pages = {1230--1246},
}

Drought stress impacts seedling establishment, survival and whole-plant productivity. Molecular responses to drought stress have been most extensively studied in herbaceous species, mostly considering only aboveground tissues. Coniferous tree species dominate boreal forests, which are predicted to be exposed to more frequent and acute drought as a result of ongoing climate change. The associated impact at all stages of the forest tree life cycle is expected to have large-scale ecological and economic impacts. However, the molecular response to drought has not been comprehensively profiled for coniferous species. We assayed the physiological and transcriptional response of Picea abies (L.) H. Karst seedling needles and roots after exposure to mild and severe drought. Shoots and needles showed an extensive reversible plasticity for physiological measures indicative of drought-response mechanisms, including changes in stomatal conductance (gs), shoot water potential and abscisic acid (ABA). In both tissues, the most commonly observed expression profiles in response to drought were highly correlated with the ABA levels. Still, root and needle transcriptional responses contrasted, with extensive root-specific down-regulation of growth. Comparison between previously characterized Arabidopsis thaliana L. drought-response genes and P. abies revealed both conservation and divergence of transcriptional response to drought. In P. abies, transcription factors belonging to the ABA responsive element(ABRE) binding/ABRE binding factors ABA-dependent pathway had a more limited role. These results highlight the importance of profiling both above- and belowground tissues, and provide a comprehensive framework to advance the understanding of the drought response of P. abies. The results demonstrate that a short-term, severe drought induces severe physiological responses coupled to extensive transcriptome modulation and highlight the susceptibility of Norway spruce seedlings to such drought events.

@article{velasquez_xyloglucan_2021,
	title = {Xyloglucan {Remodeling} {Defines} {Auxin}-{Dependent} {Differential} {Tissue} {Expansion} in {Plants}},
	volume = {22},
	issn = {1422-0067},
	doi = {10.3390/ijms22179222},
	abstract = {Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan's molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth.},
	language = {eng},
	number = {17},
	journal = {International Journal of Molecular Sciences},
	author = {Velasquez, Silvia Melina and Guo, Xiaoyuan and Gallemi, Marçal and Aryal, Bibek and Venhuizen, Peter and Barbez, Elke and Dünser, Kai Alexander and Darino, Martin and Pĕnčík, Aleš and Novák, Ondřej and Kalyna, Maria and Mouille, Gregory and Benková, Eva and P Bhalerao, Rishikesh and Mravec, Jozef and Kleine-Vehn, Jürgen},
	month = aug,
	year = {2021},
	keywords = {Arabidopsis, Cell Wall, Fluorescent Antibody Technique, Gene Expression Regulation, Plant, Glucans, Indoleacetic Acids, Peas, Plant Cells, Plant Development, Plant Physiological Phenomena, Signal Transduction, Xylans, auxin, cell wall, gravitropism, growth, hypocotyls, xyloglucans},
	pages = {9222},
}

Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan's molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth.

@article{rigal_network_2021,
	title = {A network of stress-related genes regulates hypocotyl elongation downstream of selective auxin perception},
	volume = {187},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab269},
	doi = {10.1093/plphys/kiab269},
	abstract = {The plant hormone auxin, a master coordinator of development, regulates hypocotyl elongation during seedling growth. We previously identified the synthetic molecule RubNeddin 1 (RN1), which induces degradation of the AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors INDOLE-3-ACETIC ACID-INDUCIBLE3 (IAA3) and IAA7 in planta and strongly promotes hypocotyl elongation. In the present study, we show that despite the structural similarity of RN1 to the synthetic auxin 2,4-dichlorophenoxyacetic-acid (2,4-D), direct treatments with these compounds in Arabidopsis (Arabidopsis thaliana) result in distinct effects, possibly due to enhanced uptake of RN1 and low-level, chronic release of 2,4-D from RN1 in planta. We confirm RN1-induced hypocotyl elongation occurs via specific TRANSPORT INHIBITOR RESISTANT1 (TIR1)/AUXIN SIGNALING F-BOX (AFB) receptor-mediated auxin signaling involving TIR1, AFB2, and AFB5. Using a transcriptome profiling strategy and candidate gene approach, we identify the genes ZINC FINGER OF ARABIDOPSIS THALIANA10 (ZAT10), ARABIDOPSIS TOXICOS EN LEVADURA31 (ATL31), and WRKY DNA-BINDING PROTEIN33 (WRKY33) as being rapidly upregulated by RN1, despite being downregulated by 2,4-D treatment. RN1-induced expression of these genes also occurs via TIR1/AFB-mediated auxin signaling. Our results suggest both hypocotyl elongation and transcription of these genes are induced by RN1 via the promoted degradation of the AUX/IAA transcriptional repressor IAA7. Moreover, these three genes, which are known to be stress-related, act in an inter-dependent transcriptional regulatory network controlling hypocotyl elongation. Together, our results suggest ZAT10, ATL31, and WRKY33 take part in a common gene network regulating hypocotyl elongation in Arabidopsis downstream of a selective auxin perception module likely involving TIR1, AFB2, and AFB5 and inducing the degradation of IAA7.},
	number = {1},
	urldate = {2021-10-15},
	journal = {Plant Physiology},
	author = {Rigal, Adeline and Doyle, Siamsa M. and Ritter, Andrés and Raggi, Sara and Vain, Thomas and O’Brien, José Antonio and Goossens, Alain and Pauwels, Laurens and Robert, Stéphanie},
	month = sep,
	year = {2021},
	pages = {430--445},
}

The plant hormone auxin, a master coordinator of development, regulates hypocotyl elongation during seedling growth. We previously identified the synthetic molecule RubNeddin 1 (RN1), which induces degradation of the AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors INDOLE-3-ACETIC ACID-INDUCIBLE3 (IAA3) and IAA7 in planta and strongly promotes hypocotyl elongation. In the present study, we show that despite the structural similarity of RN1 to the synthetic auxin 2,4-dichlorophenoxyacetic-acid (2,4-D), direct treatments with these compounds in Arabidopsis (Arabidopsis thaliana) result in distinct effects, possibly due to enhanced uptake of RN1 and low-level, chronic release of 2,4-D from RN1 in planta. We confirm RN1-induced hypocotyl elongation occurs via specific TRANSPORT INHIBITOR RESISTANT1 (TIR1)/AUXIN SIGNALING F-BOX (AFB) receptor-mediated auxin signaling involving TIR1, AFB2, and AFB5. Using a transcriptome profiling strategy and candidate gene approach, we identify the genes ZINC FINGER OF ARABIDOPSIS THALIANA10 (ZAT10), ARABIDOPSIS TOXICOS EN LEVADURA31 (ATL31), and WRKY DNA-BINDING PROTEIN33 (WRKY33) as being rapidly upregulated by RN1, despite being downregulated by 2,4-D treatment. RN1-induced expression of these genes also occurs via TIR1/AFB-mediated auxin signaling. Our results suggest both hypocotyl elongation and transcription of these genes are induced by RN1 via the promoted degradation of the AUX/IAA transcriptional repressor IAA7. Moreover, these three genes, which are known to be stress-related, act in an inter-dependent transcriptional regulatory network controlling hypocotyl elongation. Together, our results suggest ZAT10, ATL31, and WRKY33 take part in a common gene network regulating hypocotyl elongation in Arabidopsis downstream of a selective auxin perception module likely involving TIR1, AFB2, and AFB5 and inducing the degradation of IAA7.

@article{ma_mads-box_2021,
	title = {{MADS}-box transcription factors {MADS11} and {DAL1} interact to mediate the vegetative-to-reproductive transition in pine},
	volume = {187},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiab250},
	doi = {10.1093/plphys/kiab250},
	abstract = {The reproductive transition is an important event that is crucial for plant survival and reproduction. Relative to the thorough understanding of the vegetative phase transition in angiosperms, a little is known about this process in perennial conifers. To gain insight into the molecular basis of the regulatory mechanism in conifers, we used temporal dynamic transcriptome analysis with samples from seven different ages of Pinus tabuliformis to identify a gene module substantially associated with aging. The results first demonstrated that the phase change in P. tabuliformis occurred as an unexpectedly rapid transition rather than a slow, gradual progression. The age-related gene module contains 33 transcription factors and was enriched in genes that belong to the MADS (MCMl, AGAMOUS, DEFICIENS, SRF)-box family, including six SOC1-like genes and DAL1 and DAL10. Expression analysis in P. tabuliformis and a late-cone-setting P. bungeana mutant showed a tight association between PtMADS11 and reproductive competence. We then confirmed that MADS11 and DAL1 coordinate the aging pathway through physical interaction. Overexpression of PtMADS11 and PtDAL1 partially rescued the flowering of 35S::miR156A and spl1,2,3,4,5,6 mutants in Arabidopsis (Arabidopsis thaliana), but only PtMADS11 could rescue the flowering of the ft-10 mutant, suggesting PtMADS11 and PtDAL1 play different roles in flowering regulatory networks in Arabidopsis. The PtMADS11 could not alter the flowering phenotype of soc1-1-2, indicating it may function differently from AtSOC1 in Arabidopsis. In this study, we identified the MADS11 gene in pine as a regulatory mediator of the juvenile-to-adult transition with functions differentiated from the angiosperm SOC1.},
	number = {1},
	urldate = {2021-10-01},
	journal = {Plant Physiology},
	author = {Ma, Jing-Jing and Chen, Xi and Song, Yi-Tong and Zhang, Gui-Fang and Zhou, Xian-Qing and Que, Shu-Peng and Mao, Fei and Pervaiz, Tariq and Lin, Jin-Xing and Li, Yue and Li, Wei and Wu, Harry X. and Niu, Shi-Hui},
	month = sep,
	year = {2021},
	pages = {247--262},
}

The reproductive transition is an important event that is crucial for plant survival and reproduction. Relative to the thorough understanding of the vegetative phase transition in angiosperms, a little is known about this process in perennial conifers. To gain insight into the molecular basis of the regulatory mechanism in conifers, we used temporal dynamic transcriptome analysis with samples from seven different ages of Pinus tabuliformis to identify a gene module substantially associated with aging. The results first demonstrated that the phase change in P. tabuliformis occurred as an unexpectedly rapid transition rather than a slow, gradual progression. The age-related gene module contains 33 transcription factors and was enriched in genes that belong to the MADS (MCMl, AGAMOUS, DEFICIENS, SRF)-box family, including six SOC1-like genes and DAL1 and DAL10. Expression analysis in P. tabuliformis and a late-cone-setting P. bungeana mutant showed a tight association between PtMADS11 and reproductive competence. We then confirmed that MADS11 and DAL1 coordinate the aging pathway through physical interaction. Overexpression of PtMADS11 and PtDAL1 partially rescued the flowering of 35S::miR156A and spl1,2,3,4,5,6 mutants in Arabidopsis (Arabidopsis thaliana), but only PtMADS11 could rescue the flowering of the ft-10 mutant, suggesting PtMADS11 and PtDAL1 play different roles in flowering regulatory networks in Arabidopsis. The PtMADS11 could not alter the flowering phenotype of soc1-1-2, indicating it may function differently from AtSOC1 in Arabidopsis. In this study, we identified the MADS11 gene in pine as a regulatory mediator of the juvenile-to-adult transition with functions differentiated from the angiosperm SOC1.

@article{lutter_belowground_2021,
	title = {Belowground resource utilization in monocultures and mixtures of {Scots} pine and {Norway} spruce},
	volume = {500},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S0378112721007374},
	doi = {10.1016/j.foreco.2021.119647},
	abstract = {Mixed forests have been recommended to replace monocultures, often being more productive and resilient ecosystems. Those benefits of species mixing have been suggested to be attributed to lower competition (above- and belowground) due to potential separation of resource acquisition strategies, yet a mechanistic understanding of belowground processes has largely been missing. We applied an isotopic-labelling technique using 15N and 2H at {\textasciitilde}5 cm soil depth to study acquisition of two important resources, nitrogen (N) and water, in a replicated field experiment including mature Scots pine and Norway spruce monocultures and their mixture in boreal Sweden. Based on the isotopic data, we modelled distance-dependent N and water uptake and described the horizontal reach of active rooting areas around trees. The active root area for both N and water uptake in monocultures of both species was approximately 6–10 m2. Substantially wider areas were observed inside the mixture for N acquisition (27 m2 for pine and 21 m2 for spruce). Water was mainly acquired from within a 12–15 m2 area in mixture. The mixture and the pine monocultures exhibited similar recovery of the added 15N (3.8–4.5\%) and its uptake per unit of foliage mass. The recovery of 15N for the spruce monocultures was generally lower (2.1\%) but no difference was noted in the uptake per unit of foliage mass between spruce monoculture and mixture. No differences were found for recovery of 2H between the stand types. Mixing pine and spruce did not improve the resource uptake in comparison with the estimated theoretical mixture (according to the normalized basal area in monocultures). However, the mixing revealed significant differences between tree species whereas pines inside the mixture recovered 11.3-fold more 15N than accompanying spruce. Root overlap of 3–11 trees on 1 m2 was observed in all stand types, far exceeding the degree of canopy overlap. We discuss this overlap in terms of competition between individual trees. Spruces have proportionally larger horizontal rooting area relative to their aboveground size than pines. Scots pine and Norway spruce mixing in this type of boreal forest does not significantly enhance resource acquisition but leads to compensatory partitioning of growth, suggesting fierce interspecific competition, rather than niche separation.},
	language = {en},
	urldate = {2021-10-14},
	journal = {Forest Ecology and Management},
	author = {Lutter, Reimo and Henriksson, Nils and Lim, Hyungwoo and Blaško, Róbert and Magh, Ruth-Kristina and Näsholm, Torgny and Nordin, Annika and Lundmark, Tomas and Marshall, John D.},
	month = nov,
	year = {2021},
	keywords = {Mixed forests, Nitrogen, Root competition, Stable Isotopes, Water},
	pages = {119647},
}

Mixed forests have been recommended to replace monocultures, often being more productive and resilient ecosystems. Those benefits of species mixing have been suggested to be attributed to lower competition (above- and belowground) due to potential separation of resource acquisition strategies, yet a mechanistic understanding of belowground processes has largely been missing. We applied an isotopic-labelling technique using 15N and 2H at ~5 cm soil depth to study acquisition of two important resources, nitrogen (N) and water, in a replicated field experiment including mature Scots pine and Norway spruce monocultures and their mixture in boreal Sweden. Based on the isotopic data, we modelled distance-dependent N and water uptake and described the horizontal reach of active rooting areas around trees. The active root area for both N and water uptake in monocultures of both species was approximately 6–10 m2. Substantially wider areas were observed inside the mixture for N acquisition (27 m2 for pine and 21 m2 for spruce). Water was mainly acquired from within a 12–15 m2 area in mixture. The mixture and the pine monocultures exhibited similar recovery of the added 15N (3.8–4.5%) and its uptake per unit of foliage mass. The recovery of 15N for the spruce monocultures was generally lower (2.1%) but no difference was noted in the uptake per unit of foliage mass between spruce monoculture and mixture. No differences were found for recovery of 2H between the stand types. Mixing pine and spruce did not improve the resource uptake in comparison with the estimated theoretical mixture (according to the normalized basal area in monocultures). However, the mixing revealed significant differences between tree species whereas pines inside the mixture recovered 11.3-fold more 15N than accompanying spruce. Root overlap of 3–11 trees on 1 m2 was observed in all stand types, far exceeding the degree of canopy overlap. We discuss this overlap in terms of competition between individual trees. Spruces have proportionally larger horizontal rooting area relative to their aboveground size than pines. Scots pine and Norway spruce mixing in this type of boreal forest does not significantly enhance resource acquisition but leads to compensatory partitioning of growth, suggesting fierce interspecific competition, rather than niche separation.

@article{mahboubi_small-scale_2021,
	title = {Small-scale sequencing enables quality assessment of {Ribo}-{Seq} data: an example from {Arabidopsis} cell culture},
	volume = {17},
	issn = {1746-4811},
	shorttitle = {Small-scale sequencing enables quality assessment of {Ribo}-{Seq} data},
	url = {https://doi.org/10.1186/s13007-021-00791-w},
	doi = {10.1186/s13007-021-00791-w},
	abstract = {Translation is a tightly regulated process, controlling the rate of protein synthesis in cells. Ribosome sequencing (Ribo-Seq) is a recently developed tool for studying actively translated mRNA and can thus directly address translational regulation. Ribo-Seq libraries need to be sequenced to a great depth due to high contamination by rRNA and other contaminating nucleic acid fragments. Deep sequencing is expensive, and it generates large volumes of data, making data analysis complicated and time consuming.},
	number = {1},
	urldate = {2021-10-14},
	journal = {Plant Methods},
	author = {Mahboubi, Amir and Delhomme, Nicolas and Häggström, Sara and Hanson, Johannes},
	month = aug,
	year = {2021},
	keywords = {Evaluation of sequencing library quality, Ribo-Seq, Ribosomal profiling, Translation, Translational profiling},
	pages = {92},
}

Translation is a tightly regulated process, controlling the rate of protein synthesis in cells. Ribosome sequencing (Ribo-Seq) is a recently developed tool for studying actively translated mRNA and can thus directly address translational regulation. Ribo-Seq libraries need to be sequenced to a great depth due to high contamination by rRNA and other contaminating nucleic acid fragments. Deep sequencing is expensive, and it generates large volumes of data, making data analysis complicated and time consuming.

@article{asadi-aghbolaghi_protocol_2021,
	title = {Protocol development for somatic embryogenesis, {SSR} markers and genetic modification of {Stipagrostis} pennata ({Trin}.) {De} {Winter}},
	volume = {17},
	issn = {1746-4811},
	url = {https://doi.org/10.1186/s13007-021-00768-9},
	doi = {10.1186/s13007-021-00768-9},
	abstract = {Stipagrostis pennata (Trin.) De Winter is an important species for fixing sand in shifting and semi-fixed sandy lands, for grazing, and potentially as a source of lignocellulose fibres for pulp and paper industry. The seeds have low viability, which limits uses for revegetation. Somatic embryogenesis offers an alternative method for obtaining large numbers of plants from limited seed sources.},
	number = {1},
	urldate = {2021-10-14},
	journal = {Plant Methods},
	author = {Asadi-Aghbolaghi, Masoumeh and Dedicova, Beata and Ranade, Sonali Sachi and Le, Kim-Cuong and Sharifzadeh, Farzad and Omidi, Mansoor and Egertsdotter, Ulrika},
	month = jun,
	year = {2021},
	keywords = {Agrobacterium, Grass, Plant regeneration, SSR markers, Somatic embryogenesis, Stipagrostis pennata (Trin.) De Winter},
	pages = {70},
}

Stipagrostis pennata (Trin.) De Winter is an important species for fixing sand in shifting and semi-fixed sandy lands, for grazing, and potentially as a source of lignocellulose fibres for pulp and paper industry. The seeds have low viability, which limits uses for revegetation. Somatic embryogenesis offers an alternative method for obtaining large numbers of plants from limited seed sources.

@article{stenlund_metabolic_2021,
	title = {Metabolic {Profiling} of {Plasma} in {Patients} with {Irritable} {Bowel} {Syndrome} after a 4-{Week} {Starch}- and {Sucrose}-{Reduced} {Diet}},
	volume = {11},
	copyright = {http://creativecommons.org/licenses/by/3.0/},
	url = {https://www.mdpi.com/2218-1989/11/7/440},
	doi = {10.3390/metabo11070440},
	abstract = {A 4-week dietary intervention with a starch- and sucrose-restricted diet (SSRD) was conducted in patients with irritable bowel syndrome (IBS) to examine the metabolic profile in relation to nutrient intake and gastrointestinal symptoms. IBS patients were randomized to SSRD intervention (n = 69) or control continuing with their ordinary food habits (n = 22). Food intake was registered and the questionnaires IBS-symptoms severity scale (IBS-SSS) and visual analog scale for IBS (VAS-IBS) were completed. Metabolomics untargeted analysis was performed by gas chromatography mass spectrometry (GC-MS) and liquid chromatography mass spectrometry (LC-MS) in positive and negative ionization modes. SSRD led to marked changes in circulating metabolite concentrations at the group level, most prominent for reduced starch intake and increased polyunsaturated fat, with small changes in the control group. On an individual level, the correlations were weak. The marked reduction in gastrointestinal symptoms did not correlate with the metabolic changes. SSRD was observed by clear metabolic effects mainly related to linoleic acid metabolism, fatty acid biosynthesis, and beta-oxidation.},
	language = {en},
	number = {7},
	urldate = {2021-10-14},
	journal = {Metabolites},
	author = {Stenlund, Hans and Nilholm, Clara and Chorell, Elin and Roth, Bodil and D’Amato, Mauro and Ohlsson, Bodil},
	month = jul,
	year = {2021},
	keywords = {IBS, dietary advice, metabolic profiling, metabolomics, starch, sucrose},
	pages = {440},
}

A 4-week dietary intervention with a starch- and sucrose-restricted diet (SSRD) was conducted in patients with irritable bowel syndrome (IBS) to examine the metabolic profile in relation to nutrient intake and gastrointestinal symptoms. IBS patients were randomized to SSRD intervention (n = 69) or control continuing with their ordinary food habits (n = 22). Food intake was registered and the questionnaires IBS-symptoms severity scale (IBS-SSS) and visual analog scale for IBS (VAS-IBS) were completed. Metabolomics untargeted analysis was performed by gas chromatography mass spectrometry (GC-MS) and liquid chromatography mass spectrometry (LC-MS) in positive and negative ionization modes. SSRD led to marked changes in circulating metabolite concentrations at the group level, most prominent for reduced starch intake and increased polyunsaturated fat, with small changes in the control group. On an individual level, the correlations were weak. The marked reduction in gastrointestinal symptoms did not correlate with the metabolic changes. SSRD was observed by clear metabolic effects mainly related to linoleic acid metabolism, fatty acid biosynthesis, and beta-oxidation.

@article{chen_leveraging_2021,
	title = {Leveraging breeding programs and genomic data in {Norway} spruce ({Picea} abies {L}. {Karst}) for {GWAS} analysis},
	volume = {22},
	issn = {1474-760X},
	url = {https://doi.org/10.1186/s13059-021-02392-1},
	doi = {10.1186/s13059-021-02392-1},
	abstract = {Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.},
	number = {1},
	urldate = {2021-10-14},
	journal = {Genome Biology},
	author = {Chen, Zhi-Qiang and Zan, Yanjun and Milesi, Pascal and Zhou, Linghua and Chen, Jun and Li, Lili and Cui, BinBin and Niu, Shihui and Westin, Johan and Karlsson, Bo and García-Gil, Maria Rosario and Lascoux, Martin and Wu, Harry X.},
	month = jun,
	year = {2021},
	keywords = {Budburst stage, Frost damage, Genome-wide association study, MAP3K gene, Norway spruce, Wood quality},
	pages = {179},
}

Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.

@article{martin_exploring_2021,
	title = {Exploring the β-tubulin gene family in a benzimidazole-resistant {Parascaris} univalens population},
	volume = {17},
	issn = {2211-3207},
	url = {https://www.sciencedirect.com/science/article/pii/S2211320721000403},
	doi = {10.1016/j.ijpddr.2021.08.004},
	abstract = {Benzimidazole (BZ) drugs are frequently used to treat infections with the equine ascarid Parascaris univalens due to increasing resistance to macrocyclic lactones and pyrantel. Benzimidazole resistance is rare in ascarids in contrast to strongyle parasites where this resistance is widespread. In strongyles, single nucleotide polymorphisms (SNPs) at codons 167, 198 and 200 in a β-tubulin gene have been correlated to BZ resistance, but little is known about the β-tubulin genes and their possible involvement in BZ resistance in P. univalens and other ascarids. Previously two β-tubulin genes have been identified in P. univalens. In this study, we present five additional β-tubulin genes as well as the phylogenetic relationship of all seven genes to β-tubulins of other clade III and V nematodes. In addition, the efficacy of fenbendazole for treatment of P. univalens on a Swedish stud farm was studied in 2019 and 2020 using faecal egg count reduction test. Reductions varied from 73\% to 88\%, indicating the presence of a resistant P. univalens population on the farm. The emergence of BZ resistance emphasizes the need for development of molecular markers for rapid and more sensitive detection of resistant populations. We therefore investigated whether possible SNPs at positions 167, 198 or 200 in any of the β-tubulin genes could be used to distinguish between resistant and susceptible P. univalens populations. Amplicon sequencing covering the mutation sites 167, 198 and 200 in all seven β-tubulin genes revealed an absence of SNPs in both resistant and susceptible populations, suggesting that the mechanism behind BZ resistance in ascarids is different from that in strongyle nematodes and the search for a molecular marker for BZ resistance in P. univalens needs to continue.},
	language = {en},
	urldate = {2021-10-01},
	journal = {International Journal for Parasitology: Drugs and Drug Resistance},
	author = {Martin, Frida and Halvarsson, Peter and Delhomme, Nicolas and Höglund, Johan and Tydén, Eva},
	month = dec,
	year = {2021},
	keywords = {Amplicon sequencing, Anthelmintic resistance, Equine, Fenbendazole},
	pages = {84--91},
}

Benzimidazole (BZ) drugs are frequently used to treat infections with the equine ascarid Parascaris univalens due to increasing resistance to macrocyclic lactones and pyrantel. Benzimidazole resistance is rare in ascarids in contrast to strongyle parasites where this resistance is widespread. In strongyles, single nucleotide polymorphisms (SNPs) at codons 167, 198 and 200 in a β-tubulin gene have been correlated to BZ resistance, but little is known about the β-tubulin genes and their possible involvement in BZ resistance in P. univalens and other ascarids. Previously two β-tubulin genes have been identified in P. univalens. In this study, we present five additional β-tubulin genes as well as the phylogenetic relationship of all seven genes to β-tubulins of other clade III and V nematodes. In addition, the efficacy of fenbendazole for treatment of P. univalens on a Swedish stud farm was studied in 2019 and 2020 using faecal egg count reduction test. Reductions varied from 73% to 88%, indicating the presence of a resistant P. univalens population on the farm. The emergence of BZ resistance emphasizes the need for development of molecular markers for rapid and more sensitive detection of resistant populations. We therefore investigated whether possible SNPs at positions 167, 198 or 200 in any of the β-tubulin genes could be used to distinguish between resistant and susceptible P. univalens populations. Amplicon sequencing covering the mutation sites 167, 198 and 200 in all seven β-tubulin genes revealed an absence of SNPs in both resistant and susceptible populations, suggesting that the mechanism behind BZ resistance in ascarids is different from that in strongyle nematodes and the search for a molecular marker for BZ resistance in P. univalens needs to continue.

@article{lim_organic_2021,
	title = {Organic nitrogen enhances nitrogen nutrition and early growth of {Pinus} sylvestris seedlings},
	issn = {1758-4469},
	url = {https://doi.org/10.1093/treephys/tpab127},
	doi = {10.1093/treephys/tpab127},
	abstract = {Boreal trees are capable of taking up organic nitrogen (N) as effectively as inorganic N. Depending on the abundance of soil N forms, plants may adjust physiological and morphological traits to optimize N uptake. However, the link between these traits and N uptake in response to soil N sources is poorly understood. We examined Pinus sylvestris seedlings��� biomass growth and allocation, transpiration, and N uptake in response to additions of organic (the amino acid arginine) or inorganic N (ammonium-nitrate). We also monitored in-situ soil N fluxes in the pots following an addition of N, using a microdialysis system. Supplying organic N resulted in a stable soil N flux, whereas the inorganic N resulted in a sharp increase of nitrate flux followed by a rapid decline, demonstrating a fluctuating N supply and a risk for loss of nitrate from the growth medium. Seedlings supplied with organic N achieved a greater biomass with a higher N content, thus reaching a higher N recovery compared with those supplied inorganic N. In spite of a higher N concentration in organic N seedlings, root-to-shoot ratio and transpiration per unit leaf area were similar to those of inorganic N seedlings. We conclude that enhanced seedlings’ nutrition and growth under the organic N source may be attributed to a stable supply of N, owing to a strong retention rate in the soil medium.},
	number = {tpab127},
	urldate = {2021-10-01},
	journal = {Tree Physiology},
	author = {Lim, Hyungwoo and Jämtgård, Sandra and Oren, Ram and Gruffman, Linda and Kunz, Sabine and Näsholm, Torgny},
	month = sep,
	year = {2021},
}

Boreal trees are capable of taking up organic nitrogen (N) as effectively as inorganic N. Depending on the abundance of soil N forms, plants may adjust physiological and morphological traits to optimize N uptake. However, the link between these traits and N uptake in response to soil N sources is poorly understood. We examined Pinus sylvestris seedlings��� biomass growth and allocation, transpiration, and N uptake in response to additions of organic (the amino acid arginine) or inorganic N (ammonium-nitrate). We also monitored in-situ soil N fluxes in the pots following an addition of N, using a microdialysis system. Supplying organic N resulted in a stable soil N flux, whereas the inorganic N resulted in a sharp increase of nitrate flux followed by a rapid decline, demonstrating a fluctuating N supply and a risk for loss of nitrate from the growth medium. Seedlings supplied with organic N achieved a greater biomass with a higher N content, thus reaching a higher N recovery compared with those supplied inorganic N. In spite of a higher N concentration in organic N seedlings, root-to-shoot ratio and transpiration per unit leaf area were similar to those of inorganic N seedlings. We conclude that enhanced seedlings’ nutrition and growth under the organic N source may be attributed to a stable supply of N, owing to a strong retention rate in the soil medium.

@article{pramod_saccharification_2021,
	title = {Saccharification {Potential} of {Transgenic} {Greenhouse}- and {Field}-{Grown} {Aspen} {Engineered} for {Reduced} {Xylan} {Acetylation}},
	volume = {12},
	issn = {1664-462X},
	url = {https://www.frontiersin.org/article/10.3389/fpls.2021.704960},
	doi = {10.3389/fpls.2021.704960},
	abstract = {High acetylation of xylan in hardwoods decreases their value as biorefinery feedstocks. To counter this problem, we have constitutively suppressed RWA genes encoding acetyl-CoA transporters using the 35S promoter, or constitutively and wood-specifically (using the WP promoter) expressed fungal acetyl xylan esterases of families CE1 (AnAXE1) and CE5 (HjAXE), to reduce acetylation in hybrid aspen. All these transformations improved the saccharification of wood from greenhouse-grown trees. Here, we describe the chemical properties and saccharification potential of the resulting lines grown in a five-year field trial, and one type of them (WP:AnAXE1) in greenhouse conditions. Chemically, the lignocellulose of the field- and greenhouse-field-grown plants slightly differed, but the reductions in acetylation and saccharification improvement of engineered trees were largely maintained in the field. The main novel phenotypic observation in the field was higher lignification in lines with the WP promoter than those with the 35S promoter. Following growth in the field, saccharification glucose yields were higher from most transformed lines than from wild-type (WT) plants with no pretreatment, but there was no improvement in saccharification with acid pretreatment. Thus, acid pretreatment removes most recalcitrance caused by acetylation. We found a complex relationship between acetylation and glucose yields in saccharification without pretreatment, suggesting that other variables, for example, the acetylation pattern, affect recalcitrance. Bigger gains in glucose yields were observed in lines with the 35S promoter than in those with the WP promoter, possibly due to their lower lignin content. However, better lignocellulose saccharification of these lines was offset by a growth penalty and their glucose yield per tree was lower. In a comparison of the best lines with each construct, WP:AnAXE1 provided the highest glucose yield per tree from saccharification, with and without pretreatment, WP:HjAXE yields were similar to those of WT plants, and yields of lines with other constructs were lower. These results show that lignocellulose properties of field-grown trees can be improved by reducing cell wall acetylation using various approaches, but some affect productivity in the field. Thus, better understanding of molecular and physiological consequences of deacetylation is needed to obtain quantitatively better results.},
	urldate = {2021-09-30},
	journal = {Frontiers in Plant Science},
	author = {Pramod, Sivan and Gandla, Madhavi Latha and Derba-Maceluch, Marta and Jönsson, Leif J. and Mellerowicz, Ewa J. and Winestrand, Sandra},
	year = {2021},
	pages = {1722},
}

High acetylation of xylan in hardwoods decreases their value as biorefinery feedstocks. To counter this problem, we have constitutively suppressed RWA genes encoding acetyl-CoA transporters using the 35S promoter, or constitutively and wood-specifically (using the WP promoter) expressed fungal acetyl xylan esterases of families CE1 (AnAXE1) and CE5 (HjAXE), to reduce acetylation in hybrid aspen. All these transformations improved the saccharification of wood from greenhouse-grown trees. Here, we describe the chemical properties and saccharification potential of the resulting lines grown in a five-year field trial, and one type of them (WP:AnAXE1) in greenhouse conditions. Chemically, the lignocellulose of the field- and greenhouse-field-grown plants slightly differed, but the reductions in acetylation and saccharification improvement of engineered trees were largely maintained in the field. The main novel phenotypic observation in the field was higher lignification in lines with the WP promoter than those with the 35S promoter. Following growth in the field, saccharification glucose yields were higher from most transformed lines than from wild-type (WT) plants with no pretreatment, but there was no improvement in saccharification with acid pretreatment. Thus, acid pretreatment removes most recalcitrance caused by acetylation. We found a complex relationship between acetylation and glucose yields in saccharification without pretreatment, suggesting that other variables, for example, the acetylation pattern, affect recalcitrance. Bigger gains in glucose yields were observed in lines with the 35S promoter than in those with the WP promoter, possibly due to their lower lignin content. However, better lignocellulose saccharification of these lines was offset by a growth penalty and their glucose yield per tree was lower. In a comparison of the best lines with each construct, WP:AnAXE1 provided the highest glucose yield per tree from saccharification, with and without pretreatment, WP:HjAXE yields were similar to those of WT plants, and yields of lines with other constructs were lower. These results show that lignocellulose properties of field-grown trees can be improved by reducing cell wall acetylation using various approaches, but some affect productivity in the field. Thus, better understanding of molecular and physiological consequences of deacetylation is needed to obtain quantitatively better results.

@article{robinson_variation_2021,
	title = {Variation in non-target traits in genetically modified hybrid aspens does not exceed natural variation},
	volume = {64},
	issn = {1871-6784},
	url = {https://www.sciencedirect.com/science/article/pii/S1871678421000625},
	doi = {10.1016/j.nbt.2021.05.005},
	abstract = {Genetically modified hybrid aspens (Populus tremula L. x P. tremuloides Michx.), selected for increased growth under controlled conditions, have been grown in highly replicated field trials to evaluate how the target trait (growth) translated to natural conditions. Moreover, the variation was compared among genotypes of ecologically important non-target traits: number of shoots, bud set, pathogen infection, amount of insect herbivory, composition of the insect herbivore community and flower bud induction. This variation was compared with the variation in a population of randomly selected natural accessions of P. tremula grown in common garden trials, to estimate how the “unintended variation” present in transgenic trees, which in the future may be commercialized, compares with natural variation. The natural variation in the traits was found to be typically significantly greater. The data suggest that when authorities evaluate the potential risks associated with a field experiment or commercial introduction of transgenic trees, risk evaluation should focus on target traits and that unintentional variation in non-target traits is of less concern.},
	language = {en},
	urldate = {2021-09-21},
	journal = {New Biotechnology},
	author = {Robinson, Kathryn M. and Möller, Linus and Bhalerao, Rishikesh P. and Hertzberg, Magnus and Nilsson, Ove and Jansson, Stefan},
	month = sep,
	year = {2021},
	keywords = {European aspen, Field experiment, Genetically modified, Hybrid aspen, Natural variation, Non-target traits},
	pages = {27--36},
}

Genetically modified hybrid aspens (Populus tremula L. x P. tremuloides Michx.), selected for increased growth under controlled conditions, have been grown in highly replicated field trials to evaluate how the target trait (growth) translated to natural conditions. Moreover, the variation was compared among genotypes of ecologically important non-target traits: number of shoots, bud set, pathogen infection, amount of insect herbivory, composition of the insect herbivore community and flower bud induction. This variation was compared with the variation in a population of randomly selected natural accessions of P. tremula grown in common garden trials, to estimate how the “unintended variation” present in transgenic trees, which in the future may be commercialized, compares with natural variation. The natural variation in the traits was found to be typically significantly greater. The data suggest that when authorities evaluate the potential risks associated with a field experiment or commercial introduction of transgenic trees, risk evaluation should focus on target traits and that unintentional variation in non-target traits is of less concern.

@article{jia_chromosome-scale_2021,
	title = {Chromosome-scale assembly and evolution of the tetraploid {Salvia} splendens ({Lamiaceae}) genome},
	volume = {8},
	copyright = {2021 The Author(s)},
	issn = {2052-7276},
	url = {https://www.nature.com/articles/s41438-021-00614-y},
	doi = {10/gmskmf},
	abstract = {Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.},
	language = {en},
	number = {1},
	urldate = {2021-09-02},
	journal = {Horticulture Research},
	author = {Jia, Kai-Hua and Liu, Hui and Zhang, Ren-Gang and Xu, Jie and Zhou, Shan-Shan and Jiao, Si-Qian and Yan, Xue-Mei and Tian, Xue-Chan and Shi, Tian-Le and Luo, Hang and Li, Zhi-Chao and Bao, Yu-Tao and Nie, Shuai and Guo, Jing-Fang and Porth, Ilga and El-Kassaby, Yousry A. and Wang, Xiao-Ru and Chen, Charles and Van de Peer, Yves and Zhao, Wei and Mao, Jian-Feng},
	month = sep,
	year = {2021},
	pages = {1--15},
}

Polyploidization plays a key role in plant evolution, but the forces driving the fate of homoeologs in polyploid genomes, i.e., paralogs resulting from a whole-genome duplication (WGD) event, remain to be elucidated. Here, we present a chromosome-scale genome assembly of tetraploid scarlet sage (Salvia splendens), one of the most diverse ornamental plants. We found evidence for three WGD events following an older WGD event shared by most eudicots (the γ event). A comprehensive, spatiotemporal, genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries, which could be associated with genomic rearrangements, transposable element proximity discrepancies, coding sequence variation, selection pressure, and transcription factor binding site differences. The observed differences between homoeologs may reflect the first step toward sub- and/or neofunctionalization. This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.

@article{raizada_recursive_2021,
	title = {Recursive partitioning to prioritize morphometric traits that separate {Aspen} specialist {Chaitophorus} aphid by species and stage},
	issn = {1742-7592},
	url = {https://doi.org/10.1007/s42690-021-00620-6},
	doi = {10/gmtzbt},
	abstract = {Arthropod herbivore assemblages are used to gain insight into questions about evolution, ecology, diversity, and conservation. However, determination at the species level of small arthropods may be challenging risking underestimating diversity. Here we suggest morphometric analyses as a supplementary determination method, and we demonstrate its use for a study of Chaitophorus species collected from Aspen trees (Populus tremula). Although sampled as one colony, the aphids represented three species. Rearing the species separately allowed us to get estimates characteristic of the developmental stages from each of the three species for morphometric comparisons. Recursive partitioning (RP) was used to create a decision tree for choice of morphometric parameters that with significance (p {\textless} 0.05) could determine the aphids by species and developmental stage; this insight could then be used as a key for determination. Eight of fifteen morphometric traits were selected by RP to be used in the key. Body length was responsible for nine splits and was consequently the more consistent morphometric trait used in the key.},
	language = {en},
	urldate = {2021-09-09},
	journal = {International Journal of Tropical Insect Science},
	author = {Raizada, Richa and Gaur, Rajarshi Kumar and Albrectsen, Benedicte R.},
	month = aug,
	year = {2021},
}

Arthropod herbivore assemblages are used to gain insight into questions about evolution, ecology, diversity, and conservation. However, determination at the species level of small arthropods may be challenging risking underestimating diversity. Here we suggest morphometric analyses as a supplementary determination method, and we demonstrate its use for a study of Chaitophorus species collected from Aspen trees (Populus tremula). Although sampled as one colony, the aphids represented three species. Rearing the species separately allowed us to get estimates characteristic of the developmental stages from each of the three species for morphometric comparisons. Recursive partitioning (RP) was used to create a decision tree for choice of morphometric parameters that with significance (p \textless 0.05) could determine the aphids by species and developmental stage; this insight could then be used as a key for determination. Eight of fifteen morphometric traits were selected by RP to be used in the key. Body length was responsible for nine splits and was consequently the more consistent morphometric trait used in the key.

@article{bai_modulation_2021,
	title = {Modulation of {Arabidopsis} root growth by specialized triterpenes},
	volume = {230},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.17144},
	doi = {10.1111/nph.17144},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Bai, Yuechen and Fernández‐Calvo, Patricia and Ritter, Andrés and Huang, Ancheng C. and Morales‐Herrera, Stefania and Bicalho, Keylla U. and Karady, Michal and Pauwels, Laurens and Buyst, Dieter and Njo, Maria and Ljung, Karen and Martins, José C. and Vanneste, Steffen and Beeckman, Tom and Osbourn, Anne and Goossens, Alain and Pollier, Jacob},
	month = apr,
	year = {2021},
	pages = {228--243},
}

@article{liu_solving_2021,
	title = {Solving the {Puzzle} of {Shape} {Regulation} in {Plant} {Epidermal} {Pavement} {Cells}},
	volume = {72},
	issn = {1543-5008},
	url = {https://www.annualreviews.org/doi/10.1146/annurev-arplant-080720-081920},
	doi = {10/gkzfvc},
	abstract = {The plant epidermis serves many essential functions, including interactions with the environment, protection, mechanical strength, and regulation of tissue and organ growth. To achieve these functions, specialized epidermal cells develop into particular shapes. These include the intriguing interdigitated jigsaw puzzle shape of cotyledon and leaf pavement cells seen in many species, the precise functions of which remain rather obscure. Although pavement cell shape regulation is complex and still a long way from being fully understood, the roles of the cell wall, mechanical stresses, cytoskeleton, cytoskeletal regulatory proteins, and phytohormones are becoming clearer. Here, we provide a review of this current knowledge of pavement cell morphogenesis, generated from a wealth of experimental evidence and assisted by computational modeling approaches. We also discuss the evolution and potential functions of pavement cell interdigitation. Throughout the review, we highlight some of the thought-provoking controversies and creative theories surrounding the formation of the curious puzzle shape of these cells.},
	number = {1},
	urldate = {2021-06-21},
	journal = {Annual Review of Plant Biology},
	author = {Liu, Sijia and Jobert, François and Rahneshan, Zahra and Doyle, Siamsa M. and Robert, Stéphanie},
	month = jun,
	year = {2021},
	pages = {525--550},
}

The plant epidermis serves many essential functions, including interactions with the environment, protection, mechanical strength, and regulation of tissue and organ growth. To achieve these functions, specialized epidermal cells develop into particular shapes. These include the intriguing interdigitated jigsaw puzzle shape of cotyledon and leaf pavement cells seen in many species, the precise functions of which remain rather obscure. Although pavement cell shape regulation is complex and still a long way from being fully understood, the roles of the cell wall, mechanical stresses, cytoskeleton, cytoskeletal regulatory proteins, and phytohormones are becoming clearer. Here, we provide a review of this current knowledge of pavement cell morphogenesis, generated from a wealth of experimental evidence and assisted by computational modeling approaches. We also discuss the evolution and potential functions of pavement cell interdigitation. Throughout the review, we highlight some of the thought-provoking controversies and creative theories surrounding the formation of the curious puzzle shape of these cells.

@article{przybylatoscano_gene_2021,
	title = {Gene atlas of iron‐containing proteins in {Arabidopsis} thaliana},
	volume = {106},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.15154},
	doi = {10/gkcr7c},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {The Plant Journal},
	author = {Przybyla‐Toscano, Jonathan and Boussardon, Clément and Law, Simon R. and Rouhier, Nicolas and Keech, Olivier},
	month = apr,
	year = {2021},
	pages = {258--274},
}

@article{singh_growing_2021,
	title = {Growing in time: exploring the molecular mechanisms of tree growth},
	volume = {41},
	issn = {1758-4469},
	shorttitle = {Growing in time},
	url = {https://academic.oup.com/treephys/article/41/4/657/5848548},
	doi = {10.1093/treephys/tpaa065},
	abstract = {Abstract
            Trees cover vast areas of the Earth’s landmasses. They mitigate erosion, capture carbon dioxide, produce oxygen and support biodiversity, and also are a source of food, raw materials and energy for human populations. Understanding the growth cycles of trees is fundamental for many areas of research. Trees, like most other organisms, have evolved a circadian clock to synchronize their growth and development with the daily and seasonal cycles of the environment. These regular changes in light, daylength and temperature are perceived via a range of dedicated receptors and cause resetting of the circadian clock to local time. This allows anticipation of daily and seasonal fluctuations and enables trees to co-ordinate their metabolism and physiology to ensure vital processes occur at the optimal times. In this review, we explore the current state of knowledge concerning the regulation of growth and seasonal dormancy in trees, using information drawn from model systems such as Populus spp.},
	language = {en},
	number = {4},
	urldate = {2021-06-07},
	journal = {Tree Physiology},
	author = {Singh, Rajesh Kumar and Bhalerao, Rishikesh P. and Eriksson, Maria E.},
	editor = {Polle, Andrea},
	month = apr,
	year = {2021},
	pages = {657--678},
}

Abstract Trees cover vast areas of the Earth’s landmasses. They mitigate erosion, capture carbon dioxide, produce oxygen and support biodiversity, and also are a source of food, raw materials and energy for human populations. Understanding the growth cycles of trees is fundamental for many areas of research. Trees, like most other organisms, have evolved a circadian clock to synchronize their growth and development with the daily and seasonal cycles of the environment. These regular changes in light, daylength and temperature are perceived via a range of dedicated receptors and cause resetting of the circadian clock to local time. This allows anticipation of daily and seasonal fluctuations and enables trees to co-ordinate their metabolism and physiology to ensure vital processes occur at the optimal times. In this review, we explore the current state of knowledge concerning the regulation of growth and seasonal dormancy in trees, using information drawn from model systems such as Populus spp.

@article{bannoud_adventitious_2021,
	title = {Adventitious {Rooting} in {Populus} {Species}: {Update} and {Perspectives}},
	volume = {12},
	issn = {1664-462X},
	shorttitle = {Adventitious {Rooting} in {Populus} {Species}},
	url = {https://www.frontiersin.org/articles/10.3389/fpls.2021.668837/full},
	doi = {10/gkhp7k},
	abstract = {Populus spp. are among the most economically important species worldwide. These trees are used not only for wood and fiber production, but also in the rehabilitation of degraded lands. Since they are clonally propagated, the ability of stem cuttings to form adventitious roots is a critical point for plant establishment and survival in the field, and consequently for the forest industry. Adventitious rooting in different Populus clones has been an agronomic trait targeted in breeding programs for many years, and many factors have been identified that affect this quantitative trait. A huge variation in the rooting capacity has been observed among the species in the Populus genus, and the responses to some of the factors affecting this trait have been shown to be genotype-dependent. This review analyses similarities and differences between results obtained from studies examining the role of internal and external factors affecting rooting of Populus species cuttings. Since rooting is the most important requirement for stand establishment in clonally propagated species, understanding the physiological and genetic mechanisms that promote this trait is essential for successful commercial deployment.},
	language = {English},
	urldate = {2021-06-17},
	journal = {Frontiers in Plant Science},
	author = {Bannoud, Florencia and Bellini, Catherine},
	year = {2021},
	keywords = {Adventitious rooting, Populus, Vegetative propagation, adventitious rooting, endogenous factors, environmental factors, vegetative propagation},
}

Populus spp. are among the most economically important species worldwide. These trees are used not only for wood and fiber production, but also in the rehabilitation of degraded lands. Since they are clonally propagated, the ability of stem cuttings to form adventitious roots is a critical point for plant establishment and survival in the field, and consequently for the forest industry. Adventitious rooting in different Populus clones has been an agronomic trait targeted in breeding programs for many years, and many factors have been identified that affect this quantitative trait. A huge variation in the rooting capacity has been observed among the species in the Populus genus, and the responses to some of the factors affecting this trait have been shown to be genotype-dependent. This review analyses similarities and differences between results obtained from studies examining the role of internal and external factors affecting rooting of Populus species cuttings. Since rooting is the most important requirement for stand establishment in clonally propagated species, understanding the physiological and genetic mechanisms that promote this trait is essential for successful commercial deployment.

@article{maher_hasselquist_moving_2021,
	title = {Moving towards multi-layered, mixed-species forests in riparian buffers will enhance their long-term function in boreal landscapes},
	volume = {493},
	issn = {0378-1127},
	url = {https://www.sciencedirect.com/science/article/pii/S037811272100342X},
	doi = {10.1016/j.foreco.2021.119254},
	abstract = {Riparian buffers are the primary tool in forest management for protecting the habitat structure and function of streams. They help protect against biogeochemical perturbation, filter sediments and nutrients, prevent erosion, contribute food to aquatic organisms, regulate light and hence water temperature, contribute deadwood, and preserve biodiversity. However, in production forests of Sweden and Finland, many headwater streams have been straightened, ditched, and/or channelized, resulting in altered hydrology and reduced natural disturbance by floods, which in turn affects important riparian functions. Furthermore, in even-aged management systems as practiced in much of Fennoscandia, understory trees have usually been cleared right up to the stream’s edge during thinning operations, especially around small, headwater streams. Fire suppression has further favored succession towards shade tolerant species. In the regions within Fennoscandia that have experienced this combination of intensive management and lack of natural disturbance, riparian zones are now dominated by single-storied, native Norway spruce. When the adjacent forest is cut, thin (5 - 15m) conifer-dominated riparian buffers are typically left. These buffers do not provide the protection and subsidies, in terms of leaf litter quality, needed to maintain water quality or support riparian or aquatic biodiversity. Based on a literature review, we found compelling evidence that the ecological benefits of multi-layered, mixed-species riparian forest with a large component of broadleaved species are higher than what is now commonly found in the managed stands of Fennoscandia. To improve the functionality of riparian zones, and hence the protection of streams in managed forest landscapes, we present some basic principles that could be used to enhance the ecological function of these interfaces. These management actions should be prioritized on streams and streamside stands that have been affected by simplification either through forest management or hydrological modification. Key to these principles is the planning and managing of buffer zones as early as possible in the rotation to ensure improved function throughout the rotation cycle and not only at final felling. This is well in line with EU and national legislation which can be interpreted as requiring landscape planning at all forest ages to meet biodiversity and other environmental goals. However, it is still rare that planning for conservation is done other than at the final felling stage. Implementing this new strategy is likely to have long-term positive effects and improve the protection of surface waters from negative forestry effects and a history of fire suppression. By following these suggested management principles, there will be a longer time period with high function and greater future management flexibility in addition to the benefits provided by leaving riparian buffers at the final felling stage.},
	language = {en},
	urldate = {2021-06-17},
	journal = {Forest Ecology and Management},
	author = {Maher Hasselquist, Eliza and Kuglerová, Lenka and Sjögren, Jörgen and Hjältén, Joakim and Ring, Eva and Sponseller, Ryan A. and Andersson, Elisabet and Lundström, Johanna and Mancheva, Irina and Nordin, Annika and Laudon, Hjalmar},
	month = aug,
	year = {2021},
	keywords = {boreal, broadleaf, continuous cover forestry, deciduous, forest planning, retention forestry, uneven-aged forestry},
	pages = {119254},
}

Riparian buffers are the primary tool in forest management for protecting the habitat structure and function of streams. They help protect against biogeochemical perturbation, filter sediments and nutrients, prevent erosion, contribute food to aquatic organisms, regulate light and hence water temperature, contribute deadwood, and preserve biodiversity. However, in production forests of Sweden and Finland, many headwater streams have been straightened, ditched, and/or channelized, resulting in altered hydrology and reduced natural disturbance by floods, which in turn affects important riparian functions. Furthermore, in even-aged management systems as practiced in much of Fennoscandia, understory trees have usually been cleared right up to the stream’s edge during thinning operations, especially around small, headwater streams. Fire suppression has further favored succession towards shade tolerant species. In the regions within Fennoscandia that have experienced this combination of intensive management and lack of natural disturbance, riparian zones are now dominated by single-storied, native Norway spruce. When the adjacent forest is cut, thin (5 - 15m) conifer-dominated riparian buffers are typically left. These buffers do not provide the protection and subsidies, in terms of leaf litter quality, needed to maintain water quality or support riparian or aquatic biodiversity. Based on a literature review, we found compelling evidence that the ecological benefits of multi-layered, mixed-species riparian forest with a large component of broadleaved species are higher than what is now commonly found in the managed stands of Fennoscandia. To improve the functionality of riparian zones, and hence the protection of streams in managed forest landscapes, we present some basic principles that could be used to enhance the ecological function of these interfaces. These management actions should be prioritized on streams and streamside stands that have been affected by simplification either through forest management or hydrological modification. Key to these principles is the planning and managing of buffer zones as early as possible in the rotation to ensure improved function throughout the rotation cycle and not only at final felling. This is well in line with EU and national legislation which can be interpreted as requiring landscape planning at all forest ages to meet biodiversity and other environmental goals. However, it is still rare that planning for conservation is done other than at the final felling stage. Implementing this new strategy is likely to have long-term positive effects and improve the protection of surface waters from negative forestry effects and a history of fire suppression. By following these suggested management principles, there will be a longer time period with high function and greater future management flexibility in addition to the benefits provided by leaving riparian buffers at the final felling stage.

@article{mahmud_prokseq_2021,
	title = {{ProkSeq} for complete analysis of {RNA}-{Seq} data from prokaryotes},
	volume = {37},
	issn = {1367-4803},
	url = {https://doi.org/10.1093/bioinformatics/btaa1063},
	doi = {10/gjd6zd},
	abstract = {Since its introduction, RNA-Seq technology has been used extensively in studies of pathogenic bacteria to identify and quantify differences in gene expression across multiple samples from bacteria exposed to different conditions. With some exceptions, tools for studying gene expression, determination of differential gene expression, downstream pathway analysis and normalization of data collected in extreme biological conditions is still lacking. Here, we describe ProkSeq, a user-friendly, fully automated RNA-Seq data analysis pipeline designed for prokaryotes. ProkSeq provides a wide variety of options for analysing differential expression, normalizing expression data and visualizing data and results.ProkSeq is implemented in Python and is published under the MIT source license. The pipeline is available as a Docker container https://hub.docker.com/repository/docker/snandids/prokseq-v2.0, or can be used through Anaconda: https://anaconda.org/snandiDS/prokseq. The code is available on Github: https://github.com/snandiDS/prokseq and a detailed user documentation, including a manual and tutorial can be found at https://prokseqV20.readthedocs.io.Supplementary data are available at Bioinformatics online.},
	number = {1},
	urldate = {2021-06-10},
	journal = {Bioinformatics},
	author = {Mahmud, A K M Firoj and Delhomme, Nicolas and Nandi, Soumyadeep and Fällman, Maria},
	month = jan,
	year = {2021},
	pages = {126--128},
}

Since its introduction, RNA-Seq technology has been used extensively in studies of pathogenic bacteria to identify and quantify differences in gene expression across multiple samples from bacteria exposed to different conditions. With some exceptions, tools for studying gene expression, determination of differential gene expression, downstream pathway analysis and normalization of data collected in extreme biological conditions is still lacking. Here, we describe ProkSeq, a user-friendly, fully automated RNA-Seq data analysis pipeline designed for prokaryotes. ProkSeq provides a wide variety of options for analysing differential expression, normalizing expression data and visualizing data and results.ProkSeq is implemented in Python and is published under the MIT source license. The pipeline is available as a Docker container https://hub.docker.com/repository/docker/snandids/prokseq-v2.0, or can be used through Anaconda: https://anaconda.org/snandiDS/prokseq. The code is available on Github: https://github.com/snandiDS/prokseq and a detailed user documentation, including a manual and tutorial can be found at https://prokseqV20.readthedocs.io.Supplementary data are available at Bioinformatics online.

@article{lindgren_balanced_2021,
	title = {Balanced forest tree improvement can be enhanced by selecting among many parents but maintaining balance among grandparents},
	url = {https://core.ac.uk/display/227117724},
	abstract = {A model for a balanced tree breeding program that considers genetic gain and cost was used to assess the benefits of increasing the breeding population to allow for a component of among-parent selection while maintaining an equal contribution among grandparents, rather than relaying on within-family selection with an equal parental representation. The scenario used in this study had characteristics similar to those of the phenotypic selection strategy for Scots pine ( Pinus sylvestris L.) in Sweden. The results showed that investments in a greater number of parents and families to allow for among-parent selection resulted in a markedly higher genetic gain. The among-parent selection component increased the genetic gain by as much as 70\% in a scenario with a high budget and no family creation costs and by as much as 20\% in a scenario with a low budget and high family creation costsVytauto Didžiojo universitetasŽemės ūkio akademij},
	language = {en-gb},
	urldate = {2021-06-10},
	author = {Lindgren, Dag and Danusevičius, Darius and Rosvall, Ola},
	year = {2021},
	keywords = {⛔ No DOI found},
}

A model for a balanced tree breeding program that considers genetic gain and cost was used to assess the benefits of increasing the breeding population to allow for a component of among-parent selection while maintaining an equal contribution among grandparents, rather than relaying on within-family selection with an equal parental representation. The scenario used in this study had characteristics similar to those of the phenotypic selection strategy for Scots pine ( Pinus sylvestris L.) in Sweden. The results showed that investments in a greater number of parents and families to allow for among-parent selection resulted in a markedly higher genetic gain. The among-parent selection component increased the genetic gain by as much as 70% in a scenario with a high budget and no family creation costs and by as much as 20% in a scenario with a low budget and high family creation costsVytauto Didžiojo universitetasŽemės ūkio akademij

@article{hall_divergent_2021,
	title = {Divergent patterns between phenotypic and genetic variation in {Scots} pine},
	volume = {2},
	issn = {25903462},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2590346220301826},
	doi = {10.1016/j.xplc.2020.100139},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Plant Communications},
	author = {Hall, David and Olsson, Jenny and Zhao, Wei and Kroon, Johan and Wennström, Ulfstand and Wang, Xiao-Ru},
	month = jan,
	year = {2021},
	pages = {100139},
}

@article{lihavainen_stem_2021,
	title = {Stem girdling affects the onset of autumn senescence in aspen in interaction with metabolic signals},
	volume = {172},
	issn = {0031-9317, 1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ppl.13319},
	doi = {10.1111/ppl.13319},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Lihavainen, Jenna and Edlund, Erik and Björkén, Lars and Bag, Pushan and Robinson, Kathryn M. and Jansson, Stefan},
	month = may,
	year = {2021},
	pages = {201--217},
}

@article{przybyla-toscano_ironsulfur_2021,
	title = {Iron–sulfur proteins in plant mitochondria: roles and maturation},
	volume = {72},
	issn = {0022-0957, 1460-2431},
	shorttitle = {Iron–sulfur proteins in plant mitochondria},
	url = {https://academic.oup.com/jxb/article/72/6/2014/6029934},
	doi = {10.1093/jxb/eraa578},
	abstract = {Abstract
            Iron–sulfur (Fe–S) clusters are prosthetic groups ensuring electron transfer reactions, activating substrates for catalytic reactions, providing sulfur atoms for the biosynthesis of vitamins or other cofactors, or having protein-stabilizing effects. Hence, metalloproteins containing these cofactors are essential for numerous and diverse metabolic pathways and cellular processes occurring in the cytoplasm. Mitochondria are organelles where the Fe–S cluster demand is high, notably because the activity of the respiratory chain complexes I, II, and III relies on the correct assembly and functioning of Fe–S proteins. Several other proteins or complexes present in the matrix require Fe–S clusters as well, or depend either on Fe–S proteins such as ferredoxins or on cofactors such as lipoic acid or biotin whose synthesis relies on Fe–S proteins. In this review, we have listed and discussed the Fe–S-dependent enzymes or pathways in plant mitochondria including some potentially novel Fe–S proteins identified based on in silico analysis or on recent evidence obtained in non-plant organisms. We also provide information about recent developments concerning the molecular mechanisms involved in Fe–S cluster synthesis and trafficking steps of these cofactors from maturation factors to client apoproteins.},
	language = {en},
	number = {6},
	urldate = {2021-06-07},
	journal = {Journal of Experimental Botany},
	author = {Przybyla-Toscano, Jonathan and Christ, Loïck and Keech, Olivier and Rouhier, Nicolas},
	editor = {Dietz, Karl-Josef},
	month = mar,
	year = {2021},
	pages = {2014--2044},
}

Abstract Iron–sulfur (Fe–S) clusters are prosthetic groups ensuring electron transfer reactions, activating substrates for catalytic reactions, providing sulfur atoms for the biosynthesis of vitamins or other cofactors, or having protein-stabilizing effects. Hence, metalloproteins containing these cofactors are essential for numerous and diverse metabolic pathways and cellular processes occurring in the cytoplasm. Mitochondria are organelles where the Fe–S cluster demand is high, notably because the activity of the respiratory chain complexes I, II, and III relies on the correct assembly and functioning of Fe–S proteins. Several other proteins or complexes present in the matrix require Fe–S clusters as well, or depend either on Fe–S proteins such as ferredoxins or on cofactors such as lipoic acid or biotin whose synthesis relies on Fe–S proteins. In this review, we have listed and discussed the Fe–S-dependent enzymes or pathways in plant mitochondria including some potentially novel Fe–S proteins identified based on in silico analysis or on recent evidence obtained in non-plant organisms. We also provide information about recent developments concerning the molecular mechanisms involved in Fe–S cluster synthesis and trafficking steps of these cofactors from maturation factors to client apoproteins.

@article{van_sundert_increased_2021,
	title = {Increased tree growth following long-term optimised fertiliser application indirectly alters soil properties in a boreal forest},
	volume = {140},
	issn = {1612-4677},
	url = {https://doi.org/10.1007/s10342-020-01327-y},
	doi = {10.1007/s10342-020-01327-y},
	abstract = {It is well established that nutrient addition influences ecosystem features such as productivity, carbon storage, soil acidification and biodiversity. Less studied are long-term effects of sustained fertiliser application on forest soil characteristics and nutrient supplies, and especially direct and indirect mechanisms underlying changes. We investigated effects of 3 decades versus 1 decade of optimised fertiliser application on soil properties and nutrient supplies in a 30-year-old nutrient optimisation experiment in a Norway spruce plantation in northern Sweden. We tested for direct and indirect effects of fertiliser use through structural equation models and correlations among tree and soil variables. Results showed that soil characteristics, especially organic carbon and nutrient concentrations, were significantly affected by 10- and 30-year fertiliser application. Soil C/N was similar for the short-term versus controls, but decreased for the long-term versus short-term treatment. Although not explicitly measured, it was clear from our analyses and earlier studies at the site that litter accumulation played a key role in explaining these changes in soil properties, while foliar stoichiometry data suggest long-term effects of litter quality. Nutrient supply rates increased more after 30 than 10 years of fertiliser application. Summarized, we showed that the interplay of direct and indirect effects can yield nonlinear patterns over time, as exemplified by soil C/N. Furthermore, we conclude that lagged, indirect effects of fertilisation through altered litter quantity and quality dominate changes in soil characteristics in this forest. These soil characteristics have further relevance to nutrient availability, suggesting that nutrient optimisation can influence soil fertility also indirectly.},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {European Journal of Forest Research},
	author = {Van Sundert, Kevin and Linder, Sune and Marshall, John D. and Nordin, Annika and Vicca, Sara},
	month = feb,
	year = {2021},
	pages = {241--254},
}

It is well established that nutrient addition influences ecosystem features such as productivity, carbon storage, soil acidification and biodiversity. Less studied are long-term effects of sustained fertiliser application on forest soil characteristics and nutrient supplies, and especially direct and indirect mechanisms underlying changes. We investigated effects of 3 decades versus 1 decade of optimised fertiliser application on soil properties and nutrient supplies in a 30-year-old nutrient optimisation experiment in a Norway spruce plantation in northern Sweden. We tested for direct and indirect effects of fertiliser use through structural equation models and correlations among tree and soil variables. Results showed that soil characteristics, especially organic carbon and nutrient concentrations, were significantly affected by 10- and 30-year fertiliser application. Soil C/N was similar for the short-term versus controls, but decreased for the long-term versus short-term treatment. Although not explicitly measured, it was clear from our analyses and earlier studies at the site that litter accumulation played a key role in explaining these changes in soil properties, while foliar stoichiometry data suggest long-term effects of litter quality. Nutrient supply rates increased more after 30 than 10 years of fertiliser application. Summarized, we showed that the interplay of direct and indirect effects can yield nonlinear patterns over time, as exemplified by soil C/N. Furthermore, we conclude that lagged, indirect effects of fertilisation through altered litter quantity and quality dominate changes in soil characteristics in this forest. These soil characteristics have further relevance to nutrient availability, suggesting that nutrient optimisation can influence soil fertility also indirectly.

@article{bernhardsson_development_2021,
	title = {Development of a highly efficient {50K} single nucleotide polymorphism genotyping array for the large and complex genome of {Norway} spruce ( \textit{{Picea} abies} {L}. {Karst}) by whole genome resequencing and its transferability to other spruce species},
	volume = {21},
	issn = {1755-098X, 1755-0998},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/1755-0998.13292},
	doi = {10.1111/1755-0998.13292},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Molecular Ecology Resources},
	author = {Bernhardsson, Carolina and Zan, Yanjun and Chen, Zhiqiang and Ingvarsson, Pär K. and Wu, Harry X.},
	month = apr,
	year = {2021},
	pages = {880--896},
}

@article{ji_fully_2021,
	title = {A fully assembled plastid‐encoded {\textless}span style="font-variant:small-caps;"{\textgreater}{RNA}{\textless}/span{\textgreater} polymerase complex detected in etioplasts and proplastids in {Arabidopsis}},
	volume = {171},
	issn = {0031-9317, 1399-3054},
	shorttitle = {A fully assembled plastid‐encoded {\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ppl.13256},
	doi = {10.1111/ppl.13256},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {Physiologia Plantarum},
	author = {Ji, Yan and Lehotai, Nóra and Zan, Yanjun and Dubreuil, Carole and Díaz, Manuel Guinea and Strand, Åsa},
	month = mar,
	year = {2021},
	pages = {435--446},
}

@article{forsmark_longterm_2021,
	title = {Long‐term nitrogen enrichment does not increase microbial phosphorus mobilization in a northern coniferous forest},
	volume = {35},
	issn = {0269-8463, 1365-2435},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/1365-2435.13701},
	doi = {10.1111/1365-2435.13701},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {Functional Ecology},
	author = {Forsmark, Benjamin and Wallander, Håkan and Nordin, Annika and Gundale, Michael J.},
	editor = {Stevens, Carly},
	month = jan,
	year = {2021},
	pages = {277--287},
}

@article{jonasson_comparison_2021,
	title = {Comparison of tension wood and normal wood for oxidative nanofibrillation and network characteristics},
	volume = {28},
	issn = {0969-0239, 1572-882X},
	url = {http://link.springer.com/10.1007/s10570-020-03556-1},
	doi = {10.1007/s10570-020-03556-1},
	abstract = {Abstract
            
              Cellulose nanofibrils (CNFs) are top-down nanomaterials obtainable from abundant lignocelluloses. Despite recent advances in processing technologies, the effects of variations in the lignocellulose structure and composition on CNF isolation and properties are poorly understood. In this study, we compared the isolation of CNFs from tension wood (TW) and normal wood (NW) from
              Populus tremula
              (aspen). The TW has a higher cellulose content, native cellulose fibrils with a larger crystalline diameter, and less lignin than the NW, making it an interesting material for CNF isolation. The wood powders were oxidized directly by 2,2,6,6-tetramethylpiperidin-1-oxyl, and the morphology and mechanical behaviors of the nanofibril suspensions and networks were characterized. The TW was more difficult to fibrillate by both chemical and mechanical means. Larger nanofibrils (5–10 nm) composed of 1.2 nm structures were present in the TW CNFs, whereas the NW samples contained more of thin (1.6 nm) structures, which also comprised 77\% of the solid yield compared to the 33\% for TW. This difference was reflected in the TW CNF networks as decreased transmittance (15\% vs. 50\%), higher degree of crystallinity (85.9\% vs. 78.0\%), doubled toughness (11 MJ/m
              3
              ) and higher elongation at break (12\%) compared to NW. The difference was ascribed to greater preservation of the hierarchical, more crystalline microfibril structure, combined with a more cellulose-rich network (84\% vs. 70\%). This knowledge of the processing, structure, and properties of CNFs can facilitate the breeding and design of wood feedstocks to meet the increasing demand for nanoscale renewable materials.
            
            
              Graphic abstract},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {Cellulose},
	author = {Jonasson, Simon and Bünder, Anne and Das, Oisik and Niittylä, Totte and Oksman, Kristiina},
	month = jan,
	year = {2021},
	pages = {1085--1104},
}

Abstract Cellulose nanofibrils (CNFs) are top-down nanomaterials obtainable from abundant lignocelluloses. Despite recent advances in processing technologies, the effects of variations in the lignocellulose structure and composition on CNF isolation and properties are poorly understood. In this study, we compared the isolation of CNFs from tension wood (TW) and normal wood (NW) from Populus tremula (aspen). The TW has a higher cellulose content, native cellulose fibrils with a larger crystalline diameter, and less lignin than the NW, making it an interesting material for CNF isolation. The wood powders were oxidized directly by 2,2,6,6-tetramethylpiperidin-1-oxyl, and the morphology and mechanical behaviors of the nanofibril suspensions and networks were characterized. The TW was more difficult to fibrillate by both chemical and mechanical means. Larger nanofibrils (5–10 nm) composed of 1.2 nm structures were present in the TW CNFs, whereas the NW samples contained more of thin (1.6 nm) structures, which also comprised 77% of the solid yield compared to the 33% for TW. This difference was reflected in the TW CNF networks as decreased transmittance (15% vs. 50%), higher degree of crystallinity (85.9% vs. 78.0%), doubled toughness (11 MJ/m 3 ) and higher elongation at break (12%) compared to NW. The difference was ascribed to greater preservation of the hierarchical, more crystalline microfibril structure, combined with a more cellulose-rich network (84% vs. 70%). This knowledge of the processing, structure, and properties of CNFs can facilitate the breeding and design of wood feedstocks to meet the increasing demand for nanoscale renewable materials. Graphic abstract

@article{landberg_studies_2021,
	title = {Studies of moss reproductive development indicate that auxin biosynthesis in apical stem cells may constitute an ancestral function for focal growth control},
	volume = {229},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16914},
	doi = {10.1111/nph.16914},
	language = {en},
	number = {2},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Landberg, Katarina and Šimura, Jan and Ljung, Karin and Sundberg, Eva and Thelander, Mattias},
	month = jan,
	year = {2021},
	pages = {845--860},
}

@article{zhu_acclimation_2021,
	title = {Acclimation of leaf respiration temperature responses across thermally contrasting biomes},
	volume = {229},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16929},
	doi = {10.1111/nph.16929},
	language = {en},
	number = {3},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Zhu, Lingling and Bloomfield, Keith J. and Asao, Shinichi and Tjoelker, Mark G. and Egerton, John J.G. and Hayes, Lucy and Weerasinghe, Lasantha K. and Creek, Danielle and Griffin, Kevin L. and Hurry, Vaughan and Liddell, Michael and Meir, Patrick and Turnbull, Matthew H. and Atkin, Owen K.},
	month = feb,
	year = {2021},
	pages = {1312--1325},
}

@article{dominguez_sucrose_2021,
	title = {Sucrose synthase determines carbon allocation in developing wood and alters carbon flow at the whole tree level in aspen},
	volume = {229},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16721},
	doi = {10.1111/nph.16721},
	language = {en},
	number = {1},
	urldate = {2021-06-07},
	journal = {New Phytologist},
	author = {Dominguez, Pia Guadalupe and Donev, Evgeniy and Derba‐Maceluch, Marta and Bünder, Anne and Hedenström, Mattias and Tomášková, Ivana and Mellerowicz, Ewa J. and Niittylä, Totte},
	month = jan,
	year = {2021},
	pages = {186--198},
}

@article{pandey_plant_2021,
	title = {Plant roots sense soil compaction through restricted ethylene diffusion},
	volume = {371},
	issn = {0036-8075, 1095-9203},
	url = {https://www.sciencemag.org/lookup/doi/10.1126/science.abf3013},
	doi = {10/ghtf3b},
	abstract = {Soil compaction represents a major challenge for modern agriculture. Compaction is intuitively thought to reduce root growth by limiting the ability of roots to penetrate harder soils. We report that root growth in compacted soil is instead actively suppressed by the volatile hormone ethylene. We found that mutant
              Arabidopsis
              and rice roots that were insensitive to ethylene penetrated compacted soil more effectively than did wild-type roots. Our results indicate that soil compaction lowers gas diffusion through a reduction in air-filled pores, thereby causing ethylene to accumulate in root tissues and trigger hormone responses that restrict growth. We propose that ethylene acts as an early warning signal for roots to avoid compacted soils, which would be relevant to research into the breeding of crops resilient to soil compaction.},
	language = {en},
	number = {6526},
	urldate = {2021-06-04},
	journal = {Science},
	author = {Pandey, Bipin K. and Huang, Guoqiang and Bhosale, Rahul and Hartman, Sjon and Sturrock, Craig J. and Jose, Lottie and Martin, Olivier C. and Karady, Michal and Voesenek, Laurentius A. C. J. and Ljung, Karin and Lynch, Jonathan P. and Brown, Kathleen M. and Whalley, William R. and Mooney, Sacha J. and Zhang, Dabing and Bennett, Malcolm J.},
	month = jan,
	year = {2021},
	pages = {276--280},
}

Soil compaction represents a major challenge for modern agriculture. Compaction is intuitively thought to reduce root growth by limiting the ability of roots to penetrate harder soils. We report that root growth in compacted soil is instead actively suppressed by the volatile hormone ethylene. We found that mutant Arabidopsis and rice roots that were insensitive to ethylene penetrated compacted soil more effectively than did wild-type roots. Our results indicate that soil compaction lowers gas diffusion through a reduction in air-filled pores, thereby causing ethylene to accumulate in root tissues and trigger hormone responses that restrict growth. We propose that ethylene acts as an early warning signal for roots to avoid compacted soils, which would be relevant to research into the breeding of crops resilient to soil compaction.

@article{diacci_diurnal_2021,
	title = {Diurnal in vivo xylem sap glucose and sucrose monitoring using implantable organic electrochemical transistor sensors},
	volume = {24},
	issn = {25890042},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S2589004220311639},
	doi = {10/gjgsjg},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {iScience},
	author = {Diacci, Chiara and Abedi, Tayebeh and Lee, Jee Woong and Gabrielsson, Erik O. and Berggren, Magnus and Simon, Daniel T. and Niittylä, Totte and Stavrinidou, Eleni},
	month = jan,
	year = {2021},
	pages = {101966},
}

@article{galbraith_best_2021,
	title = {Best practices in plant cytometry},
	volume = {99},
	issn = {1552-4922, 1552-4930},
	url = {https://onlinelibrary.wiley.com/doi/10.1002/cyto.a.24295},
	doi = {10/gkcr59},
	language = {en},
	number = {4},
	urldate = {2021-06-03},
	journal = {Cytometry Part A},
	author = {Galbraith, David and Loureiro, João and Antoniadi, Ioanna and Bainard, Jillian and Bureš, Petr and Cápal, Petr and Castro, Mariana and Castro, Sílvia and Čertner, Martin and Čertnerová, Dora and Chumová, Zuzana and Doležel, Jaroslav and Giorgi, Debora and Husband, Brian C. and Kolář, Filip and Koutecký, Petr and Kron, Paul and Leitch, Ilia J. and Ljung, Karin and Lopes, Sara and Lučanová, Magdalena and Lucretti, Sergio and Ma, Wen and Melzer, Susanne and Molnár, István and Novák, Ondřej and Poulton, Nicole and Skalický, Vladimír and Sliwinska, Elwira and Šmarda, Petr and Smith, Tyler W. and Sun, Guiling and Talhinhas, Pedro and Tárnok, Attila and Temsch, Eva M. and Trávníček, Pavel and Urfus, Tomáš},
	month = apr,
	year = {2021},
	pages = {311--317},
}

@article{parizkova_new_2021,
	title = {New fluorescent auxin probes visualise tissue‐specific and subcellular distributions of auxin in {Arabidopsis}},
	volume = {230},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.17183},
	doi = {10/gkcr7d},
	language = {en},
	number = {2},
	urldate = {2021-06-03},
	journal = {New Phytologist},
	author = {Pařízková, Barbora and Žukauskaitė, Asta and Vain, Thomas and Grones, Peter and Raggi, Sara and Kubeš, Martin F. and Kieffer, Martin and Doyle, Siamsa M. and Strnad, Miroslav and Kepinski, Stefan and Napier, Richard and Doležal, Karel and Robert, Stéphanie and Novák, Ondřej},
	month = apr,
	year = {2021},
	pages = {535--549},
}

@article{baral_external_2021,
	title = {External {Mechanical} {Cues} {Reveal} a {Katanin}-{Independent} {Mechanism} behind {Auxin}-{Mediated} {Tissue} {Bending} in {Plants}},
	volume = {56},
	issn = {15345807},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1534580720309837},
	doi = {10/ghtbf9},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {Developmental Cell},
	author = {Baral, Anirban and Aryal, Bibek and Jonsson, Kristoffer and Morris, Emily and Demes, Elsa and Takatani, Shogo and Verger, Stéphane and Xu, Tongda and Bennett, Malcolm and Hamant, Olivier and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2021},
	pages = {67--80.e3},
}

@article{vaughanhirsch_function_2021,
	title = {Function of the pseudo phosphotransfer proteins has diverged between rice and {Arabidopsis}},
	volume = {106},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.15156},
	doi = {10/gkcr6p},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {The Plant Journal},
	author = {Vaughan‐Hirsch, John and Tallerday, Emily J. and Burr, Christian A. and Hodgens, Charlie and Boeshore, Samantha L. and Beaver, Kevin and Melling, Allison and Sari, Kartika and Kerr, Ian D. and Šimura, Jan and Ljung, Karin and Xu, Dawei and Liang, Wanqi and Bhosale, Rahul and Schaller, G. Eric and Bishopp, Anthony and Kieber, Joseph J.},
	month = apr,
	year = {2021},
	pages = {159--173},
}

@article{le_evaluation_2021,
	title = {Evaluation of parameters to characterise germination-competent mature somatic embryos of {Norway} spruce ({Picea} abies)},
	volume = {203},
	issn = {15375110},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S1537511020303457},
	doi = {10/gkcr7h},
	language = {en},
	urldate = {2021-06-03},
	journal = {Biosystems Engineering},
	author = {Le, Kim-Cuong and Weerasekara, Aruna B. and Ranade, Sonali S. and Egertsdotter, E-M Ulrika},
	month = mar,
	year = {2021},
	pages = {55--59},
}

@article{ranade_molecular_2021,
	title = {Molecular signatures of local adaptation to light in {Norway} spruce},
	volume = {253},
	issn = {0032-0935, 1432-2048},
	url = {http://link.springer.com/10.1007/s00425-020-03517-9},
	doi = {10/gjd69n},
	abstract = {Abstract
            
              Main conclusion
              Transcriptomic and exome capture analysis reveal an adaptive cline for shade tolerance in Norway spruce. Genes involved in the lignin pathway and immunity seem to play a potential role in contributing towards local adaptation to light.
            
            
              Abstract
              The study of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. Norway spruce is a shade-tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. The objective of the study is to characterize the genetic control of local adaptation to light enriched in far-red in Norway spruce, motivated by a latitudinal gradient for the Red:Far-red (R:FR) ratio to which Norway spruce has been proven to be genetically adapted. We have established the genomic signatures of local adaptation by conducting transcriptomic (total RNA-sequencing) and genomic analyses (exome capture), for the identification of genes differentially regulated along the cline. RNA-sequencing revealed 274 differentially expressed genes in response to SHADE (low R:FR light), between the southern and northern natural populations in Sweden. Exome capture included analysis of a uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway, and cold acclimation and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation, and immunity. Based on these results, we suggest that the northern populations might not only be able to adjust their growing season in response to low R:FR light, but they may also be better adapted towards disease resistance by up-regulation of the lignin pathway that is linked to immunity. This forms a concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.},
	language = {en},
	number = {2},
	urldate = {2021-06-03},
	journal = {Planta},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario},
	month = feb,
	year = {2021},
	pages = {53},
}

Abstract Main conclusion Transcriptomic and exome capture analysis reveal an adaptive cline for shade tolerance in Norway spruce. Genes involved in the lignin pathway and immunity seem to play a potential role in contributing towards local adaptation to light. Abstract The study of natural variation is an efficient method to elucidate how plants adapt to local climatic conditions, a key process for the evolution of a species. Norway spruce is a shade-tolerant conifer in which the requirement of far-red light for growth increases latitudinally northwards. The objective of the study is to characterize the genetic control of local adaptation to light enriched in far-red in Norway spruce, motivated by a latitudinal gradient for the Red:Far-red (R:FR) ratio to which Norway spruce has been proven to be genetically adapted. We have established the genomic signatures of local adaptation by conducting transcriptomic (total RNA-sequencing) and genomic analyses (exome capture), for the identification of genes differentially regulated along the cline. RNA-sequencing revealed 274 differentially expressed genes in response to SHADE (low R:FR light), between the southern and northern natural populations in Sweden. Exome capture included analysis of a uniquely large data set (1654 trees) that revealed missense variations in coding regions of nine differentially expressed candidate genes, which followed a latitudinal cline in allele and genotype frequencies. These genes included five transcription factors involved in vital processes like bud-set/bud-flush, lignin pathway, and cold acclimation and other genes that take part in cell-wall remodeling, secondary cell-wall thickening, response to starvation, and immunity. Based on these results, we suggest that the northern populations might not only be able to adjust their growing season in response to low R:FR light, but they may also be better adapted towards disease resistance by up-regulation of the lignin pathway that is linked to immunity. This forms a concrete basis for local adaptation to light quality in Norway spruce, one of the most economically important conifer tree species in Sweden.

@article{kleczkowski_magnesium_2021,
	title = {Magnesium {Signaling} in {Plants}},
	volume = {22},
	issn = {1422-0067},
	url = {https://www.mdpi.com/1422-0067/22/3/1159},
	doi = {10/gjd692},
	abstract = {Free magnesium (Mg2+) is a signal of the adenylate (ATP+ADP+AMP) status in the cells. It results from the equilibrium of adenylate kinase (AK), which uses Mg-chelated and Mg-free adenylates as substrates in both directions of its reaction. The AK-mediated primary control of intracellular [Mg2+] is finely interwoven with the operation of membrane-bound adenylate- and Mg2+-translocators, which in a given compartment control the supply of free adenylates and Mg2+ for the AK-mediated equilibration. As a result, [Mg2+] itself varies both between and within the compartments, depending on their energetic status and environmental clues. Other key nucleotide-utilizing/producing enzymes (e.g., nucleoside diphosphate kinase) may also be involved in fine-tuning of the intracellular [Mg2+]. Changes in [Mg2+] regulate activities of myriads of Mg-utilizing/requiring enzymes, affecting metabolism under both normal and stress conditions, and impacting photosynthetic performance, respiration, phloem loading and other processes. In compartments controlled by AK equilibrium (cytosol, chloroplasts, mitochondria, nucleus), the intracellular [Mg2+] can be calculated from total adenylate contents, based on the dependence of the apparent equilibrium constant of AK on [Mg2+]. Magnesium signaling, reflecting cellular adenylate status, is likely widespread in all eukaryotic and prokaryotic organisms, due simply to the omnipresent nature of AK and to its involvement in adenylate equilibration.},
	language = {en},
	number = {3},
	urldate = {2021-06-03},
	journal = {International Journal of Molecular Sciences},
	author = {Kleczkowski, Leszek A. and Igamberdiev, Abir U.},
	month = jan,
	year = {2021},
	pages = {1159},
}

Free magnesium (Mg2+) is a signal of the adenylate (ATP+ADP+AMP) status in the cells. It results from the equilibrium of adenylate kinase (AK), which uses Mg-chelated and Mg-free adenylates as substrates in both directions of its reaction. The AK-mediated primary control of intracellular [Mg2+] is finely interwoven with the operation of membrane-bound adenylate- and Mg2+-translocators, which in a given compartment control the supply of free adenylates and Mg2+ for the AK-mediated equilibration. As a result, [Mg2+] itself varies both between and within the compartments, depending on their energetic status and environmental clues. Other key nucleotide-utilizing/producing enzymes (e.g., nucleoside diphosphate kinase) may also be involved in fine-tuning of the intracellular [Mg2+]. Changes in [Mg2+] regulate activities of myriads of Mg-utilizing/requiring enzymes, affecting metabolism under both normal and stress conditions, and impacting photosynthetic performance, respiration, phloem loading and other processes. In compartments controlled by AK equilibrium (cytosol, chloroplasts, mitochondria, nucleus), the intracellular [Mg2+] can be calculated from total adenylate contents, based on the dependence of the apparent equilibrium constant of AK on [Mg2+]. Magnesium signaling, reflecting cellular adenylate status, is likely widespread in all eukaryotic and prokaryotic organisms, due simply to the omnipresent nature of AK and to its involvement in adenylate equilibration.

@article{bandau_european_2021,
	title = {European aspen with high compared to low constitutive tannin defenses grow taller in response to anthropogenic nitrogen enrichment},
	volume = {487},
	issn = {03781127},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0378112721000748},
	doi = {10/gjd7k2},
	language = {en},
	urldate = {2021-06-03},
	journal = {Forest Ecology and Management},
	author = {Bandau, Franziska and Albrectsen, Benedicte Riber and Robinson, Kathryn M. and Gundale, Michael J.},
	month = may,
	year = {2021},
	pages = {118985},
}

@article{schneider_comparative_2021,
	title = {Comparative {Fungal} {Community} {Analyses} {Using} {Metatranscriptomics} and {Internal} {Transcribed} {Spacer} {Amplicon} {Sequencing} from {Norway} {Spruce}},
	volume = {6},
	issn = {2379-5077},
	url = {https://journals.asm.org/doi/10.1128/mSystems.00884-20},
	doi = {10/gjnmqq},
	abstract = {A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present.
          , 
            ABSTRACT
            
              The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species
              Picea abies
              (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus
              Cortinarius
              .
            
            
              IMPORTANCE
              A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {mSystems},
	author = {Schneider, Andreas N. and Sundh, John and Sundström, Görel and Richau, Kerstin and Delhomme, Nicolas and Grabherr, Manfred and Hurry, Vaughan and Street, Nathaniel R.},
	editor = {McClure, Ryan},
	month = feb,
	year = {2021},
}

A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. , ABSTRACT The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius . IMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.

@article{gandla_overexpression_2021,
	title = {Overexpression of vesicle-associated membrane protein {PttVAP27}-17 as a tool to improve biomass production and the overall saccharification yields in {Populus} trees},
	volume = {14},
	issn = {1754-6834},
	url = {https://biotechnologyforbiofuels.biomedcentral.com/articles/10.1186/s13068-021-01895-0},
	doi = {10/gjd7kj},
	abstract = {Abstract
            
              Background
              Bioconversion of wood into bioproducts and biofuels is hindered by the recalcitrance of woody raw material to bioprocesses such as enzymatic saccharification. Targeted modification of the chemical composition of the feedstock can improve saccharification but this gain is often abrogated by concomitant reduction in tree growth.
            
            
              Results
              
                In this study, we report on transgenic hybrid aspen (
                Populus tremula
                ×
                tremuloides
                ) lines that showed potential to increase biomass production both in the greenhouse and after 5 years of growth in the field. The transgenic lines carried an overexpression construct for
                Populus tremula
                ×
                tremuloides
                vesicle-associated membrane protein (VAMP)-associated protein
                PttVAP27-17
                that was selected from a gene-mining program for novel regulators of wood formation. Analytical-scale enzymatic saccharification without any pretreatment revealed for all greenhouse-grown transgenic lines, compared to the wild type, a 20–44\% increase in the glucose yield per dry weight after enzymatic saccharification, even though it was statistically significant only for one line. The glucose yield after enzymatic saccharification with a prior hydrothermal pretreatment step with sulfuric acid was not increased in the greenhouse-grown transgenic trees on a dry-weight basis, but increased by 26–50\% when calculated on a whole biomass basis in comparison to the wild-type control. Tendencies to increased glucose yields by up to 24\% were present on a whole tree biomass basis after acidic pretreatment and enzymatic saccharification also in the transgenic trees grown for 5 years on the field when compared to the wild-type control.
              
            
            
              Conclusions
              The results demonstrate the usefulness of gene-mining programs to identify novel genes with the potential to improve biofuel production in tree biotechnology programs. Furthermore, multi-omic analyses, including transcriptomic, proteomic and metabolomic analyses, performed here provide a toolbox for future studies on the function of VAP27 proteins in plants.},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {Biotechnology for Biofuels},
	author = {Gandla, Madhavi Latha and Mähler, Niklas and Escamez, Sacha and Skotare, Tomas and Obudulu, Ogonna and Möller, Linus and Abreu, Ilka N. and Bygdell, Joakim and Hertzberg, Magnus and Hvidsten, Torgeir R. and Moritz, Thomas and Wingsle, Gunnar and Trygg, Johan and Tuominen, Hannele and Jönsson, Leif J.},
	month = dec,
	year = {2021},
	pages = {43},
}

Abstract Background Bioconversion of wood into bioproducts and biofuels is hindered by the recalcitrance of woody raw material to bioprocesses such as enzymatic saccharification. Targeted modification of the chemical composition of the feedstock can improve saccharification but this gain is often abrogated by concomitant reduction in tree growth. Results In this study, we report on transgenic hybrid aspen ( Populus tremula × tremuloides ) lines that showed potential to increase biomass production both in the greenhouse and after 5 years of growth in the field. The transgenic lines carried an overexpression construct for Populus tremula × tremuloides vesicle-associated membrane protein (VAMP)-associated protein PttVAP27-17 that was selected from a gene-mining program for novel regulators of wood formation. Analytical-scale enzymatic saccharification without any pretreatment revealed for all greenhouse-grown transgenic lines, compared to the wild type, a 20–44% increase in the glucose yield per dry weight after enzymatic saccharification, even though it was statistically significant only for one line. The glucose yield after enzymatic saccharification with a prior hydrothermal pretreatment step with sulfuric acid was not increased in the greenhouse-grown transgenic trees on a dry-weight basis, but increased by 26–50% when calculated on a whole biomass basis in comparison to the wild-type control. Tendencies to increased glucose yields by up to 24% were present on a whole tree biomass basis after acidic pretreatment and enzymatic saccharification also in the transgenic trees grown for 5 years on the field when compared to the wild-type control. Conclusions The results demonstrate the usefulness of gene-mining programs to identify novel genes with the potential to improve biofuel production in tree biotechnology programs. Furthermore, multi-omic analyses, including transcriptomic, proteomic and metabolomic analyses, performed here provide a toolbox for future studies on the function of VAP27 proteins in plants.

@article{azeez_early_2021,
	title = {{EARLY} {BUD}-{BREAK} 1 and {EARLY} {BUD}-{BREAK} 3 control resumption of poplar growth after winter dormancy},
	volume = {12},
	issn = {2041-1723},
	url = {http://www.nature.com/articles/s41467-021-21449-0},
	doi = {10/gkcr78},
	abstract = {Abstract
            
              Bud-break is an economically and environmentally important process in trees and shrubs from boreal and temperate latitudes, but its molecular mechanisms are poorly understood. Here, we show that two previously reported transcription factors, EARLY BUD BREAK 1 (EBB1) and SHORT VEGETATIVE PHASE-Like (SVL) directly interact to control bud-break. EBB1 is a positive regulator of bud-break, whereas SVL is a negative regulator of bud-break. EBB1 directly and negatively regulates
              SVL
              expression. We further report the identification and characterization of the EBB3 gene. EBB3 is a temperature-responsive, epigenetically-regulated, positive regulator of bud-break that provides a direct link to activation of the cell cycle during bud-break. EBB3 is an AP2/ERF transcription factor that positively and directly regulates
              CYCLIND3.1
              gene. Our results reveal the architecture of a putative regulatory module that links temperature-mediated control of bud-break with activation of cell cycle.},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {Nature Communications},
	author = {Azeez, Abdul and Zhao, Yiru Chen and Singh, Rajesh Kumar and Yordanov, Yordan S. and Dash, Madhumita and Miskolczi, Pal and Stojkovič, Katja and Strauss, Steve H. and Bhalerao, Rishikesh P. and Busov, Victor B.},
	month = dec,
	year = {2021},
	pages = {1123},
}

Abstract Bud-break is an economically and environmentally important process in trees and shrubs from boreal and temperate latitudes, but its molecular mechanisms are poorly understood. Here, we show that two previously reported transcription factors, EARLY BUD BREAK 1 (EBB1) and SHORT VEGETATIVE PHASE-Like (SVL) directly interact to control bud-break. EBB1 is a positive regulator of bud-break, whereas SVL is a negative regulator of bud-break. EBB1 directly and negatively regulates SVL expression. We further report the identification and characterization of the EBB3 gene. EBB3 is a temperature-responsive, epigenetically-regulated, positive regulator of bud-break that provides a direct link to activation of the cell cycle during bud-break. EBB3 is an AP2/ERF transcription factor that positively and directly regulates CYCLIND3.1 gene. Our results reveal the architecture of a putative regulatory module that links temperature-mediated control of bud-break with activation of cell cycle.

@article{henriksson_mycorrhizal_2021,
	title = {The mycorrhizal tragedy of the commons},
	volume = {24},
	issn = {1461-023X, 1461-0248},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/ele.13737},
	doi = {10/gkcr8h},
	language = {en},
	number = {6},
	urldate = {2021-06-03},
	journal = {Ecology Letters},
	author = {Henriksson, Nils and Franklin, Oskar and Tarvainen, Lasse and Marshall, John and Lundberg‐Felten, Judith and Eilertsen, Lill and Näsholm, Torgny},
	editor = {Selosse, Marc‐André},
	month = jun,
	year = {2021},
	pages = {1215--1224},
}

@article{gauchan_annulohypoxylon_2021,
	title = {Annulohypoxylon sp. strain {MUS1}, an endophytic fungus isolated from {Taxus} wallichiana {Zucc}., produces taxol and other bioactive metabolites},
	volume = {11},
	issn = {2190-572X, 2190-5738},
	url = {http://link.springer.com/10.1007/s13205-021-02693-z},
	doi = {10/gkcr8j},
	language = {en},
	number = {3},
	urldate = {2021-06-03},
	journal = {3 Biotech},
	author = {Gauchan, Dhurva Prasad and Vélëz, Heriberto and Acharya, Ashesh and Östman, Johnny R. and Lundén, Karl and Elfstrand, Malin and García-Gil, M. Rosario},
	month = mar,
	year = {2021},
	pages = {152},
}

@article{woude_chemical_2021,
	title = {The chemical compound ‘{Heatin}’ stimulates hypocotyl elongation and interferes with the {Arabidopsis} {NIT1}‐subfamily of nitrilases},
	issn = {0960-7412, 1365-313X},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/tpj.15250},
	doi = {10/gkcr8m},
	language = {en},
	urldate = {2021-06-03},
	journal = {The Plant Journal},
	author = {Woude, Lennard and Piotrowski, Markus and Klaasse, Gruson and Paulus, Judith K. and Krahn, Daniel and Ninck, Sabrina and Kaschani, Farnusch and Kaiser, Markus and Novák, Ondřej and Ljung, Karin and Bulder, Suzanne and Verk, Marcel and Snoek, Basten L. and Fiers, Martijn and Martin, Nathaniel I. and Hoorn, Renier A. L. and Robert, Stéphanie and Smeekens, Sjef and Zanten, Martijn},
	month = may,
	year = {2021},
	pages = {tpj.15250},
}

@article{yang_mirna_2021,
	title = {{miRNA} {Mediated} {Regulation} and {Interaction} between {Plants} and {Pathogens}},
	volume = {22},
	issn = {1422-0067},
	url = {https://www.mdpi.com/1422-0067/22/6/2913},
	doi = {10/gjjv65},
	abstract = {Plants have evolved diverse molecular mechanisms that enable them to respond to a wide range of pathogens. It has become clear that microRNAs, a class of short single-stranded RNA molecules that regulate gene expression at the transcriptional or post-translational level, play a crucial role in coordinating plant-pathogen interactions. Specifically, miRNAs have been shown to be involved in the regulation of phytohormone signals, reactive oxygen species, and NBS-LRR gene expression, thereby modulating the arms race between hosts and pathogens. Adding another level of complexity, it has recently been shown that specific lncRNAs (ceRNAs) can act as decoys that interact with and modulate the activity of miRNAs. Here we review recent findings regarding the roles of miRNA in plant defense, with a focus on the regulatory modes of miRNAs and their possible applications in breeding pathogen-resistance plants including crops and trees. Special emphasis is placed on discussing the role of miRNA in the arms race between hosts and pathogens, and the interaction between disease-related miRNAs and lncRNAs.},
	language = {en},
	number = {6},
	urldate = {2021-06-03},
	journal = {International Journal of Molecular Sciences},
	author = {Yang, Xiaoqian and Zhang, Lichun and Yang, Yuzhang and Schmid, Markus and Wang, Yanwei},
	month = mar,
	year = {2021},
	pages = {2913},
}

Plants have evolved diverse molecular mechanisms that enable them to respond to a wide range of pathogens. It has become clear that microRNAs, a class of short single-stranded RNA molecules that regulate gene expression at the transcriptional or post-translational level, play a crucial role in coordinating plant-pathogen interactions. Specifically, miRNAs have been shown to be involved in the regulation of phytohormone signals, reactive oxygen species, and NBS-LRR gene expression, thereby modulating the arms race between hosts and pathogens. Adding another level of complexity, it has recently been shown that specific lncRNAs (ceRNAs) can act as decoys that interact with and modulate the activity of miRNAs. Here we review recent findings regarding the roles of miRNA in plant defense, with a focus on the regulatory modes of miRNAs and their possible applications in breeding pathogen-resistance plants including crops and trees. Special emphasis is placed on discussing the role of miRNA in the arms race between hosts and pathogens, and the interaction between disease-related miRNAs and lncRNAs.

@article{forsmark_anthropogenic_2021,
	title = {Anthropogenic nitrogen enrichment increased the efficiency of belowground biomass production in a boreal forest},
	volume = {155},
	issn = {00380717},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0038071721000262},
	doi = {10/gjdqgb},
	language = {en},
	urldate = {2021-06-03},
	journal = {Soil Biology and Biochemistry},
	author = {Forsmark, Benjamin and Nordin, Annika and Rosenstock, Nicholas P. and Wallander, Håkan and Gundale, Michael J.},
	month = apr,
	year = {2021},
	pages = {108154},
}

@article{siddique_mycobiomes_2021,
	title = {Mycobiomes of {Young} {Beech} {Trees} {Are} {Distinguished} by {Organ} {Rather} {Than} by {Habitat}, and {Community} {Analyses} {Suggest} {Competitive} {Interactions} {Among} {Twig} {Fungi}},
	volume = {12},
	issn = {1664-302X},
	url = {https://www.frontiersin.org/articles/10.3389/fmicb.2021.646302/full},
	doi = {10/gjrpd2},
	abstract = {Beech trees (
              Fagus sylvatica
              ) are prominent keystone species of great economic and environmental value for central Europe, hosting a diverse mycobiome. The composition of endophyte communities may depend on tree health, plant organ or tissue, and growth habitat. To evaluate mycobiome communalities at local scales, buds, and twigs were sampled from two young healthy mountain beech stands in Bavaria, Germany, four kilometers apart. With Illumina high-throughput sequencing, we found 113 fungal taxa from 0.7 million high-quality reads that mainly consisted of Ascomycota (52\%) and Basidiomycota (26\%) taxa. Significant correlations between richness and diversity indices were observed (
              p
              \< 0.05), and mycobiomes did not differ between habitats in the current study. Species richness and diversity were higher in twigs compared to spring buds, and the assemblages in twigs shared most similarities. Interaction network analyses revealed that twig-bound fungi shared similar numbers of (interaction) links with others, dominated by negative co-occurrences, suggesting that competitive exclusion may be the predominant ecological interaction in the highly connected twig mycobiome. Combining community and network analyses strengthened the evidence that plant organs may filter endophytic communities directly through colonization access and indirectly by facilitating competitive interactions between the fungi.},
	urldate = {2021-06-03},
	journal = {Frontiers in Microbiology},
	author = {Siddique, Abu Bakar and Biella, Paolo and Unterseher, Martin and Albrectsen, Benedicte Riber},
	month = apr,
	year = {2021},
	pages = {646302},
}

Beech trees ( Fagus sylvatica ) are prominent keystone species of great economic and environmental value for central Europe, hosting a diverse mycobiome. The composition of endophyte communities may depend on tree health, plant organ or tissue, and growth habitat. To evaluate mycobiome communalities at local scales, buds, and twigs were sampled from two young healthy mountain beech stands in Bavaria, Germany, four kilometers apart. With Illumina high-throughput sequencing, we found 113 fungal taxa from 0.7 million high-quality reads that mainly consisted of Ascomycota (52%) and Basidiomycota (26%) taxa. Significant correlations between richness and diversity indices were observed ( p < 0.05), and mycobiomes did not differ between habitats in the current study. Species richness and diversity were higher in twigs compared to spring buds, and the assemblages in twigs shared most similarities. Interaction network analyses revealed that twig-bound fungi shared similar numbers of (interaction) links with others, dominated by negative co-occurrences, suggesting that competitive exclusion may be the predominant ecological interaction in the highly connected twig mycobiome. Combining community and network analyses strengthened the evidence that plant organs may filter endophytic communities directly through colonization access and indirectly by facilitating competitive interactions between the fungi.

@article{kloth_sli1_2021,
	title = {{SLI1} confers broad‐spectrum resistance to phloem‐feeding insects},
	issn = {0140-7791, 1365-3040},
	shorttitle = {{\textless}span style="font-variant},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/pce.14064},
	doi = {10/gjzng9},
	language = {en},
	urldate = {2021-06-03},
	journal = {Plant, Cell \& Environment},
	author = {Kloth, Karen J. and Shah, Parth and Broekgaarden, Colette and Ström, Cecilia and Albrectsen, Benedicte R. and Dicke, Marcel},
	month = may,
	year = {2021},
	pages = {pce.14064},
}

@article{jonasson_effect_2021,
	title = {The {Effect} of {High} {Lignin} {Content} on {Oxidative} {Nanofibrillation} of {Wood} {Cell} {Wall}},
	volume = {11},
	issn = {2079-4991},
	url = {https://www.mdpi.com/2079-4991/11/5/1179},
	doi = {10/gjznf2},
	abstract = {Wood from field-grown poplars with different genotypes and varying lignin content (17.4 wt \% to 30.0 wt \%) were subjected to one-pot 2,2,6,6-Tetramethylpiperidin-1-yl)oxyl catalyzed oxidation and high-pressure homogenization in order to investigate nanofibrillation following simultaneous delignification and cellulose oxidation. When comparing low and high lignin wood it was found that the high lignin wood was more easily fibrillated as indicated by a higher nanofibril yield (68\% and 45\%) and suspension viscosity (27 and 15 mPa·s). The nanofibrils were monodisperse with diameter ranging between 1.2 and 2.0 nm as measured using atomic force microscopy. Slightly less cellulose oxidation (0.44 and 0.68 mmol·g−1) together with a reduced process yield (36\% and 44\%) was also found which showed that the removal of a larger amount of lignin increased the efficiency of the homogenization step despite slightly reduced oxidation of the nanofibril surfaces. The surface area of oxidized high lignin wood was also higher than low lignin wood (114 m2·g−1 and 76 m2·g−1) which implicates porosity as a factor that can influence cellulose nanofibril isolation from wood in a beneficial manner.},
	language = {en},
	number = {5},
	urldate = {2021-06-03},
	journal = {Nanomaterials},
	author = {Jonasson, Simon and Bünder, Anne and Berglund, Linn and Hertzberg, Magnus and Niittylä, Totte and Oksman, Kristiina},
	month = apr,
	year = {2021},
	pages = {1179},
}

Wood from field-grown poplars with different genotypes and varying lignin content (17.4 wt % to 30.0 wt %) were subjected to one-pot 2,2,6,6-Tetramethylpiperidin-1-yl)oxyl catalyzed oxidation and high-pressure homogenization in order to investigate nanofibrillation following simultaneous delignification and cellulose oxidation. When comparing low and high lignin wood it was found that the high lignin wood was more easily fibrillated as indicated by a higher nanofibril yield (68% and 45%) and suspension viscosity (27 and 15 mPa·s). The nanofibrils were monodisperse with diameter ranging between 1.2 and 2.0 nm as measured using atomic force microscopy. Slightly less cellulose oxidation (0.44 and 0.68 mmol·g−1) together with a reduced process yield (36% and 44%) was also found which showed that the removal of a larger amount of lignin increased the efficiency of the homogenization step despite slightly reduced oxidation of the nanofibril surfaces. The surface area of oxidized high lignin wood was also higher than low lignin wood (114 m2·g−1 and 76 m2·g−1) which implicates porosity as a factor that can influence cellulose nanofibril isolation from wood in a beneficial manner.

@article{nzayisenga_metabolomic_2021,
	title = {Metabolomic {Study} of {Heterotrophically} {Grown} {Chlorella} sp. {Isolated} from {Wastewater} in {Northern} {Sweden}},
	volume = {26},
	issn = {1420-3049},
	url = {https://www.mdpi.com/1420-3049/26/9/2410},
	doi = {10/gj6zk8},
	abstract = {There are numerous strains of Chlorella with a corresponding variety of metabolic pathways. A strain we previously isolated from wastewater in northern Sweden can grow heterotrophically as well as autotrophically in light and has higher lipid contents under heterotrophic growth conditions. The aims of the present study were to characterize metabolic changes associated with the higher lipid contents in order to enhance our understanding of lipid production in microalgae and potentially identify new compounds with utility in sustainable development. Inter alia, the amino acids glutamine and lysine were 7-fold more abundant under heterotrophic conditions, the key metabolic intermediate alpha-ketoglutarate was more abundant under heterotrophic conditions with glucose, and maltose was more abundant under heterotrophic conditions with glycerol than under autotrophic conditions. The metabolite 3-hydroxy-butyric acid, the direct precursor of the biodegradable plastic PHB (poly-3-hydroxy-butyric acid), was also more abundant under heterotrophic conditions. Our metabolomic analysis has provided new insights into the alga’s lipid production pathways and identified metabolites with potential use in sustainable development, such as the production of renewable, biodegradable plastics, cosmetics, and nutraceuticals, with reduced pollution and improvements in both ecological and human health.},
	language = {en},
	number = {9},
	urldate = {2021-06-03},
	journal = {Molecules},
	author = {Nzayisenga, Jean Claude and Sellstedt, Anita},
	month = apr,
	year = {2021},
	pages = {2410},
}

There are numerous strains of Chlorella with a corresponding variety of metabolic pathways. A strain we previously isolated from wastewater in northern Sweden can grow heterotrophically as well as autotrophically in light and has higher lipid contents under heterotrophic growth conditions. The aims of the present study were to characterize metabolic changes associated with the higher lipid contents in order to enhance our understanding of lipid production in microalgae and potentially identify new compounds with utility in sustainable development. Inter alia, the amino acids glutamine and lysine were 7-fold more abundant under heterotrophic conditions, the key metabolic intermediate alpha-ketoglutarate was more abundant under heterotrophic conditions with glucose, and maltose was more abundant under heterotrophic conditions with glycerol than under autotrophic conditions. The metabolite 3-hydroxy-butyric acid, the direct precursor of the biodegradable plastic PHB (poly-3-hydroxy-butyric acid), was also more abundant under heterotrophic conditions. Our metabolomic analysis has provided new insights into the alga’s lipid production pathways and identified metabolites with potential use in sustainable development, such as the production of renewable, biodegradable plastics, cosmetics, and nutraceuticals, with reduced pollution and improvements in both ecological and human health.

@article{kohorn_effects_2021,
	title = {Effects of {Arabidopsis} wall associated kinase mutations on {ESMERALDA1} and elicitor induced {ROS}},
	volume = {16},
	issn = {1932-6203},
	url = {https://dx.plos.org/10.1371/journal.pone.0251922},
	doi = {10/gkct4r},
	abstract = {Angiosperm cell adhesion is dependent on interactions between pectin polysaccharides which make up a significant portion of the plant cell wall. Cell adhesion in Arabidopsis may also be regulated through a pectin-related signaling cascade mediated by a putative O-fucosyltransferase ESMERALDA1 (ESMD1), and the Epidermal Growth Factor (EGF) domains of the pectin binding Wall associated Kinases (WAKs) are a primary candidate substrate for ESMD1 activity. Genetic interactions between WAKs and ESMD1 were examined using a dominant hyperactive allele of WAK2,
              WAK2cTAP
              , and a mutant of the putative O-fucosyltransferase ESMD1. WAK2cTAP expression results in a dwarf phenotype and activation of the stress response and reactive oxygen species (ROS) production, while
              esmd1
              is a suppressor of a pectin deficiency induced loss of adhesion. Here we find that
              esmd1
              suppresses the WAK2cTAP dwarf and stress response phenotype, including ROS accumulation and gene expression. Additional analysis suggests that mutations of the potential WAK EGF O-fucosylation site also abate the WAK2cTAP phenotype, yet only evidence for an N-linked but not O-linked sugar addition can be found. Moreover, a
              WAK
              locus deletion allele has no effect on the ability of
              esmd1
              to suppress an adhesion deficiency, indicating WAKs and their modification are not a required component of the potential ESMD1 signaling mechanism involved in the control of cell adhesion. The WAK locus deletion does however affect the induction of ROS but not the transcriptional response induced by the elicitors Flagellin, Chitin and oligogalacturonides (OGs).},
	language = {en},
	number = {5},
	urldate = {2021-06-03},
	journal = {PLOS ONE},
	author = {Kohorn, Bruce D. and Greed, Bridgid E. and Mouille, Gregory and Verger, Stéphane and Kohorn, Susan L.},
	editor = {Zabotina, Olga A.},
	month = may,
	year = {2021},
	pages = {e0251922},
}

Angiosperm cell adhesion is dependent on interactions between pectin polysaccharides which make up a significant portion of the plant cell wall. Cell adhesion in Arabidopsis may also be regulated through a pectin-related signaling cascade mediated by a putative O-fucosyltransferase ESMERALDA1 (ESMD1), and the Epidermal Growth Factor (EGF) domains of the pectin binding Wall associated Kinases (WAKs) are a primary candidate substrate for ESMD1 activity. Genetic interactions between WAKs and ESMD1 were examined using a dominant hyperactive allele of WAK2, WAK2cTAP , and a mutant of the putative O-fucosyltransferase ESMD1. WAK2cTAP expression results in a dwarf phenotype and activation of the stress response and reactive oxygen species (ROS) production, while esmd1 is a suppressor of a pectin deficiency induced loss of adhesion. Here we find that esmd1 suppresses the WAK2cTAP dwarf and stress response phenotype, including ROS accumulation and gene expression. Additional analysis suggests that mutations of the potential WAK EGF O-fucosylation site also abate the WAK2cTAP phenotype, yet only evidence for an N-linked but not O-linked sugar addition can be found. Moreover, a WAK locus deletion allele has no effect on the ability of esmd1 to suppress an adhesion deficiency, indicating WAKs and their modification are not a required component of the potential ESMD1 signaling mechanism involved in the control of cell adhesion. The WAK locus deletion does however affect the induction of ROS but not the transcriptional response induced by the elicitors Flagellin, Chitin and oligogalacturonides (OGs).

@article{majda_elongation_2021,
	title = {Elongation of wood fibers combines features of diffuse and tip growth},
	issn = {0028-646X, 1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.17468},
	doi = {10/gj3qbx},
	language = {en},
	urldate = {2021-06-03},
	journal = {New Phytologist},
	author = {Majda, Mateusz and Kozlova, Liudmila and Banasiak, Alicja and Derba‐Maceluch, Marta and Iashchishyn, Igor A. and Morozova‐Roche, Ludmilla A. and Smith, Richard S. and Gorshkova, Tatyana and Mellerowicz, Ewa J.},
	month = may,
	year = {2021},
	pages = {nph.17468},
}

@article{ahmad_sucrose-dependent_2021,
	title = {Sucrose-dependent production of biomass and low-caloric steviol glycosides in adventitious root cultures of {Stevia} rebaudiana ({Bert}.)},
	volume = {164},
	issn = {09266690},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0926669021001461},
	doi = {10/gj6thz},
	language = {en},
	urldate = {2021-06-03},
	journal = {Industrial Crops and Products},
	author = {Ahmad, Naveed and Rab, Abdur and Sajid, Muhammad and Ahmad, Nisar and Fazal, Hina and Ali, Mohammad and Egertsdotter, Ulrika},
	month = jun,
	year = {2021},
	pages = {113382},
}

@article{ranade_silico_2021,
	title = {In silico characterization of putative gene homologues involved in somatic embryogenesis suggests that some conifer species may lack {LEC2}, one of the key regulators of initiation of the process},
	volume = {22},
	issn = {1471-2164},
	url = {https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-07718-8},
	doi = {10/gkbhh3},
	abstract = {Abstract
            
              Background
              Somatic embryogenesis (SE) is the process in which somatic embryos develop from somatic tissue in vitro on medium in most cases supplemented with growth regulators. Knowledge of genes involved in regulation of initiation and of development of somatic embryos is crucial for application of SE as an efficient tool to enable genetic improvement across genotypes by clonal propagation.
            
            
              Results
              
                Current work presents in silico identification of putative homologues of central regulators of SE initiation and development in conifers focusing mainly on key transcription factors (TFs) e.g.
                BBM
                ,
                LEC1
                ,
                LEC1-LIKE, LEC2
                and
                FUSCA3
                , based on sequence similarity using BLASTP. Protein sequences of well-characterised candidates genes from
                Arabidopsis thaliana
                were used to query the databases (Gymno PLAZA, Congenie, GenBank) including whole-genome sequence data from two representative species from the genus
                Picea
                (
                Picea abies
                ) and
                Pinus
                (
                Pinus taeda
                ), for finding putative conifer homologues, using BLASTP. Identification of corresponding conifer proteins was further confirmed by domain search (Conserved Domain Database), alignment (MUSCLE) with respective sequences of
                Arabidopsis thaliana
                proteins and phylogenetic analysis (Phylogeny.fr).
              
            
            
              Conclusions
              
                This in silico analysis suggests absence of
                LEC2
                in
                Picea abies
                and
                Pinus taeda
                , the conifer species whose genomes have been sequenced. Based on available sequence data to date,
                LEC2
                was also not detected in the other conifer species included in the study.
                LEC2
                is one of the key TFs associated with initiation and regulation of the process of SE in angiosperms. Potential alternative mechanisms that might be functional in conifers to compensate the lack of
                LEC2
                are discussed.},
	language = {en},
	number = {1},
	urldate = {2021-06-03},
	journal = {BMC Genomics},
	author = {Ranade, Sonali Sachin and Egertsdotter, Ulrika},
	month = dec,
	year = {2021},
	pages = {392},
}

Abstract Background Somatic embryogenesis (SE) is the process in which somatic embryos develop from somatic tissue in vitro on medium in most cases supplemented with growth regulators. Knowledge of genes involved in regulation of initiation and of development of somatic embryos is crucial for application of SE as an efficient tool to enable genetic improvement across genotypes by clonal propagation. Results Current work presents in silico identification of putative homologues of central regulators of SE initiation and development in conifers focusing mainly on key transcription factors (TFs) e.g. BBM , LEC1 , LEC1-LIKE, LEC2 and FUSCA3 , based on sequence similarity using BLASTP. Protein sequences of well-characterised candidates genes from Arabidopsis thaliana were used to query the databases (Gymno PLAZA, Congenie, GenBank) including whole-genome sequence data from two representative species from the genus Picea ( Picea abies ) and Pinus ( Pinus taeda ), for finding putative conifer homologues, using BLASTP. Identification of corresponding conifer proteins was further confirmed by domain search (Conserved Domain Database), alignment (MUSCLE) with respective sequences of Arabidopsis thaliana proteins and phylogenetic analysis (Phylogeny.fr). Conclusions This in silico analysis suggests absence of LEC2 in Picea abies and Pinus taeda , the conifer species whose genomes have been sequenced. Based on available sequence data to date, LEC2 was also not detected in the other conifer species included in the study. LEC2 is one of the key TFs associated with initiation and regulation of the process of SE in angiosperms. Potential alternative mechanisms that might be functional in conifers to compensate the lack of LEC2 are discussed.

@article{mboene_noah_dynamics_2021,
	title = {Dynamics of {Auxin} and {Cytokinin} {Metabolism} during {Early} {Root} and {Hypocotyl} {Growth} in {Theobroma} cacao},
	volume = {10},
	issn = {2223-7747},
	url = {https://www.mdpi.com/2223-7747/10/5/967},
	doi = {10/gkcr5m},
	abstract = {The spatial location and timing of plant developmental events are largely regulated by the well balanced effects of auxin and cytokinin phytohormone interplay. Together with transport, localized metabolism regulates the concentration gradients of their bioactive forms, ultimately eliciting growth responses. In order to explore the dynamics of auxin and cytokinin metabolism during early seedling growth in Theobroma cacao (cacao), we have performed auxin and cytokinin metabolite profiling in hypocotyls and root developmental sections at different times by using ultra-high-performance liquid chromatography-electrospray tandem mass spectrometry (UHPLC-MS/MS). Our work provides quantitative characterization of auxin and cytokinin metabolites throughout early root and hypocotyl development and identifies common and distinctive features of auxin and cytokinin metabolism during cacao seedling development.},
	language = {en},
	number = {5},
	urldate = {2021-06-03},
	journal = {Plants},
	author = {Mboene Noah, Alexandre and Casanova-Sáez, Rubén and Makondy Ango, Rolande Eugenie and Antoniadi, Ioanna and Karady, Michal and Novák, Ondřej and Niemenak, Nicolas and Ljung, Karin},
	month = may,
	year = {2021},
	pages = {967},
}

The spatial location and timing of plant developmental events are largely regulated by the well balanced effects of auxin and cytokinin phytohormone interplay. Together with transport, localized metabolism regulates the concentration gradients of their bioactive forms, ultimately eliciting growth responses. In order to explore the dynamics of auxin and cytokinin metabolism during early seedling growth in Theobroma cacao (cacao), we have performed auxin and cytokinin metabolite profiling in hypocotyls and root developmental sections at different times by using ultra-high-performance liquid chromatography-electrospray tandem mass spectrometry (UHPLC-MS/MS). Our work provides quantitative characterization of auxin and cytokinin metabolites throughout early root and hypocotyl development and identifies common and distinctive features of auxin and cytokinin metabolism during cacao seedling development.