@article{birkeland_updated_2025,
	title = {An updated perspective: what genes make a tree a tree?},
	issn = {1360-1385},
	shorttitle = {An updated perspective},
	url = {https://www.sciencedirect.com/science/article/pii/S1360138525002821},
	doi = {10.1016/j.tplants.2025.09.006},
	abstract = {We learn early on how to tell trees apart from other plants. However, it has proved hard to distinguish trees from other plants at the genetic level, and it is believed that there are no unique ‘tree genes’. With the rapid increase in available tree genomes, we can perform new comparative and evolutionary analyses of plant life histories and growth forms. Here we provide a fresh perspective on the genetic foundation for woodiness and perenniality in angiosperms by analyzing selection pressures and gene family evolution in the rosids using genomic data. We examine genes distinguishing trees from herbs and discuss future directions for uncovering the genetic factors that define a tree in this new era of tree genomics.},
	urldate = {2025-10-24},
	journal = {Trends in Plant Science},
	author = {Birkeland, Siri and Soldado, Eduardo R. and Ranade, Sonali S. and García-Gil, M. Rosario and Choudhary, Shruti and Kumar, Vikash and Tuominen, Hannele and Mellerowicz, Ewa J. and Street, Nathaniel R. and Hvidsten, Torgeir R.},
	month = oct,
	year = {2025},
	keywords = {comparative genomics, plant growth forms, plant life histories, rosids, tree genomics, woodiness},
}

We learn early on how to tell trees apart from other plants. However, it has proved hard to distinguish trees from other plants at the genetic level, and it is believed that there are no unique ‘tree genes’. With the rapid increase in available tree genomes, we can perform new comparative and evolutionary analyses of plant life histories and growth forms. Here we provide a fresh perspective on the genetic foundation for woodiness and perenniality in angiosperms by analyzing selection pressures and gene family evolution in the rosids using genomic data. We examine genes distinguishing trees from herbs and discuss future directions for uncovering the genetic factors that define a tree in this new era of tree genomics.

@article{ye_cambium_2025,
	title = {Cambium {LBDs} promote radial growth by regulating {PLL}-mediated pectin metabolism},
	copyright = {2025 The Author(s)},
	issn = {2055-0278},
	url = {https://www.nature.com/articles/s41477-025-02151-1},
	doi = {10.1038/s41477-025-02151-1},
	abstract = {Plant growth originates from the interlinked action of cell division and cell growth. During radial growth of secondary tissues, bifacial cambial stem cells grow and divide to produce xylem and phloem precursors, which subsequently undergo expansion characteristic of their respective differentiation processes. In Arabidopsis roots, cytokinins and four downstream LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors are key players in promoting radial growth, though the underlying mechanisms remain unknown. Here our results indicate that these LBD genes primarily regulate cell growth rather than proliferation. Through a large-scale CRISPR–Cas9-aided reverse genetic screen, we identified a set of PECTATE LYASE-LIKE (PLL) genes that function downstream of cytokinin and the LBDs in the regulation of radial growth. We show that at least one of these PLLs, PLL18, possesses pectate lyase activity. In accordance with this activity, PLLs and LBDs promote radial growth by modifying the pectin composition and mechanical properties of the primary cell wall. Our findings thus connect the central role of cytokinins in radial growth with cell wall remodelling and pave a way for further research on hormone-mediated plant growth regulation and cell wall metabolism.},
	language = {en},
	urldate = {2025-11-21},
	journal = {Nature Plants},
	author = {Ye, Lingling and Wang, Xin and Valle-Delgado, Juan José and Vainonen, Julia P. and Wopereis, Isaac and Kesari, Kavindra Kumar and Takahashi, Junko and Sierla, Maija and Mähönen, Ari Pekka},
	month = nov,
	year = {2025},
	note = {Publisher: Nature Publishing Group},
	keywords = {Cell wall, Cytokinin, Plant morphogenesis, Transgenic plants},
	pages = {1--16},
}

Plant growth originates from the interlinked action of cell division and cell growth. During radial growth of secondary tissues, bifacial cambial stem cells grow and divide to produce xylem and phloem precursors, which subsequently undergo expansion characteristic of their respective differentiation processes. In Arabidopsis roots, cytokinins and four downstream LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors are key players in promoting radial growth, though the underlying mechanisms remain unknown. Here our results indicate that these LBD genes primarily regulate cell growth rather than proliferation. Through a large-scale CRISPR–Cas9-aided reverse genetic screen, we identified a set of PECTATE LYASE-LIKE (PLL) genes that function downstream of cytokinin and the LBDs in the regulation of radial growth. We show that at least one of these PLLs, PLL18, possesses pectate lyase activity. In accordance with this activity, PLLs and LBDs promote radial growth by modifying the pectin composition and mechanical properties of the primary cell wall. Our findings thus connect the central role of cytokinins in radial growth with cell wall remodelling and pave a way for further research on hormone-mediated plant growth regulation and cell wall metabolism.

@article{sullivan_airborne_2025,
	title = {Airborne {eDNA} captures three decades of ecosystem biodiversity},
	volume = {16},
	copyright = {2025 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-025-67676-7},
	doi = {10.1038/s41467-025-67676-7},
	abstract = {Biodiversity loss threatens ecosystems and human well-being, making accurate, large-scale monitoring crucial. Environmental DNA (eDNA) has enabled species detection from substrates such as water, without the need for direct observation. Lately, airborne eDNA has been showing promise for tracking organisms from insects to mammals in terrestrial ecosystems. Conventional biodiversity assessments are often labor-intensive and limited in scope, leaving gaps in our understanding of ecosystem response to environmental change. Here, we demonstrate that airborne eDNA can detect organisms across the tree of life, quantify changes in abundance congruent with traditional monitoring, and reveal land-use induced regional decline of diversity in a northern boreal ecosystem over more than three decades. By analyzing 34 years of archived aerosol filters, we reconstruct weekly temporal relative abundance data for more than 2700 genera using non-targeted methods. This study provides unified, ecosystem-scale biodiversity surveillance spanning multiple decades, with data collected at weekly intervals on both the individual species and community level. Previously, large scale analyses of ecosystem changes, targeting all types of organisms, has been prohibitively expensive and difficult to attempt. Here, we present a way of holistically doing this type of analysis in a single framework.},
	language = {en},
	number = {1},
	urldate = {2026-01-09},
	journal = {Nature Communications},
	author = {Sullivan, Alexis R. and Karlsson, Edvin and Svensson, Daniel and Brindefalk, Björn and Villegas, Jose Antonio and Mikko, Amanda and Bellieny, Daniel and Siddique, Abu Bakar and Johansson, Anna-Mia and Grahn, Håkan and Sundell, David and Norman, Anita and Esseen, Per-Anders and Sjödin, Andreas and Singh, Navinder J. and Brodin, Tomas and Forsman, Mats and Stenberg, Per},
	month = dec,
	year = {2025},
	note = {Publisher: Nature Publishing Group},
	keywords = {Biodiversity, Molecular ecology},
	pages = {11281},
}

Biodiversity loss threatens ecosystems and human well-being, making accurate, large-scale monitoring crucial. Environmental DNA (eDNA) has enabled species detection from substrates such as water, without the need for direct observation. Lately, airborne eDNA has been showing promise for tracking organisms from insects to mammals in terrestrial ecosystems. Conventional biodiversity assessments are often labor-intensive and limited in scope, leaving gaps in our understanding of ecosystem response to environmental change. Here, we demonstrate that airborne eDNA can detect organisms across the tree of life, quantify changes in abundance congruent with traditional monitoring, and reveal land-use induced regional decline of diversity in a northern boreal ecosystem over more than three decades. By analyzing 34 years of archived aerosol filters, we reconstruct weekly temporal relative abundance data for more than 2700 genera using non-targeted methods. This study provides unified, ecosystem-scale biodiversity surveillance spanning multiple decades, with data collected at weekly intervals on both the individual species and community level. Previously, large scale analyses of ecosystem changes, targeting all types of organisms, has been prohibitively expensive and difficult to attempt. Here, we present a way of holistically doing this type of analysis in a single framework.

@article{goretti_splicing_2025,
	title = {The splicing genes {SmEa} and {SmEb} regulate plant development during vegetative growth in poplar},
	volume = {25},
	issn = {1471-2229},
	url = {https://doi.org/10.1186/s12870-025-07676-3},
	doi = {10.1186/s12870-025-07676-3},
	abstract = {Spliceosomes are large evolutionary conserved ribonucleoprotein complexes containing at their core heptameric rings of Sm (or LSm) proteins and U-rich snRNAs. The role of Sm proteins in animal development is well established, and recent research has begun to link mutations in these genes to growth defects in plants. One of the most studied Sm genes is SmE1/PCP, mutants of which display a temperature-dependent phenotype in Arabidopsis thaliana.},
	language = {en},
	number = {1},
	urldate = {2026-01-09},
	journal = {BMC Plant Biology},
	author = {Goretti, Daniela and Collani, Silvio and Marcon, Alice and Nilsson, Ove and Schmid, Markus},
	month = dec,
	year = {2025},
	keywords = {CRISPR/Cas9, Development, Poplar, Sm, Splicing},
	pages = {1723},
}

Spliceosomes are large evolutionary conserved ribonucleoprotein complexes containing at their core heptameric rings of Sm (or LSm) proteins and U-rich snRNAs. The role of Sm proteins in animal development is well established, and recent research has begun to link mutations in these genes to growth defects in plants. One of the most studied Sm genes is SmE1/PCP, mutants of which display a temperature-dependent phenotype in Arabidopsis thaliana.

@article{parizkova_l-glutamine_2026,
	title = {L-{Glutamine} {Modulates} {Root} {Architecture} and {Hormonal} {Balance} in {Arabidopsis}},
	volume = {178},
	copyright = {© 2025 The Author(s). Physiologia Plantarum published by John Wiley \& Sons Ltd on behalf of Scandinavian Plant Physiology Society.},
	issn = {1399-3054},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ppl.70723},
	doi = {10.1111/ppl.70723},
	abstract = {Nitrogen (N) availability is a key determinant of plant growth and development. Here, we investigate how different N sources shape Arabidopsis thaliana root system architecture, metabolism and hormone dynamics. L-glutamine (L-GLN) significantly enhances root biomass compared to nitrate (KNO3) without compromising shoot growth. This effect emerges after 2 weeks and is independent of L-GLN's role as a carbon or ammonium source or of potential L-GLN-induced pH changes due to ammonium release, indicating a specific function of L-GLN as a N source and signaling molecule. A reverse genetic screen identified AMINO ACID PERMEASE 1 (AAP1)-mediated uptake and GLUTAMINE SYNTHETASE (GS)-dependent assimilation as essential for L-GLN-induced root biomass. In contrast, the N-sensing regulators NITRATE TRANSPORTER 1.1 (NRT1.1) and AMMONIUM TRANSPORTER (AMT) family members contribute to the differential root responses between KNO3 and L-GLN. Metabolic profiling revealed distinct amino acid signatures under these N sources, irrespective of genotype. Hormonal analyses showed that L-GLN modulates auxin homeostasis, with auxin supplementation restoring primary root growth and lateral root symmetry under L-GLN conditions. L-GLN also reconfigures cytokinin balance by elevating cZ while reducing tZ, collectively shaping root system architecture through hormone-dependent regulation. Together, these findings establish L-GLN as an integrator of N metabolism and hormone signaling in root development, highlighting its signaling capacity beyond nutrient supply and offering new perspectives for improving N use efficiency.},
	language = {en},
	number = {1},
	urldate = {2026-01-09},
	journal = {Physiologia Plantarum},
	author = {Pařízková, Barbora and Johansson, Annika I. and Juvany, Marta and Šimura, Jan and Ljung, Karin and Antoniadi, Ioanna},
	year = {2026},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70723},
	keywords = {KNO3, L-GLN, auxin, cytokinin, organic N, root growth, root system architecture},
	pages = {e70723},
}

Nitrogen (N) availability is a key determinant of plant growth and development. Here, we investigate how different N sources shape Arabidopsis thaliana root system architecture, metabolism and hormone dynamics. L-glutamine (L-GLN) significantly enhances root biomass compared to nitrate (KNO3) without compromising shoot growth. This effect emerges after 2 weeks and is independent of L-GLN's role as a carbon or ammonium source or of potential L-GLN-induced pH changes due to ammonium release, indicating a specific function of L-GLN as a N source and signaling molecule. A reverse genetic screen identified AMINO ACID PERMEASE 1 (AAP1)-mediated uptake and GLUTAMINE SYNTHETASE (GS)-dependent assimilation as essential for L-GLN-induced root biomass. In contrast, the N-sensing regulators NITRATE TRANSPORTER 1.1 (NRT1.1) and AMMONIUM TRANSPORTER (AMT) family members contribute to the differential root responses between KNO3 and L-GLN. Metabolic profiling revealed distinct amino acid signatures under these N sources, irrespective of genotype. Hormonal analyses showed that L-GLN modulates auxin homeostasis, with auxin supplementation restoring primary root growth and lateral root symmetry under L-GLN conditions. L-GLN also reconfigures cytokinin balance by elevating cZ while reducing tZ, collectively shaping root system architecture through hormone-dependent regulation. Together, these findings establish L-GLN as an integrator of N metabolism and hormone signaling in root development, highlighting its signaling capacity beyond nutrient supply and offering new perspectives for improving N use efficiency.