@article{mazumdar_damage_2025,
	title = {Damage activates \textit{{EXG1}} and \textit{{RLP44}} to suppress vascular differentiation during regeneration in {Arabidopsis}},
	issn = {2590-3462},
	url = {https://www.sciencedirect.com/science/article/pii/S2590346225000185},
	doi = {10.1016/j.xplc.2025.101256},
	abstract = {Plants possess remarkable regenerative abilities to form de novo vasculature after damage and in response to pathogens that invade and withdraw nutrients. To look for common factors that affect vascular formation upon stress, we searched for Arabidopsis thaliana genes differentially expressed upon Agrobacterium infection, nematode infection and plant grafting. One such gene was cell wall related and highly induced by all three stresses and was named ENHANCED XYLEM AND GRAFTING1 (EXG1) since mutations in it promoted ectopic xylem formation in Vascular cell Induction culture System Using Arabidopsis Leaves (VISUAL) and enhanced graft formation. Further observations revealed that exg1 mutants inhibited cambium development and callus formation but enhanced tissue attachment, syncytium size, phloem reconnection and xylem formation. Given that brassinosteroids also promote xylem differentiation, we analyzed brassinosteroid-related genes and found that mutations in a receptor-like protein, RLP44, caused similar regeneration-related phenotypes as mutations in EXG1. Like EXG1, RLP44 expression was induced by grafting and wounding. Mutations in EXG1 and RLP44 affected the expression of many genes in common including those related to cell walls and genes important for vascular regeneration. We propose that EXG1 integrates information from wounding or pathogen stresses and functions with RLP44 to suppress vascular differentiation during regeneration and healing.},
	urldate = {2025-01-24},
	journal = {Plant Communications},
	author = {Mazumdar, Shamik and Augstein, Frauke and Zhang, Ai and Musseau, Constance and Anjam, Muhammad Shahzad and Marhavy, Peter and Melnyk, Charles W.},
	month = jan,
	year = {2025},
	keywords = {Cell wall, Grafting, Regeneration, Stress, Wounding, Xylem},
	pages = {101256},
}

Plants possess remarkable regenerative abilities to form de novo vasculature after damage and in response to pathogens that invade and withdraw nutrients. To look for common factors that affect vascular formation upon stress, we searched for Arabidopsis thaliana genes differentially expressed upon Agrobacterium infection, nematode infection and plant grafting. One such gene was cell wall related and highly induced by all three stresses and was named ENHANCED XYLEM AND GRAFTING1 (EXG1) since mutations in it promoted ectopic xylem formation in Vascular cell Induction culture System Using Arabidopsis Leaves (VISUAL) and enhanced graft formation. Further observations revealed that exg1 mutants inhibited cambium development and callus formation but enhanced tissue attachment, syncytium size, phloem reconnection and xylem formation. Given that brassinosteroids also promote xylem differentiation, we analyzed brassinosteroid-related genes and found that mutations in a receptor-like protein, RLP44, caused similar regeneration-related phenotypes as mutations in EXG1. Like EXG1, RLP44 expression was induced by grafting and wounding. Mutations in EXG1 and RLP44 affected the expression of many genes in common including those related to cell walls and genes important for vascular regeneration. We propose that EXG1 integrates information from wounding or pathogen stresses and functions with RLP44 to suppress vascular differentiation during regeneration and healing.

@article{baral_typhon_2025,
	title = {{TYPHON} proteins are {RAB}-dependent mediators of the trans-{Golgi} network secretory pathway},
	volume = {37},
	issn = {1040-4651},
	url = {https://doi.org/10.1093/plcell/koae280},
	doi = {10.1093/plcell/koae280},
	abstract = {The trans-Golgi network (TGN), a key compartment in endomembrane trafficking, participates in both secretion to and endocytosis from the plasma membrane. Consequently, the TGN plays a key role in plant growth and development. Understanding how proteins are sorted for secretion or endocytic recycling at the TGN is critical for elucidating mechanisms of plant development. We previously showed that the protein ECHIDNA is essential for phytohormonal control of hypocotyl bending because it mediates secretion of cell wall components and the auxin influx carrier AUXIN RESISTANT 1 (AUX1) from the TGN. Despite the critical role of ECHIDNA in TGN-mediated trafficking, its mode of action remains unknown in Arabidopsis (Arabidopsis thaliana). We therefore performed a suppressor screen on the ech mutant. Here, we report the identification of TGN-localized TYPHON 1 (TPN1) and TPN2 proteins. A single amino acid change in either TPN protein causes dominant suppression of the ech mutant's defects in growth and AUX1 secretion, while also restoring wild-type (WT)-like ethylene-responsive hypocotyl bending. Importantly, genetic and cell biological evidence shows that TPN1 acts through RAS-ASSOCIATED BINDING H1b (RABH1b), a TGN-localized RAB-GTPase. These results provide insights into ECHIDNA-mediated secretory trafficking of cell wall and auxin carriers at the TGN, as well as its role in controlling plant growth.},
	number = {1},
	urldate = {2025-01-20},
	journal = {The Plant Cell},
	author = {Baral, Anirban and Gendre, Delphine and Aryal, Bibek and Fougère, Louise and Di Fino, Luciano Martin and Ohori, Chihiro and Sztojka, Bernadette and Uemura, Tomohiro and Ueda, Takashi and Marhavý, Peter and Boutté, Yohann and Bhalerao, Rishikesh P},
	month = jan,
	year = {2025},
	pages = {koae280},
}

The trans-Golgi network (TGN), a key compartment in endomembrane trafficking, participates in both secretion to and endocytosis from the plasma membrane. Consequently, the TGN plays a key role in plant growth and development. Understanding how proteins are sorted for secretion or endocytic recycling at the TGN is critical for elucidating mechanisms of plant development. We previously showed that the protein ECHIDNA is essential for phytohormonal control of hypocotyl bending because it mediates secretion of cell wall components and the auxin influx carrier AUXIN RESISTANT 1 (AUX1) from the TGN. Despite the critical role of ECHIDNA in TGN-mediated trafficking, its mode of action remains unknown in Arabidopsis (Arabidopsis thaliana). We therefore performed a suppressor screen on the ech mutant. Here, we report the identification of TGN-localized TYPHON 1 (TPN1) and TPN2 proteins. A single amino acid change in either TPN protein causes dominant suppression of the ech mutant's defects in growth and AUX1 secretion, while also restoring wild-type (WT)-like ethylene-responsive hypocotyl bending. Importantly, genetic and cell biological evidence shows that TPN1 acts through RAS-ASSOCIATED BINDING H1b (RABH1b), a TGN-localized RAB-GTPase. These results provide insights into ECHIDNA-mediated secretory trafficking of cell wall and auxin carriers at the TGN, as well as its role in controlling plant growth.

@article{fino_cellular_2025,
	title = {Cellular damage triggers mechano-chemical control of cell wall dynamics and patterned cell divisions in plant healing},
	volume = {0},
	issn = {1534-5807},
	url = {https://www.cell.com/developmental-cell/abstract/S1534-5807(24)00771-8},
	doi = {10.1016/j.devcel.2024.12.032},
	language = {English},
	number = {0},
	urldate = {2025-01-15},
	journal = {Developmental Cell},
	author = {Fino, Luciano Martín Di and Anjam, Muhammad Shahzad and Besten, Maarten and Mentzelopoulou, Andriani and Papadakis, Vassilis and Zahid, Nageena and Baez, Luis Alonso and Trozzi, Nicola and Majda, Mateusz and Ma, Xuemin and Hamann, Thorsten and Sprakel, Joris and Moschou, Panagiotis N. and Smith, Richard S. and Marhavý, Peter},
	month = jan,
	year = {2025},
	pmid = {39809282},
	note = {Publisher: Elsevier},
	keywords = {cell division, cell wall, ethylene, mechanobiology, pectin, regeneration, single-cell laser ablation, xylem-pole-pericycle},
}

@article{wieloch_new_2025,
	title = {New insights into the mechanisms of plant isotope fractionation from combined analysis of intramolecular {13C} and deuterium abundances in {Pinus} nigra tree-ring glucose},
	volume = {245},
	copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20113},
	doi = {10.1111/nph.20113},
	abstract = {Understanding isotope fractionation mechanisms is fundamental for analyses of plant ecophysiology and paleoclimate based on tree-ring isotope data. To gain new insights into isotope fractionation, we analysed intramolecular 13C discrimination in tree-ring glucose (Δi′, i = C-1 to C-6) and metabolic deuterium fractionation at H1 and H2 (εmet) combinedly. This dual-isotope approach was used for isotope-signal deconvolution. We found evidence for metabolic processes affecting Δ1′ and Δ3′, which respond to air vapour pressure deficit (VPD), and processes affecting Δ1′, Δ2′, and εmet, which respond to precipitation but not VPD. These relationships exhibit change points dividing a period of homeostasis (1961–1980) from a period of metabolic adjustment (1983–1995). Homeostasis may result from sufficient groundwater availability. Additionally, we found Δ5′ and Δ6′ relationships with radiation and temperature, which are temporally stable and consistent with previously proposed isotope fractionation mechanisms. Based on the multitude of climate covariables, intramolecular carbon isotope analysis has a remarkable potential for climate reconstruction. While isotope fractionation beyond leaves is currently considered to be constant, we propose significant parts of the carbon and hydrogen isotope variation in tree-ring glucose originate in stems (precipitation-dependent signals). As basis for follow-up studies, we propose mechanisms introducing Δ1′, Δ2′, Δ3′, and εmet variability.},
	language = {en},
	number = {3},
	urldate = {2025-01-10},
	journal = {New Phytologist},
	author = {Wieloch, Thomas and Holloway-Phillips, Meisha and Yu, Jun and Niittylä, Totte},
	month = feb,
	year = {2025},
	keywords = {carbon stable isotopes, hydrogen stable isotopes, intramolecular isotope analysis, isotope fractionation mechanisms, leaf water status, plant–environment interactions, stem water status, tree rings},
	pages = {1000--1017},
}

Understanding isotope fractionation mechanisms is fundamental for analyses of plant ecophysiology and paleoclimate based on tree-ring isotope data. To gain new insights into isotope fractionation, we analysed intramolecular 13C discrimination in tree-ring glucose (Δi′, i = C-1 to C-6) and metabolic deuterium fractionation at H1 and H2 (εmet) combinedly. This dual-isotope approach was used for isotope-signal deconvolution. We found evidence for metabolic processes affecting Δ1′ and Δ3′, which respond to air vapour pressure deficit (VPD), and processes affecting Δ1′, Δ2′, and εmet, which respond to precipitation but not VPD. These relationships exhibit change points dividing a period of homeostasis (1961–1980) from a period of metabolic adjustment (1983–1995). Homeostasis may result from sufficient groundwater availability. Additionally, we found Δ5′ and Δ6′ relationships with radiation and temperature, which are temporally stable and consistent with previously proposed isotope fractionation mechanisms. Based on the multitude of climate covariables, intramolecular carbon isotope analysis has a remarkable potential for climate reconstruction. While isotope fractionation beyond leaves is currently considered to be constant, we propose significant parts of the carbon and hydrogen isotope variation in tree-ring glucose originate in stems (precipitation-dependent signals). As basis for follow-up studies, we propose mechanisms introducing Δ1′, Δ2′, Δ3′, and εmet variability.

@article{li_unravelling_2024,
	title = {Unravelling the novel sex determination genotype with ‘{ZY}’ and a distinctive 2.15–2.95 {Mb} inversion among poplar species through haplotype-resolved genome assembly and comparative genomics analysis},
	volume = {24},
	copyright = {© 2024 John Wiley \& Sons Ltd.},
	issn = {1755-0998},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.14002},
	doi = {10.1111/1755-0998.14002},
	abstract = {Populus tomentosa, an indigenous tree species, is widely distributed and cultivated over 1,000,000 km2 in China, contributing significantly to forest production, ecological conservation and urban–rural greening. Although a reference genome is available for P. tomentosa, the intricate interspecific hybrid origins, chromosome structural variations (SVs) and sex determination mechanisms remain confusion and unclear due to its broad and even overlapping geographical distribution, extensive morphological variations and cross infiltration among white poplar species. We conducted a haplotype-resolved de novo assembly of P. tomentosa elite individual GM107, which comprises subgenomes a and b with a total genome size of 714.9 Mb. We then analysed the formation of hybrid species and the phylogenetic evolution and sex differentiation across the entire genus. Phylogenomic analyses suggested that GM107 likely originated from a hybridisation event between P. alba (♀) and P. davidiana (♂) which diverged at approximately 3.8 Mya. A total of 1551 chromosome SVs were identified between the two subgenomes. More noteworthily, a distinctive inversion structure spanning 2.15–2.95 Mb was unveiled among Populus, Tacamahaca, Turaga, Aigeiros poplar species and Salix, highlighting a unique evolutionary feature. Intriguingly, a novel sex genotype of the ZY type, which represents a crossover between XY and ZW systems, was identified and confirmed through both natural and artificial hybrids populations. These novel insights offer significant theoretical value for the study of the species' evolutionary origins and serve as a valuable resource for ecological genetics and forest biotechnology.},
	language = {en},
	number = {7},
	urldate = {2024-08-09},
	journal = {Molecular Ecology Resources},
	author = {Li, Juan and Chen, Tingting and Gao, Kai and Xue, Yinxuan and Wu, Ruqian and Guo, Bin and Chen, Zhong and Li, Shanwen and Zhang, Ren-Gang and Jia, Kai-Hua and Mao, Jian-Feng and An, Xinmin},
	month = oct,
	year = {2024},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1755-0998.14002},
	keywords = {Populus tomentosa, chromosome structural variations, haplotype-resolved genome assembly, interspecific hybrid, parental origin, sex determination},
	pages = {e14002},
}

Populus tomentosa, an indigenous tree species, is widely distributed and cultivated over 1,000,000 km2 in China, contributing significantly to forest production, ecological conservation and urban–rural greening. Although a reference genome is available for P. tomentosa, the intricate interspecific hybrid origins, chromosome structural variations (SVs) and sex determination mechanisms remain confusion and unclear due to its broad and even overlapping geographical distribution, extensive morphological variations and cross infiltration among white poplar species. We conducted a haplotype-resolved de novo assembly of P. tomentosa elite individual GM107, which comprises subgenomes a and b with a total genome size of 714.9 Mb. We then analysed the formation of hybrid species and the phylogenetic evolution and sex differentiation across the entire genus. Phylogenomic analyses suggested that GM107 likely originated from a hybridisation event between P. alba (♀) and P. davidiana (♂) which diverged at approximately 3.8 Mya. A total of 1551 chromosome SVs were identified between the two subgenomes. More noteworthily, a distinctive inversion structure spanning 2.15–2.95 Mb was unveiled among Populus, Tacamahaca, Turaga, Aigeiros poplar species and Salix, highlighting a unique evolutionary feature. Intriguingly, a novel sex genotype of the ZY type, which represents a crossover between XY and ZW systems, was identified and confirmed through both natural and artificial hybrids populations. These novel insights offer significant theoretical value for the study of the species' evolutionary origins and serve as a valuable resource for ecological genetics and forest biotechnology.