@article{pandey_variable_2026,
	title = {Variable temperature processing by plasmodesmata regulates robust bud dormancy release},
	volume = {17},
	copyright = {2026 The Author(s)},
	issn = {2041-1723},
	url = {https://www.nature.com/articles/s41467-025-67260-z},
	doi = {10.1038/s41467-025-67260-z},
	abstract = {Dormancy is a key mechanism in perennial plants in boreal and temperate regions, protecting buds from winter damage by repressing precocious bud break before spring onset. How plants robustly time dormancy release under fluctuating environments remains unknown. Here, we show that, rather than simply sensing cold duration, buds leverage warm spikes to sense winter progression and time dormancy release. This timing mechanism is mediated by previously unrecognized regulation of plasmodesmata by warm spikes acting through tree ortholog of FLOWERING LOCUS T (FT1) and the gibberellic acid pathway. Our results reveal FT1 as a previously unrecognized, suppressor of callose levels and show that warm spikes repress cold induction of FT1 and GA pathway to suppress PD opening and dormancy release. Importantly, buds exhibit heterogeneity in bud break. This heterogeneity in bud break crucial for bet hedging is amplified under temperature fluctuations and is associated with the thermal responsiveness of plasmodesmata. Altogether, our work reveals dynamic plasmodesmata regulation as a crucial tissue-level mediator of variable temperature processing by buds, enabling robust adaptation of trees to seasonal changes.},
	language = {en},
	number = {1},
	urldate = {2026-01-16},
	journal = {Nature Communications},
	author = {Pandey, Shashank K. and Moraes, Tatiana S. and Nair, Aswin and Aryal, Bibek and Azeez, Abdul and Miskolczi, Pal and Maucort, Guillaume and Cordelières, Fabrice P. and Brocard, Lysiane and Davis, Gwendolyn V. and Dromiack, Hannah and Khanapurkar, Swanand and Walker, Sara I. and Bassel, George W. and Bayer, Emmanuelle M. and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2026},
	note = {Publisher: Nature Publishing Group},
	keywords = {Plant molecular biology, Plant physiology, Shoot apical meristem},
	pages = {348},
}

Dormancy is a key mechanism in perennial plants in boreal and temperate regions, protecting buds from winter damage by repressing precocious bud break before spring onset. How plants robustly time dormancy release under fluctuating environments remains unknown. Here, we show that, rather than simply sensing cold duration, buds leverage warm spikes to sense winter progression and time dormancy release. This timing mechanism is mediated by previously unrecognized regulation of plasmodesmata by warm spikes acting through tree ortholog of FLOWERING LOCUS T (FT1) and the gibberellic acid pathway. Our results reveal FT1 as a previously unrecognized, suppressor of callose levels and show that warm spikes repress cold induction of FT1 and GA pathway to suppress PD opening and dormancy release. Importantly, buds exhibit heterogeneity in bud break. This heterogeneity in bud break crucial for bet hedging is amplified under temperature fluctuations and is associated with the thermal responsiveness of plasmodesmata. Altogether, our work reveals dynamic plasmodesmata regulation as a crucial tissue-level mediator of variable temperature processing by buds, enabling robust adaptation of trees to seasonal changes.

@article{castellano_genome_2025,
	title = {Genome {Assembly} of a {Living} {Fossil}, the {Atlantic} {Horseshoe} {Crab} {Limulus} polyphemus, {Reveals} {Lineage}-{Specific} {Whole}-{Genome} {Duplications}, {Transposable} {Element}-{Based} {Centromeres}, and a {ZW} {Sex} {Chromosome} {System}},
	volume = {42},
	issn = {1537-1719},
	url = {https://doi.org/10.1093/molbev/msaf021},
	doi = {10.1093/molbev/msaf021},
	abstract = {Horseshoe crabs, considered living fossils with a stable morphotype spanning ∼445 million years, are evolutionarily, ecologically, and biomedically important species experiencing rapid population decline. Of the four extant species of horseshoe crabs, the Atlantic horseshoe crab, Limulus polyphemus, has become an essential component of the modern medicine toolkit. Here, we present the first chromosome-level genome assembly, and the most contiguous and complete assembly to date, for L. polyphemus using nanopore long-read sequencing and chromatin conformation analysis. We find support for three horseshoe crab-specific whole-genome duplications, but none shared with Arachnopulmonata (spiders and scorpions). Moreover, we discovered tandem duplicates of endotoxin detection pathway components Factors C and G, identify candidate centromeres consisting of Gypsy retroelements, and classify the ZW sex chromosome system for this species and a sister taxon, Carcinoscorpius rotundicauda. Finally, we revealed this species has been experiencing a steep population decline over the last 5 million years, highlighting the need for international conservation interventions and fisheries-based management for this critical species.},
	number = {2},
	urldate = {2026-01-16},
	journal = {Molecular Biology and Evolution},
	author = {Castellano, Kate R and Neitzey, Michelle L and Starovoitov, Andrew and Barrett, Gabriel A and Reid, Noah M and Vuruputoor, Vidya S and Webster, Cynthia N and Storer, Jessica M and Pauloski, Nicole R and Ameral, Natalie J and McEvoy, Susan L and McManus, M Conor and Puritz, Jonathan B and Wegrzyn, Jill L and O’Neill, Rachel J},
	month = feb,
	year = {2025},
	pages = {msaf021},
}

Horseshoe crabs, considered living fossils with a stable morphotype spanning ∼445 million years, are evolutionarily, ecologically, and biomedically important species experiencing rapid population decline. Of the four extant species of horseshoe crabs, the Atlantic horseshoe crab, Limulus polyphemus, has become an essential component of the modern medicine toolkit. Here, we present the first chromosome-level genome assembly, and the most contiguous and complete assembly to date, for L. polyphemus using nanopore long-read sequencing and chromatin conformation analysis. We find support for three horseshoe crab-specific whole-genome duplications, but none shared with Arachnopulmonata (spiders and scorpions). Moreover, we discovered tandem duplicates of endotoxin detection pathway components Factors C and G, identify candidate centromeres consisting of Gypsy retroelements, and classify the ZW sex chromosome system for this species and a sister taxon, Carcinoscorpius rotundicauda. Finally, we revealed this species has been experiencing a steep population decline over the last 5 million years, highlighting the need for international conservation interventions and fisheries-based management for this critical species.

@article{urbancsok_wood-specific_2025,
	title = {Wood-specific modification of glucuronoxylan can enhance growth in {Populus}},
	issn = {0022-0957},
	url = {https://doi.org/10.1093/jxb/eraf364},
	doi = {10.1093/jxb/eraf364},
	abstract = {Xylem cells are surrounded by primary and secondary cell walls. Formation of primary walls is regulated by the cell wall integrity surveillance system, but it is unclear if the deposition of secondary walls is similarly regulated. To study this question, we introduced to aspen three different enzymes cleaving cell wall-localized xylan and we suppressed xylan synthase components either ubiquitously or specifically during secondary wall formation using Populus trichocarpa GT43B promoter. When xylan was ubiquitously altered, 95\% of lines showed reduced growth, whereas when it was altered during secondary wall deposition, 30\% of lines grew better with the rest having no growth impairment, suggesting opposite effects of primary and secondary wall disturbances. To detect mechanism of growth stimulation by disturbed deposition of secondary wall, we analyzed changes in wood quality traits, chemistry, transcriptomics, metabolomics and hormonomics in transgenic lines. We found increased tension wood production, reduced S- and H-lignin, and changes in several metabolites in common in these lines. Remorin REM1.3 and NRL2 (NPH3 family) transcripts increased and changes in jasmonates, ABA and SA occurred in secondary wall-forming xylem suggesting their involvement in secondary wall integrity surveyance and signaling. The data indicate that a unique program mediates responses to secondary wall impairment that induces growth.},
	urldate = {2025-08-29},
	journal = {Journal of Experimental Botany},
	author = {Urbancsok, János and Donev, Evgeniy N and Derba-Maceluch, Marta and Sivan, Pramod and Barbut, Félix R and Mitra, Madhusree and Yassin, Zakiya and Cermanová, Kateřina and Šimura, Jan and Karady, Michal and Scheepers, Gerhard and Mellerowicz, Ewa J},
	month = aug,
	year = {2025},
	pages = {eraf364},
}

Xylem cells are surrounded by primary and secondary cell walls. Formation of primary walls is regulated by the cell wall integrity surveillance system, but it is unclear if the deposition of secondary walls is similarly regulated. To study this question, we introduced to aspen three different enzymes cleaving cell wall-localized xylan and we suppressed xylan synthase components either ubiquitously or specifically during secondary wall formation using Populus trichocarpa GT43B promoter. When xylan was ubiquitously altered, 95% of lines showed reduced growth, whereas when it was altered during secondary wall deposition, 30% of lines grew better with the rest having no growth impairment, suggesting opposite effects of primary and secondary wall disturbances. To detect mechanism of growth stimulation by disturbed deposition of secondary wall, we analyzed changes in wood quality traits, chemistry, transcriptomics, metabolomics and hormonomics in transgenic lines. We found increased tension wood production, reduced S- and H-lignin, and changes in several metabolites in common in these lines. Remorin REM1.3 and NRL2 (NPH3 family) transcripts increased and changes in jasmonates, ABA and SA occurred in secondary wall-forming xylem suggesting their involvement in secondary wall integrity surveyance and signaling. The data indicate that a unique program mediates responses to secondary wall impairment that induces growth.

@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.