@article{wu_population_2025,
	title = {Population genomics of \textit{{Marchantia} polymorpha} subsp. \textit{ruderalis} reveals evidence of climate adaptation},
	volume = {35},
	issn = {0960-9822},
	url = {https://www.sciencedirect.com/science/article/pii/S0960982225000089},
	doi = {10.1016/j.cub.2025.01.008},
	abstract = {Sexual reproduction results in the development of haploid and diploid cell states during the life cycle. In bryophytes, the dominant multicellular haploid phase produces motile sperm that swim through water to the egg to effect fertilization from which a relatively small diploid phase develops. In angiosperms, the reduced multicellular haploid phase produces non-motile sperm that is delivered to the egg through a pollen tube to effect fertilization from which the dominant diploid phase develops. These different life cycle characteristics are likely to impact the distribution of genetic variation among populations. However, little is known about the distribution of genetic variation among wild populations of bryophytes. To investigate how genetic variation is distributed among populations of a bryophyte and to establish the foundation for population genetics research in bryophytes, we described the genetic diversity of collections of Marchantia polymorpha subsp. ruderalis, a cosmopolitan ruderal liverwort. We identified 78 genetically unique (non-clonal) from a total of 209 sequenced accessions collected from 37 sites in Europe and Japan. There was no detectable population structure among European populations but significant genetic differentiation between Japanese and European populations. By associating genetic variation across the genome with global climate data, we showed that temperature and precipitation influence the frequency of potentially adaptive alleles. This collection establishes the core of an experimental platform that exploits natural genetic variation to answer diverse questions in biology.},
	number = {5},
	urldate = {2025-03-28},
	journal = {Current Biology},
	author = {Wu, Shuangyang and Jandrasits, Katharina and Swarts, Kelly and Roetzer, Johannes and Akimcheva, Svetlana and Shimamura, Masaki and Hisanaga, Tetsuya and Berger, Frédéric and Dolan, Liam},
	month = mar,
	year = {2025},
	pages = {970--980.e3},
}

Sexual reproduction results in the development of haploid and diploid cell states during the life cycle. In bryophytes, the dominant multicellular haploid phase produces motile sperm that swim through water to the egg to effect fertilization from which a relatively small diploid phase develops. In angiosperms, the reduced multicellular haploid phase produces non-motile sperm that is delivered to the egg through a pollen tube to effect fertilization from which the dominant diploid phase develops. These different life cycle characteristics are likely to impact the distribution of genetic variation among populations. However, little is known about the distribution of genetic variation among wild populations of bryophytes. To investigate how genetic variation is distributed among populations of a bryophyte and to establish the foundation for population genetics research in bryophytes, we described the genetic diversity of collections of Marchantia polymorpha subsp. ruderalis, a cosmopolitan ruderal liverwort. We identified 78 genetically unique (non-clonal) from a total of 209 sequenced accessions collected from 37 sites in Europe and Japan. There was no detectable population structure among European populations but significant genetic differentiation between Japanese and European populations. By associating genetic variation across the genome with global climate data, we showed that temperature and precipitation influence the frequency of potentially adaptive alleles. This collection establishes the core of an experimental platform that exploits natural genetic variation to answer diverse questions in biology.

@article{ranade_metabolomic_2025,
	title = {Metabolomic profiling of shade response and in silico analysis of {PAL} homologs imply the potential presence of bifunctional ammonia lyases in conifers},
	volume = {177},
	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.70175},
	doi = {10.1111/ppl.70175},
	abstract = {Norway spruce and Scots pine show enhanced lignin synthesis under shade, along with differential expression of defense-related genes that render disease resilience. In general, phenylalanine (Phe) is the precursor for lignin synthesis in plants, and tyrosine (Tyr) forms an additional lignin precursor specifically in grasses. Phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) from the lignin biosynthesis pathway use either Phe or Tyr as precursors for lignin production, respectively. Grasses possess a bifunctional phenylalanine/tyrosine ammonia-lyase (PTAL) that potentially can use both Phe and Tyr for lignin biosynthesis. Metabolomic profiles of seedlings revealed higher levels of Phe and Tyr under shade in Scots pine, while Norway spruce showed differential regulation of only Tyr under shade. Sequence analysis and phylogeny of PAL homologs in the two conifers, coupled with correlation of up-regulation of precursors for lignin synthesis (Phe/Tyr) and enhanced lignin synthesis along with differential expression of PAL homologs under shade, suggest the potential presence of a bifunctional ammonia-lyases (BAL) in conifers. This finding is novel and comparable to PTALs in grasses. Exome sequence analysis revealed a latitudinal variation in allele frequencies of SNPs from coding regions of putative PAL and BAL in Norway spruce, which may impact enzyme activity affecting lignin synthesis. Metabolomic analysis additionally identified metabolites involved in plant immunity, defense and stress response.},
	language = {en},
	number = {2},
	urldate = {2025-03-28},
	journal = {Physiologia Plantarum},
	author = {Ranade, Sonali Sachin and García-Gil, María Rosario},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/ppl.70175},
	pages = {e70175},
}

Norway spruce and Scots pine show enhanced lignin synthesis under shade, along with differential expression of defense-related genes that render disease resilience. In general, phenylalanine (Phe) is the precursor for lignin synthesis in plants, and tyrosine (Tyr) forms an additional lignin precursor specifically in grasses. Phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) from the lignin biosynthesis pathway use either Phe or Tyr as precursors for lignin production, respectively. Grasses possess a bifunctional phenylalanine/tyrosine ammonia-lyase (PTAL) that potentially can use both Phe and Tyr for lignin biosynthesis. Metabolomic profiles of seedlings revealed higher levels of Phe and Tyr under shade in Scots pine, while Norway spruce showed differential regulation of only Tyr under shade. Sequence analysis and phylogeny of PAL homologs in the two conifers, coupled with correlation of up-regulation of precursors for lignin synthesis (Phe/Tyr) and enhanced lignin synthesis along with differential expression of PAL homologs under shade, suggest the potential presence of a bifunctional ammonia-lyases (BAL) in conifers. This finding is novel and comparable to PTALs in grasses. Exome sequence analysis revealed a latitudinal variation in allele frequencies of SNPs from coding regions of putative PAL and BAL in Norway spruce, which may impact enzyme activity affecting lignin synthesis. Metabolomic analysis additionally identified metabolites involved in plant immunity, defense and stress response.

@article{nair_elf3_2025,
	title = {{ELF3} coordinates temperature and photoperiodic control of seasonal growth in hybrid aspen},
	issn = {0960-9822},
	url = {https://www.cell.com/current-biology/abstract/S0960-9822(25)00190-3},
	doi = {10.1016/j.cub.2025.02.027},
	abstract = {{\textless}h2{\textgreater}Summary{\textless}/h2{\textgreater}{\textless}p{\textgreater}Timely growth cessation before winter is crucial for the survival of perennial plants in temperate and boreal regions. Short photoperiod (SP) and low temperature (LT) are major seasonal cues regulating growth cessation. SP, sensed in the leaves, initiates growth cessation by downregulating \textit{FLOWERING LOCUS T 2} \textit{(FT2)} expression, but how LT regulates seasonal growth is unclear. Genetic and cell biological approaches identified a hybrid aspen \textit{EARLY FLOWERING 3}(\textit{ELF3}) ortholog with a prion-like domain (PrLD) that undergoes LT-responsive phase separation as a key mediator of LT-induced growth cessation. In contrast with SP, LT acts independently of \textit{FT2} downregulation and targets the AIL1-BRC1 transcription factor network and hormonal pathways via ELF3 to induce growth cessation. Intriguingly, ELF3 also functions in SP-mediated growth cessation by downregulating \textit{FT2} in leaves. Our work thus reveals a previously unrecognized role of ELF3 in growth cessation and in coordinating temperature and photoperiodic pathways to enable robust adaptation to seasonal change.{\textless}/p{\textgreater}},
	language = {English},
	urldate = {2025-03-14},
	journal = {Current Biology},
	author = {Nair, Aswin and Maurya, Jay P. and Pandey, Shashank K. and Singh, Rajesh Kumar and Miskolczi, Pal C. and Aryal, Bibek and Bhalerao, Rishikesh P.},
	month = mar,
	year = {2025},
	pmid = {40054469},
	note = {Publisher: Elsevier},
}

\textlessh2\textgreaterSummary\textless/h2\textgreater\textlessp\textgreaterTimely growth cessation before winter is crucial for the survival of perennial plants in temperate and boreal regions. Short photoperiod (SP) and low temperature (LT) are major seasonal cues regulating growth cessation. SP, sensed in the leaves, initiates growth cessation by downregulating FLOWERING LOCUS T 2 (FT2) expression, but how LT regulates seasonal growth is unclear. Genetic and cell biological approaches identified a hybrid aspen EARLY FLOWERING 3(ELF3) ortholog with a prion-like domain (PrLD) that undergoes LT-responsive phase separation as a key mediator of LT-induced growth cessation. In contrast with SP, LT acts independently of FT2 downregulation and targets the AIL1-BRC1 transcription factor network and hormonal pathways via ELF3 to induce growth cessation. Intriguingly, ELF3 also functions in SP-mediated growth cessation by downregulating FT2 in leaves. Our work thus reveals a previously unrecognized role of ELF3 in growth cessation and in coordinating temperature and photoperiodic pathways to enable robust adaptation to seasonal change.\textless/p\textgreater

@article{holloway-phillips_is_2025,
	title = {Is {Photosynthesis}-{Derived} {NADPH} {Really} a {Source} of {2H}-{Depleted} {Hydrogen} in {Plant} {Compounds}?},
	copyright = {© 2025 John Wiley \& Sons Ltd.},
	issn = {1365-3040},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.15403},
	doi = {10.1111/pce.15403},
	abstract = {statement We provide evidence that photosynthetically produced NADPH is not the major source of 2H-depletion in carbohydrates.},
	urldate = {2025-01-31},
	journal = {Plant, Cell \& Environment},
	author = {Holloway-Phillips, Meisha and Tcherkez, Guillaume and Wieloch, Thomas and Lehmann, Marco M. and Werner, Roland A.},
	month = jan,
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.15403},
}

statement We provide evidence that photosynthetically produced NADPH is not the major source of 2H-depletion in carbohydrates.

@article{jonsson_asymmetry_2025,
	title = {The asymmetry engine: how plants harness asymmetries to shape their bodies},
	volume = {245},
	copyright = {© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.},
	issn = {1469-8137},
	shorttitle = {The asymmetry engine},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20413},
	doi = {10.1111/nph.20413},
	abstract = {Plant development depends on growth asymmetry to establish body plans and adapt to environmental stimuli. We explore how plants initiate, propagate, and regulate organ-wide growth asymmetries. External cues, such as light and gravity, and internal signals, including stochastic cellular growth variability, drive these asymmetries. The plant hormone auxin orchestrates growth asymmetry through its distribution and transport. Mechanochemical feedback loops, exemplified by apical hook formation, further amplify growth asymmetries, illustrating the dynamic interplay between biochemical signals and physical forces. Growth asymmetry itself can serve as a continuous cue, influencing subsequent growth decisions. By examining specific cellular programs and their responses to asymmetric cues, we propose that the decision to either amplify or dampen these asymmetries is key to shaping plant organs.},
	language = {en},
	number = {6},
	urldate = {2025-01-31},
	journal = {New Phytologist},
	author = {Jonsson, Kristoffer and Routier-Kierzkowska, Anne-Lise and Bhalerao, Rishikesh P.},
	month = jan,
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20413},
	keywords = {auxin, cell wall, development, feedback mechanisms, growth coordination, mechanics, morphogenesis, tropism},
	pages = {2422--2427},
}

Plant development depends on growth asymmetry to establish body plans and adapt to environmental stimuli. We explore how plants initiate, propagate, and regulate organ-wide growth asymmetries. External cues, such as light and gravity, and internal signals, including stochastic cellular growth variability, drive these asymmetries. The plant hormone auxin orchestrates growth asymmetry through its distribution and transport. Mechanochemical feedback loops, exemplified by apical hook formation, further amplify growth asymmetries, illustrating the dynamic interplay between biochemical signals and physical forces. Growth asymmetry itself can serve as a continuous cue, influencing subsequent growth decisions. By examining specific cellular programs and their responses to asymmetric cues, we propose that the decision to either amplify or dampen these asymmetries is key to shaping plant organs.