@article{liang_pan-genome_2025,
	title = {Pan-{Genome} {Analysis} {Reveals} {Local} {Adaptation} to {Climate} {Driven} by {Introgression} in {Oak} {Species}},
	volume = {42},
	issn = {1537-1719},
	url = {https://doi.org/10.1093/molbev/msaf088},
	doi = {10.1093/molbev/msaf088},
	abstract = {The genetic base of local adaptation has been extensively studied in natural populations. However, a comprehensive genome-wide perspective on the contribution of structural variants (SVs) and adaptive introgression to local adaptation remains limited. In this study, we performed de novo assembly and annotation of 22 representative accessions of Quercus variabilis, identifying a total of 543,372 SVs. These SVs play crucial roles in shaping genomic structure and influencing gene expression. By analyzing range-wide genomic data, we identified both SNPs and SVs associated with local adaptation in Q. variabilis and Quercus acutissima. Notably, SV-outliers exhibit selection signals that did not overlap with SNP-outliers, indicating that SNP-based analyses may not detect the same candidate genes associated with SV-outliers. Remarkably, 29\%−37\% of candidate SNPs were located in a 250 kb region on chromosome 9, referred to as Chr9-ERF. This region contains 8 duplicated ethylene-responsive factor (ERF) genes, which may have contributed to local adaptation of Q. variabilis and Q. acutissima. We also found that a considerable number of candidate SNPs were shared between Q. variabilis and Q. acutissima in the Chr9-ERF region, suggesting a pattern of repeated selection. We further demonstrated that advantageous variants in this region were introgressed from western populations of Q. acutissima into Q. variabilis, providing compelling evidence that introgression facilitates local adaptation. This study offers a valuable genomic resource for future studies on oak species and highlights the importance of pan-genome analysis in understating mechanism driving adaptation and evolution.},
	number = {5},
	urldate = {2025-05-16},
	journal = {Molecular Biology and Evolution},
	author = {Liang, Yi-Ye and Liu, Hui and Lin, Qiong-Qiong and Shi, Yong and Zhou, Biao-Feng and Wang, Jing-Shu and Chen, Xue-Yan and Shen, Zhao and Qiao, Liang-Jing and Niu, Jing-Wei and Ling, Shao-Jun and Luo, Wen-Ji and Zhao, Wei and Liu, Jian-Feng and Kuang, Yuan-Wen and Ingvarsson, Pär K and Guo, Ya-Long and Wang, Baosheng},
	month = may,
	year = {2025},
	pages = {msaf088},
}

The genetic base of local adaptation has been extensively studied in natural populations. However, a comprehensive genome-wide perspective on the contribution of structural variants (SVs) and adaptive introgression to local adaptation remains limited. In this study, we performed de novo assembly and annotation of 22 representative accessions of Quercus variabilis, identifying a total of 543,372 SVs. These SVs play crucial roles in shaping genomic structure and influencing gene expression. By analyzing range-wide genomic data, we identified both SNPs and SVs associated with local adaptation in Q. variabilis and Quercus acutissima. Notably, SV-outliers exhibit selection signals that did not overlap with SNP-outliers, indicating that SNP-based analyses may not detect the same candidate genes associated with SV-outliers. Remarkably, 29%−37% of candidate SNPs were located in a 250 kb region on chromosome 9, referred to as Chr9-ERF. This region contains 8 duplicated ethylene-responsive factor (ERF) genes, which may have contributed to local adaptation of Q. variabilis and Q. acutissima. We also found that a considerable number of candidate SNPs were shared between Q. variabilis and Q. acutissima in the Chr9-ERF region, suggesting a pattern of repeated selection. We further demonstrated that advantageous variants in this region were introgressed from western populations of Q. acutissima into Q. variabilis, providing compelling evidence that introgression facilitates local adaptation. This study offers a valuable genomic resource for future studies on oak species and highlights the importance of pan-genome analysis in understating mechanism driving adaptation and evolution.

@article{koehler_node_2025,
	title = {Node of origin matters: comparative analysis of soil water limitation effects on nodal root anatomy in maize ({Zea} mays {L}.)},
	issn = {0305-7364},
	shorttitle = {Node of origin matters},
	url = {https://doi.org/10.1093/aob/mcaf075},
	doi = {10.1093/aob/mcaf075},
	urldate = {2025-05-16},
	journal = {Annals of Botany},
	author = {Koehler, Tina and Kim, Yunhee and Tung, Shu-Yin and Heymans, Adrien and Tyborski, Nicolas and Steiner, Franziska and Wild, Andreas J and Pausch, Johanna and Ahmed, Mutez A and Schneider, Hannah M},
	month = may,
	year = {2025},
	pages = {mcaf075},
}

@article{biancucci_mutations_2025,
	title = {Mutations in {HEADING} {DATE} 1 affect transcription and cell wall composition in rice},
	volume = {197},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiaf120},
	doi = {10.1093/plphys/kiaf120},
	abstract = {Plants utilize environmental information to modify their developmental trajectories for optimal survival and reproduction. Over a century ago, day length (photoperiod) was identified as a major factor influencing developmental transitions, particularly the shift from vegetative to reproductive growth. In rice (Oryza sativa), exposure to day lengths shorter than a critical threshold accelerates flowering, while longer days inhibit this process. This response is mediated by HEADING DATE 1 (Hd1), a zinc finger transcription factor that is central in the photoperiodic flowering network. Hd1 acts as a repressor of flowering under long days but functions as a promoter of flowering under short days. However, how global transcription of genes downstream of Hd1 changes in response to the photoperiod is still not fully understood. Furthermore, it is unclear whether Hd1 target genes are solely involved in flowering time control or mediate additional functions. In this study, we utilized RNA-Seq to analyze the transcriptome of hd1 mutants under both long and short day conditions. We identified genes involved in the phenylpropanoid pathway that are deregulated under long days in the mutant. Quantitative profiling of cell wall components and abiotic stress assays suggested that Hd1 is involved in processes considered unrelated to flowering control. This indicates that day length perception and responses are intertwined with physiological processes beyond flowering.},
	number = {4},
	urldate = {2025-05-09},
	journal = {Plant Physiology},
	author = {Biancucci, Marco and Chirivì, Daniele and Baldini, Alessio and Badenhorst, Eugene and Dobetti, Fabio and Khahani, Bahman and Formentin, Elide and Eguen, Tenai and Turck, Franziska and Moore, John P and Tavakol, Elahe and Wenkel, Stephan and Lo Schiavo, Fiorella and Ezquer, Ignacio and Brambilla, Vittoria and Horner, David and Chiara, Matteo and Perrella, Giorgio and Betti, Camilla and Fornara, Fabio},
	month = apr,
	year = {2025},
	pages = {kiaf120},
}

Plants utilize environmental information to modify their developmental trajectories for optimal survival and reproduction. Over a century ago, day length (photoperiod) was identified as a major factor influencing developmental transitions, particularly the shift from vegetative to reproductive growth. In rice (Oryza sativa), exposure to day lengths shorter than a critical threshold accelerates flowering, while longer days inhibit this process. This response is mediated by HEADING DATE 1 (Hd1), a zinc finger transcription factor that is central in the photoperiodic flowering network. Hd1 acts as a repressor of flowering under long days but functions as a promoter of flowering under short days. However, how global transcription of genes downstream of Hd1 changes in response to the photoperiod is still not fully understood. Furthermore, it is unclear whether Hd1 target genes are solely involved in flowering time control or mediate additional functions. In this study, we utilized RNA-Seq to analyze the transcriptome of hd1 mutants under both long and short day conditions. We identified genes involved in the phenylpropanoid pathway that are deregulated under long days in the mutant. Quantitative profiling of cell wall components and abiotic stress assays suggested that Hd1 is involved in processes considered unrelated to flowering control. This indicates that day length perception and responses are intertwined with physiological processes beyond flowering.

@article{asao_leaf_2025,
	title = {Leaf nonstructural carbohydrate residence time, not concentration, correlates with leaf functional traits following the leaf economic spectrum in woody plants},
	volume = {246},
	copyright = {© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.},
	issn = {1469-8137},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.20315},
	doi = {10.1111/nph.20315},
	abstract = {Nonstructural carbohydrate (NSC) concentrations might reflect the strategies described in the leaf economic spectrum (LES) due to their dependence on photosynthesis and respiration. We examined if NSC concentrations correlate with leaf structure, chemistry, and physiology traits for 114 species from 19 sites and 5 biomes around the globe. Total leaf NSC concentrations varied greatly from 16 to 199 mg g−1 dry mass and were mostly independent of leaf gas exchange and the LES traits. By contrast, leaf NSC residence time was shorter in species with higher rates of photosynthesis, following the fast-slow strategies in the LES. An average leaf held an amount of NSCs that could sustain one night of leaf respiration and could be replenished in just a few hours of photosynthesis under saturating light, indicating that most daily carbon gain is exported. Our results suggest that NSC export is clearly linked to the economics of return on resource investment.},
	language = {en},
	number = {4},
	urldate = {2025-05-09},
	journal = {New Phytologist},
	author = {Asao, Shinichi and Way, Danielle A. and Turnbull, Matthew H. and Stitt, Mark and McDowell, Nate G. and Reich, Peter B. and Bloomfield, Keith J. and Zaragoza-Castells, Joana and Creek, Danielle and O'Sullivan, Odhran and Crous, Kristine Y. and Egerton, John J.G. and Mirotchnick, Nicholas and Weerasinghe, Lasantha K. and Griffin, Kevin L. and Hurry, Vaughan and Meir, Patrick and Sitch, Stephen and Atkin, Owen K.},
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.20315},
	keywords = {export, leaf economic spectrum, leaf functional traits, nonstructural carbohydrate, residence time},
	pages = {1505--1519},
}

Nonstructural carbohydrate (NSC) concentrations might reflect the strategies described in the leaf economic spectrum (LES) due to their dependence on photosynthesis and respiration. We examined if NSC concentrations correlate with leaf structure, chemistry, and physiology traits for 114 species from 19 sites and 5 biomes around the globe. Total leaf NSC concentrations varied greatly from 16 to 199 mg g−1 dry mass and were mostly independent of leaf gas exchange and the LES traits. By contrast, leaf NSC residence time was shorter in species with higher rates of photosynthesis, following the fast-slow strategies in the LES. An average leaf held an amount of NSCs that could sustain one night of leaf respiration and could be replenished in just a few hours of photosynthesis under saturating light, indicating that most daily carbon gain is exported. Our results suggest that NSC export is clearly linked to the economics of return on resource investment.

@article{chubanava_nad_2025,
	title = {{NAD} depletion in skeletal muscle does not compromise muscle function or accelerate aging},
	issn = {1550-4131},
	url = {https://www.sciencedirect.com/science/article/pii/S1550413125002128},
	doi = {10.1016/j.cmet.2025.04.002},
	abstract = {Nicotinamide adenine dinucleotide (NAD) is a ubiquitous electron carrier essential for energy metabolism and post-translational modification of numerous regulatory proteins. Dysregulations of NAD metabolism are widely regarded as detrimental to health, with NAD depletion commonly implicated in aging. However, the extent to which cellular NAD concentration can decline without adverse consequences remains unclear. To investigate this, we generated a mouse model in which nicotinamide phosphoribosyltransferase (NAMPT)-mediated NAD+ biosynthesis was disrupted in adult skeletal muscle. The intervention resulted in an 85\% reduction in muscle NAD+ abundance while maintaining tissue integrity and functionality, as demonstrated by preserved muscle morphology, contractility, and exercise tolerance. This absence of functional impairments was further supported by intact mitochondrial respiratory capacity and unaltered muscle transcriptomic and proteomic profiles. Furthermore, lifelong NAD depletion did not accelerate muscle aging or impair whole-body metabolism. Collectively, these findings suggest that NAD depletion does not contribute to age-related decline in skeletal muscle function.},
	urldate = {2025-05-09},
	journal = {Cell Metabolism},
	author = {Chubanava, Sabina and Karavaeva, Iuliia and Ehrlich, Amy M. and Justicia, Roger M. and Basse, Astrid L. and Kulik, Ivan and Dalbram, Emilie and Ahwazi, Danial and Heaselgrave, Samuel R. and Trošt, Kajetan and Stocks, Ben and Hodek, Ondřej and Rodrigues, Raissa N. and Havelund, Jesper F. and Schlabs, Farina L. and Larsen, Steen and Yonamine, Caio Y. and Henriquez-Olguín, Carlos and Giustarini, Daniela and Rossi, Ranieri and Gerhart-Hines, Zachary and Moritz, Thomas and Zierath, Juleen R. and Sakamoto, Kei and Jensen, Thomas E. and Færgeman, Nils J. and Lavery, Gareth G. and Deshmukh, Atul S. and Treebak, Jonas T.},
	month = apr,
	year = {2025},
	keywords = {NAD biosynthesis, NAD metabolism, NAMPT, aging, epigenetic clock, exercise, mitochondrial supercomplexes, nicotinamide, reactive oxygen species, skeletal muscle},
}

Nicotinamide adenine dinucleotide (NAD) is a ubiquitous electron carrier essential for energy metabolism and post-translational modification of numerous regulatory proteins. Dysregulations of NAD metabolism are widely regarded as detrimental to health, with NAD depletion commonly implicated in aging. However, the extent to which cellular NAD concentration can decline without adverse consequences remains unclear. To investigate this, we generated a mouse model in which nicotinamide phosphoribosyltransferase (NAMPT)-mediated NAD+ biosynthesis was disrupted in adult skeletal muscle. The intervention resulted in an 85% reduction in muscle NAD+ abundance while maintaining tissue integrity and functionality, as demonstrated by preserved muscle morphology, contractility, and exercise tolerance. This absence of functional impairments was further supported by intact mitochondrial respiratory capacity and unaltered muscle transcriptomic and proteomic profiles. Furthermore, lifelong NAD depletion did not accelerate muscle aging or impair whole-body metabolism. Collectively, these findings suggest that NAD depletion does not contribute to age-related decline in skeletal muscle function.