@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.

@article{tian_plantlncboost_2025,
	title = {{PlantLncBoost}: key features for plant {lncRNA} identification and significant improvement in accuracy and generalization},
	copyright = {© 2025 The Author(s). New Phytologist © 2025 New Phytologist Foundation.},
	issn = {1469-8137},
	shorttitle = {{PlantLncBoost}},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/nph.70211},
	doi = {10.1111/nph.70211},
	abstract = {Long noncoding RNAs (lncRNAs) are critical regulators of numerous biological processes in plants. Nevertheless, their identification is challenging due to the low sequence conservation across various species. Existing computational methods for lncRNA identification often face difficulties in generalizing across diverse plant species, highlighting the need for more robust and versatile identification models. Here, we present PlantLncBoost, a novel computational tool designed to improve the generalization in plant lncRNA identification. By integrating advanced gradient boosting algorithms with comprehensive feature selection, our approach achieves both high accuracy and generalizability. We conducted an extensive analysis of 1662 features and identified three key features – ORF coverage, complex Fourier average, and atomic Fourier amplitude – that effectively distinguish lncRNAs from mRNAs. We assessed the performance of PlantLncBoost using comprehensive datasets from 20 plant species. The model exhibited exceptional performance, with an accuracy of 96.63\%, a sensitivity of 98.42\%, and a specificity of 94.93\%, significantly outperforming existing tools. Further analysis revealed that the features we selected effectively capture the differences between lncRNAs and mRNAs across a variety of plant species. PlantLncBoost represents a significant advancement in plant lncRNA identification. It is freely accessible on GitHub (https://github.com/xuechantian/PlantLncBoost) and has been integrated into a comprehensive analysis pipeline, Plant-LncRNA-pipeline v.2 (https://github.com/xuechantian/Plant-LncRNA-pipeline-v2).},
	language = {en},
	urldate = {2025-05-30},
	journal = {New Phytologist},
	author = {Tian, Xue-Chan and Nie, Shuai and Domingues, Douglas and Rossi Paschoal, Alexandre and Jiang, Li-Bo and Mao, Jian-Feng},
	month = may,
	year = {2025},
	note = {\_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/nph.70211},
	keywords = {Fourier transform, ORF coverage, feature selection, gradient boosting algorithms, long noncoding RNAs (lncRNAs), model selection},
}

Long noncoding RNAs (lncRNAs) are critical regulators of numerous biological processes in plants. Nevertheless, their identification is challenging due to the low sequence conservation across various species. Existing computational methods for lncRNA identification often face difficulties in generalizing across diverse plant species, highlighting the need for more robust and versatile identification models. Here, we present PlantLncBoost, a novel computational tool designed to improve the generalization in plant lncRNA identification. By integrating advanced gradient boosting algorithms with comprehensive feature selection, our approach achieves both high accuracy and generalizability. We conducted an extensive analysis of 1662 features and identified three key features – ORF coverage, complex Fourier average, and atomic Fourier amplitude – that effectively distinguish lncRNAs from mRNAs. We assessed the performance of PlantLncBoost using comprehensive datasets from 20 plant species. The model exhibited exceptional performance, with an accuracy of 96.63%, a sensitivity of 98.42%, and a specificity of 94.93%, significantly outperforming existing tools. Further analysis revealed that the features we selected effectively capture the differences between lncRNAs and mRNAs across a variety of plant species. PlantLncBoost represents a significant advancement in plant lncRNA identification. It is freely accessible on GitHub (https://github.com/xuechantian/PlantLncBoost) and has been integrated into a comprehensive analysis pipeline, Plant-LncRNA-pipeline v.2 (https://github.com/xuechantian/Plant-LncRNA-pipeline-v2).

@article{safronov_independent_2025,
	title = {Independent evolution of betulin biosynthesis in {Inonotus} obliquus},
	volume = {15},
	copyright = {2025 The Author(s)},
	issn = {2045-2322},
	url = {https://www.nature.com/articles/s41598-025-05414-1},
	doi = {10.1038/s41598-025-05414-1},
	abstract = {Chaga mushroom (Inonotus obliquus) is a fungal species in the family Hymenochaetaceae (Basidiomycota) and the causative agent of white rot decay in Betula species. We assembled a high-quality 50.7 Mbp genome from PacBio sequencing and identified a lineage-specific whole genome duplication event approximately 1.3 million years ago, which has contributed to a major increase in biochemical diversity in the species through preferential retention of cytochrome P450 superfamily members. Secondary metabolism has further evolved through small-scale segmental duplications, such as tandem duplications within fungal biosynthetic gene clusters. Metabolomic fingerprinting confirmed increased complexity in terpene biosynthesis chemistry compared to related species that lacked the duplication event. This metabolic diversity may have arisen from co-evolution with the primary host species, which evolved high betulin content in its bark 4–8 million years ago.},
	language = {en},
	number = {1},
	urldate = {2025-07-04},
	journal = {Scientific Reports},
	author = {Safronov, Omid and Bal, Güleycan Lutfullahoglu and Sipari, Nina and Wilkens, Maya and Safdari, Pezhman and Smolander, Olli-Pekka and Laine, Pia K. and Lihavainen, Jenna and Silvan, Niko and Rajaraman, Sitaram and Paulin, Lars G. and Teeri, Teemu H. and Auvinen, Petri and Sarjala, Tytti and Overmyer, Kirk and Richter, Uwe and Salojärvi, Jarkko},
	month = jul,
	year = {2025},
	note = {Publisher: Nature Publishing Group},
	keywords = {Coevolution, Genomics, Molecular evolution},
	pages = {21319},
}

Chaga mushroom (Inonotus obliquus) is a fungal species in the family Hymenochaetaceae (Basidiomycota) and the causative agent of white rot decay in Betula species. We assembled a high-quality 50.7 Mbp genome from PacBio sequencing and identified a lineage-specific whole genome duplication event approximately 1.3 million years ago, which has contributed to a major increase in biochemical diversity in the species through preferential retention of cytochrome P450 superfamily members. Secondary metabolism has further evolved through small-scale segmental duplications, such as tandem duplications within fungal biosynthetic gene clusters. Metabolomic fingerprinting confirmed increased complexity in terpene biosynthesis chemistry compared to related species that lacked the duplication event. This metabolic diversity may have arisen from co-evolution with the primary host species, which evolved high betulin content in its bark 4–8 million years ago.

@article{liu_genomic_2025,
	title = {Genomic insights into the evolution of {Chinese} sweetgum and its autumn leaf coloration},
	volume = {198},
	issn = {0032-0889},
	url = {https://doi.org/10.1093/plphys/kiaf218},
	doi = {10.1093/plphys/kiaf218},
	abstract = {Chinese sweetgum (Liquidambar formosana) is valued as a source of resin and timber and is an important ornamental tree due to its showy fall foliage. Here, we report the chromosome-level assembly of the Chinese sweetgum genome. Phylogenomic analyses showed the basal phylogenetic position of Chinese sweetgum in core eudicots. Comparative genomic analyses revealed that the well-known gamma event in the common ancestors of core eudicots is evident in the Chinese sweetgum genome, and ancestral triplicated blocks resulting from that event are more intact in Chinese sweetgum than in grapevine (Vitis vinifera). Because of its conserved genome structure, very slow rate of evolution, and basal phylogenetic position, the Chinese sweetgum genome is a good reference for comparative genome studies. Further, we reconstructed the entire metabolic pathway for anthocyanins and potential regulatory networks of autumn leaf coloration of this species via metabolomics and transcriptomics. The transcription factors LfMYB69, basic helix–loop–helix (LfbHLH4), and WD40-repeat (LfWDR1) may collectively regulate the transcription of anthocyanin biosynthetic genes. The regulation of chalcone synthase genes (LfCHS1-3) and dihydroflavonol 4-reductase genes (LfDFR1-2) by the LfMYB69–LfbHLH4–LfWDR1 complex was confirmed by luciferase assays. Epigenomic analyses revealed that 5 structural genes, including LfCHS1, and 2 regulatory LfMYBs are epigenetically regulated. This study expands our understanding of autumn leaf coloration and provides valuable genomic resources for comparative biology, breeding, and biotechnology.},
	number = {2},
	urldate = {2025-06-13},
	journal = {Plant Physiology},
	author = {Liu, Ping-Li and Jing, Zhao-Yang and Zhang, Ren-Gang and Chen, Ye and Zhu, Zhixin and Zhang, Xi and Jiang, Chen-Kun and Li, Ruili and Xie, Jian-Bo and Niu, Shihui and Zhang, Jinfeng and Kong, Lisheng and Zhao, Jian and Ma, Yongpeng and Zeisler-Diehl, Viktoria V and Schreiber, Lukas and Karahara, Ichirou and Mao, Jian-Feng and Jiao, Yuannian and Ge, Song and Lin, Jinxing},
	month = jun,
	year = {2025},
	pages = {kiaf218},
}

Chinese sweetgum (Liquidambar formosana) is valued as a source of resin and timber and is an important ornamental tree due to its showy fall foliage. Here, we report the chromosome-level assembly of the Chinese sweetgum genome. Phylogenomic analyses showed the basal phylogenetic position of Chinese sweetgum in core eudicots. Comparative genomic analyses revealed that the well-known gamma event in the common ancestors of core eudicots is evident in the Chinese sweetgum genome, and ancestral triplicated blocks resulting from that event are more intact in Chinese sweetgum than in grapevine (Vitis vinifera). Because of its conserved genome structure, very slow rate of evolution, and basal phylogenetic position, the Chinese sweetgum genome is a good reference for comparative genome studies. Further, we reconstructed the entire metabolic pathway for anthocyanins and potential regulatory networks of autumn leaf coloration of this species via metabolomics and transcriptomics. The transcription factors LfMYB69, basic helix–loop–helix (LfbHLH4), and WD40-repeat (LfWDR1) may collectively regulate the transcription of anthocyanin biosynthetic genes. The regulation of chalcone synthase genes (LfCHS1-3) and dihydroflavonol 4-reductase genes (LfDFR1-2) by the LfMYB69–LfbHLH4–LfWDR1 complex was confirmed by luciferase assays. Epigenomic analyses revealed that 5 structural genes, including LfCHS1, and 2 regulatory LfMYBs are epigenetically regulated. This study expands our understanding of autumn leaf coloration and provides valuable genomic resources for comparative biology, breeding, and biotechnology.

@article{li_ecophysiological_2025,
	title = {Ecophysiological transition mediated by hybridization in a hybrid pine species complex},
	issn = {2468-2659},
	url = {https://www.sciencedirect.com/science/article/pii/S2468265925000952},
	doi = {10.1016/j.pld.2025.05.009},
	abstract = {Hybridization is a driving force in ecological transitions and speciation, yet direct evidence linking it to adaptive differentiation in natural systems remains limited. This study evaluates the role of hybridization in the speciation of Pinus densata, a keystone forest species on the southeastern Tibetan Plateau. By creating artificial interspecific F1s and a long-term common garden experiment on the plateau, we provide in situ assessments on 44 growth and physiological traits across four seasons, along with RNA sequencing. We found significant phenotypic divergence between P. densata and its putative parental species P. tabuliformis and P. yunnanensis, with P. densata demonstrating superior growth and dynamic balance between photosynthesis and photoprotection. The F1s closely resembled P. densata in most traits. Gene expression revealed 19\%–10\% of 34,000 examined genes as differentially expressed in P. densata and F1s relative to mid-parent expression values. Both additive (4\%) and non-additive gene actions (5\%–6\% in F1s, 10\%–12\% in P. densata) were common, while transgressive expression occurred more frequently in the stabilized natural hybrids, illustrating transcriptomic reprogramming brought by hybridization and further divergence by natural selection. We provide compelling evidence for hybridization-derived phenotypic divergence at both physiological and gene expression levels that could have contributed to the adaptation of P. densata to high plateau habitat where both parental species have low fitness. The altered physiology and gene expression in hybrids serve both as a substrate for novel ecological adaptation and as a mechanism for the initiation of reproductive isolation.},
	urldate = {2025-07-04},
	journal = {Plant Diversity},
	author = {Li, Zhi-Chao and Xu, Chao-Qun and Zhao, Wei and Nie, Shuai and Bao, Yu-Tao and Liu, Hui and Xing, Zhen and Mao, Jian-Feng and Wang, Xiao-Ru},
	month = may,
	year = {2025},
	keywords = {Ecological divergence, Gene action, Homoploid hybrid speciation, Physiological traits, RNA-Seq, Tibetan plateau},
}

Hybridization is a driving force in ecological transitions and speciation, yet direct evidence linking it to adaptive differentiation in natural systems remains limited. This study evaluates the role of hybridization in the speciation of Pinus densata, a keystone forest species on the southeastern Tibetan Plateau. By creating artificial interspecific F1s and a long-term common garden experiment on the plateau, we provide in situ assessments on 44 growth and physiological traits across four seasons, along with RNA sequencing. We found significant phenotypic divergence between P. densata and its putative parental species P. tabuliformis and P. yunnanensis, with P. densata demonstrating superior growth and dynamic balance between photosynthesis and photoprotection. The F1s closely resembled P. densata in most traits. Gene expression revealed 19%–10% of 34,000 examined genes as differentially expressed in P. densata and F1s relative to mid-parent expression values. Both additive (4%) and non-additive gene actions (5%–6% in F1s, 10%–12% in P. densata) were common, while transgressive expression occurred more frequently in the stabilized natural hybrids, illustrating transcriptomic reprogramming brought by hybridization and further divergence by natural selection. We provide compelling evidence for hybridization-derived phenotypic divergence at both physiological and gene expression levels that could have contributed to the adaptation of P. densata to high plateau habitat where both parental species have low fitness. The altered physiology and gene expression in hybrids serve both as a substrate for novel ecological adaptation and as a mechanism for the initiation of reproductive isolation.