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The landscape of N6-methyladenosine in localized primary prostate cancer
IF 30.8 1区 生物学
Nature genetics Pub Date : 2025-03-24 DOI: 10.1038/s41588-025-02128-y
Xin Xu, Helen Zhu, Rupert Hugh-White, Julie Livingstone, Stefan Eng, Nicole Zeltser, Yujuan Wang, Kinga Pajdzik, Sujun Chen, Kathleen E. Houlahan, Wenqin Luo, Shun Liu, Xi Xu, Minzhi Sheng, Wang Yuan Guo, Jaron Arbet, Yuxi Song, Miranda Wang, Yong Zeng, Shiyan Wang, Guanghui Zhu, Tingxiao Gao, Wei Chen, Xinpei Ci, Wenjie Xu, Kexin Xu, Michele Orain, Valerie Picard, Helene Hovington, Alain Bergeron, Louis Lacombe, Bernard Têtu, Yves Fradet, Mathieu Lupien, Gong-Hong Wei, Marianne Koritzinsky, Robert G. Bristow, Neil E. Fleshner, Xue Wu, Yang Shao, Chuan He, Alejandro Berlin, Theodorus van der Kwast, Hon Leong, Paul C. Boutros, Housheng Hansen He
{"title":"The landscape of N6-methyladenosine in localized primary prostate cancer","authors":"Xin Xu, Helen Zhu, Rupert Hugh-White, Julie Livingstone, Stefan Eng, Nicole Zeltser, Yujuan Wang, Kinga Pajdzik, Sujun Chen, Kathleen E. Houlahan, Wenqin Luo, Shun Liu, Xi Xu, Minzhi Sheng, Wang Yuan Guo, Jaron Arbet, Yuxi Song, Miranda Wang, Yong Zeng, Shiyan Wang, Guanghui Zhu, Tingxiao Gao, Wei Chen, Xinpei Ci, Wenjie Xu, Kexin Xu, Michele Orain, Valerie Picard, Helene Hovington, Alain Bergeron, Louis Lacombe, Bernard Têtu, Yves Fradet, Mathieu Lupien, Gong-Hong Wei, Marianne Koritzinsky, Robert G. Bristow, Neil E. Fleshner, Xue Wu, Yang Shao, Chuan He, Alejandro Berlin, Theodorus van der Kwast, Hon Leong, Paul C. Boutros, Housheng Hansen He","doi":"10.1038/s41588-025-02128-y","DOIUrl":"https://doi.org/10.1038/s41588-025-02128-y","url":null,"abstract":"<p><i>N</i><sup>6</sup>-methyladenosine (m<sup>6</sup>A), the most abundant internal RNA modification in humans, regulates most aspects of RNA processing. Prostate cancer is characterized by widespread transcriptomic dysregulation; therefore, we characterized the m<sup>6</sup>A landscape of 162 localized prostate tumors with matched DNA, RNA and protein profiling. m<sup>6</sup>A abundance varied dramatically across tumors, with global patterns emerging via complex germline–somatic cooperative regulation. Individual germline polymorphisms regulated m<sup>6</sup>A abundance, cooperating with somatic mutation of cancer driver genes and m<sup>6</sup>A regulators. The resulting complex patterns were associated with prognostic clinical features and established the biomarker potential of global and locus-specific m<sup>6</sup>A patterns. Tumor hypoxia dysregulates m<sup>6</sup>A profiles, bridging prior genomic and proteomic observations. Specific m<sup>6</sup>A sites, such as those in <i>VCAN</i>, drive disease aggression, associating with poor outcomes, tumor growth and metastasis. m<sup>6</sup>A dysregulation is thus associated with key events in the natural history of prostate cancer: germline risk, microenvironmental dysregulation, somatic mutation and metastasis.</p>","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"9 1","pages":""},"PeriodicalIF":30.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143677657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reply to: An alternative model for maternal mtDNA inheritance
IF 30.8 1区 生物学
Nature genetics Pub Date : 2025-03-20 DOI: 10.1038/s41588-025-02150-0
William Lee, Angelica Zamudio-Ochoa, Gina Buchel, Petar Podlesniy, Nuria Marti Gutierrez, Aleksei Mikhalchenko, Ramon Trullas, Shoukhrat Mitalipov, Dmitry Temiakov
{"title":"Reply to: An alternative model for maternal mtDNA inheritance","authors":"William Lee, Angelica Zamudio-Ochoa, Gina Buchel, Petar Podlesniy, Nuria Marti Gutierrez, Aleksei Mikhalchenko, Ramon Trullas, Shoukhrat Mitalipov, Dmitry Temiakov","doi":"10.1038/s41588-025-02150-0","DOIUrl":"https://doi.org/10.1038/s41588-025-02150-0","url":null,"abstract":"<p><span>replying to</span> M. Alexeyev &amp; Y. Bai <b><i>Nature Genetics</i></b> https://doi.org/10.1038/s41588-025-02149-7 (2025)</p><p>The dogma of uniparental inheritance of mitochondrial DNA (mtDNA) represents a fascinating aspect of genetics and the evolution of all living organisms. The processes underlying this trait involve molecular mechanisms that act before and after oocyte fertilization. The former involves elimination of mtDNA during spermatogenesis, the process of sperm cell maturation<sup>1,2,3</sup>. Post-fertilization mechanisms include removal of sperm mitochondria through autophagy and ubiquitin-mediated proteolysis after the cell penetrates an oocyte<sup>4,5</sup>.</p>","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"91 1","pages":""},"PeriodicalIF":30.8,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143660365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
An alternative model for maternal mtDNA inheritance
IF 30.8 1区 生物学
Nature genetics Pub Date : 2025-03-20 DOI: 10.1038/s41588-025-02149-7
Mikhail Alexeyev, Yidong Bai
{"title":"An alternative model for maternal mtDNA inheritance","authors":"Mikhail Alexeyev, Yidong Bai","doi":"10.1038/s41588-025-02149-7","DOIUrl":"https://doi.org/10.1038/s41588-025-02149-7","url":null,"abstract":"<p><span>arising from</span> W. Lee et al. <i>Nature Genetics</i> https://doi.org/10.1038/s41588-023-01505-9 (2023)</p><p>The exact mechanism preventing paternal mitochondrial DNA (mtDNA) inheritance in humans remains unresolved. In their recent report, ‘Molecular basis for maternal inheritance of human mitochondrial DNA’, Lee et al. propose that this process is controlled by phosphorylation of the mitochondrial transcription factor A (TFAM) on two serine residues located in the matrix targeting sequence (MTS), which blocks this protein’s mitochondrial import, thus uncoating mtDNA and exposing it to attack and destruction by unspecified mitochondrial nuclease(s), which prevents paternal mtDNA from entering the oocyte during fertilization. We argue that the experimental evidence presented in the article is inconclusive and also supports an alternative possibility: that mtDNA turnover following the loss of expression of key mtDNA replication proteins might be responsible. Therefore, additional experimentation is needed to resolve the two competing mechanisms that align with the experimental data presented by Lee et al.</p>","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"124 1","pages":""},"PeriodicalIF":30.8,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661030","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A likelihood-based framework for demographic inference from genealogical trees
IF 30.8 1区 生物学
Nature genetics Pub Date : 2025-03-20 DOI: 10.1038/s41588-025-02129-x
Caoqi Fan, Jordan L. Cahoon, Bryan L. Dinh, Diego Ortega-Del Vecchyo, Christian D. Huber, Michael D. Edge, Nicholas Mancuso, Charleston W. K. Chiang
{"title":"A likelihood-based framework for demographic inference from genealogical trees","authors":"Caoqi Fan, Jordan L. Cahoon, Bryan L. Dinh, Diego Ortega-Del Vecchyo, Christian D. Huber, Michael D. Edge, Nicholas Mancuso, Charleston W. K. Chiang","doi":"10.1038/s41588-025-02129-x","DOIUrl":"https://doi.org/10.1038/s41588-025-02129-x","url":null,"abstract":"<p>The demographic history of a population underlies patterns of genetic variation and is encoded in the gene-genealogical trees of the sampled haplotypes. Here we propose a demographic inference framework called the genealogical likelihood (gLike). Our method uses a graph-based structure to summarize the relationships among all lineages in a gene-genealogical tree with all possible trajectories of population memberships through time and derives the full likelihood across trees under a parameterized demographic model. We show through simulations and empirical applications that for populations that have experienced multiple admixtures, gLike can accurately estimate dozens of demographic parameters, including ancestral population sizes, admixture timing and admixture proportions, and it outperforms conventional demographic inference methods using the site frequency spectrum. Taken together, our proposed gLike framework harnesses underused genealogical information to offer high sensitivity and accuracy in inferring complex demographies for humans and other species.</p>","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"91 1","pages":""},"PeriodicalIF":30.8,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143660367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A structured coalescent model reveals deep ancestral structure shared by all modern humans
IF 30.8 1区 生物学
Nature genetics Pub Date : 2025-03-18 DOI: 10.1038/s41588-025-02117-1
Trevor Cousins, Aylwyn Scally, Richard Durbin
{"title":"A structured coalescent model reveals deep ancestral structure shared by all modern humans","authors":"Trevor Cousins, Aylwyn Scally, Richard Durbin","doi":"10.1038/s41588-025-02117-1","DOIUrl":"https://doi.org/10.1038/s41588-025-02117-1","url":null,"abstract":"<p>Understanding the history of admixture events and population size changes leading to modern humans is central to human evolutionary genetics. Here we introduce a coalescence-based hidden Markov model, cobraa, that explicitly represents an ancestral population split and rejoin, and demonstrate its application on simulated and real data across multiple species. Using cobraa, we present evidence for an extended period of structure in the history of all modern humans, in which two ancestral populations that diverged ~1.5 million years ago came together in an admixture event ~300 thousand years ago, in a ratio of ~80:20%. Immediately after their divergence, we detect a strong bottleneck in the major ancestral population. We inferred regions of the present-day genome derived from each ancestral population, finding that material from the minority correlates strongly with distance to coding sequence, suggesting it was deleterious against the majority background. Moreover, we found a strong correlation between regions of majority ancestry and human–Neanderthal or human–Denisovan divergence, suggesting the majority population was also ancestral to those archaic humans.</p>","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"6 1","pages":""},"PeriodicalIF":30.8,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143640502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Quantitative characterization of cell niches in spatially resolved omics data
IF 30.8 1区 生物学
Nature genetics Pub Date : 2025-03-18 DOI: 10.1038/s41588-025-02120-6
Sebastian Birk, Irene Bonafonte-Pardàs, Adib Miraki Feriz, Adam Boxall, Eneritz Agirre, Fani Memi, Anna Maguza, Anamika Yadav, Erick Armingol, Rong Fan, Gonçalo Castelo-Branco, Fabian J. Theis, Omer Ali Bayraktar, Carlos Talavera-López, Mohammad Lotfollahi
{"title":"Quantitative characterization of cell niches in spatially resolved omics data","authors":"Sebastian Birk, Irene Bonafonte-Pardàs, Adib Miraki Feriz, Adam Boxall, Eneritz Agirre, Fani Memi, Anna Maguza, Anamika Yadav, Erick Armingol, Rong Fan, Gonçalo Castelo-Branco, Fabian J. Theis, Omer Ali Bayraktar, Carlos Talavera-López, Mohammad Lotfollahi","doi":"10.1038/s41588-025-02120-6","DOIUrl":"https://doi.org/10.1038/s41588-025-02120-6","url":null,"abstract":"<p>Spatial omics enable the characterization of colocalized cell communities that coordinate specific functions within tissues. These communities, or niches, are shaped by interactions between neighboring cells, yet existing computational methods rarely leverage such interactions for their identification and characterization. To address this gap, here we introduce NicheCompass, a graph deep-learning method that models cellular communication to learn interpretable cell embeddings that encode signaling events, enabling the identification of niches and their underlying processes. Unlike existing methods, NicheCompass quantitatively characterizes niches based on communication pathways and consistently outperforms alternatives. We show its versatility by mapping tissue architecture during mouse embryonic development and delineating tumor niches in human cancers, including a spatial reference mapping application. Finally, we extend its capabilities to spatial multi-omics, demonstrate cross-technology integration with datasets from different sequencing platforms and construct a whole mouse brain spatial atlas comprising 8.4 million cells, highlighting NicheCompass’ scalability. Overall, NicheCompass provides a scalable framework for identifying and analyzing niches through signaling events.</p>","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"125 1","pages":""},"PeriodicalIF":30.8,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143640506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project
IF 30.8 1区 生物学
Nature genetics Pub Date : 2025-03-17 DOI: 10.1038/s41588-025-02121-5
Lingzhao Fang, Jinyan Teng, Qing Lin, Zhonghao Bai, Shuli Liu, Dailu Guan, Bingjie Li, Yahui Gao, Yali Hou, Mian Gong, Zhangyuan Pan, Ying Yu, Emily L. Clark, Jacqueline Smith, Konrad Rawlik, Ruidong Xiang, Amanda J. Chamberlain, Michael E. Goddard, Mathew Littlejohn, Greger Larson, David E. MacHugh, John F. O’Grady, Peter Sørensen, Goutam Sahana, Mogens Sandø Lund, Zhihua Jiang, Xiangchun Pan, Wentao Gong, Haihan Zhang, Xi He, Yuebo Zhang, Ning Gao, Jun He, Guoqiang Yi, Yuwen Liu, Zhonglin Tang, Pengju Zhao, Yang Zhou, Liangliang Fu, Xiao Wang, Dan Hao, Lei Liu, Siqian Chen, Robert S. Young, Xia Shen, Charley Xia, Hao Cheng, Li Ma, John B. Cole, Ransom L. Baldwin, Cong-jun Li, Curtis P. Van Tassell, Benjamin D. Rosen, Nayan Bhowmik, Joan Lunney, Wansheng Liu, Leluo Guan, Xin Zhao, Eveline M. Ibeagha-Awemu, Yonglun Luo, Lin Lin, Oriol Canela-Xandri, Martijn F. L. Derks, Richard P. M. A. Crooijmans, Marta Gòdia, Ole Madsen, Martien A. M. Groenen, James E. Koltes, Christopher K. Tuggle, Fiona M. McCarthy, Dominique Rocha, Elisabetta Giuffra, Marcel Amills, Alex Clop, Maria Ballester, Gwenola Tosser-Klopp, Jing Li, Chao Fang, Ming Fang, Qishan Wang, Zhuocheng Hou, Qin Wang, Fuping Zhao, Lin Jiang, Guiping Zhao, Zhengkui Zhou, Rong Zhou, Hehe Liu, Juan Deng, Long Jin, Mingzhou Li, Delin Mo, Xiaohong Liu, Yaosheng Chen, Xiaolong Yuan, Jiaqi Li, Shuhong Zhao, Yi Zhang, Xiangdong Ding, Dongxiao Sun, Hui-Zeng Sun, Cong Li, Yu Wang, Yu Jiang, Dongdong Wu, Wenwen Wang, Xinzhong Fan, Qin Zhang, Kui Li, Hao Zhang, Ning Yang, Xiaoxiang Hu, Wen Huang, Jiuzhou Song, Yang Wu, Jian Yang, Weiwei Wu, Claudia Kasper, Xinfeng Liu, Xiaofei Yu, Leilei Cui, Xiang Zhou, Seyoung Kim, Wei Li, Hae Kyung Im, Edward S. Buckler, Bing Ren, Michael C. Schatz, Jingyi Jessica Li, Abraham A. Palmer, Laurent Frantz, Huaijun Zhou, Zhe Zhang, George E. Liu
{"title":"The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project","authors":"Lingzhao Fang, Jinyan Teng, Qing Lin, Zhonghao Bai, Shuli Liu, Dailu Guan, Bingjie Li, Yahui Gao, Yali Hou, Mian Gong, Zhangyuan Pan, Ying Yu, Emily L. Clark, Jacqueline Smith, Konrad Rawlik, Ruidong Xiang, Amanda J. Chamberlain, Michael E. Goddard, Mathew Littlejohn, Greger Larson, David E. MacHugh, John F. O’Grady, Peter Sørensen, Goutam Sahana, Mogens Sandø Lund, Zhihua Jiang, Xiangchun Pan, Wentao Gong, Haihan Zhang, Xi He, Yuebo Zhang, Ning Gao, Jun He, Guoqiang Yi, Yuwen Liu, Zhonglin Tang, Pengju Zhao, Yang Zhou, Liangliang Fu, Xiao Wang, Dan Hao, Lei Liu, Siqian Chen, Robert S. Young, Xia Shen, Charley Xia, Hao Cheng, Li Ma, John B. Cole, Ransom L. Baldwin, Cong-jun Li, Curtis P. Van Tassell, Benjamin D. Rosen, Nayan Bhowmik, Joan Lunney, Wansheng Liu, Leluo Guan, Xin Zhao, Eveline M. Ibeagha-Awemu, Yonglun Luo, Lin Lin, Oriol Canela-Xandri, Martijn F. L. Derks, Richard P. M. A. Crooijmans, Marta Gòdia, Ole Madsen, Martien A. M. Groenen, James E. Koltes, Christopher K. Tuggle, Fiona M. McCarthy, Dominique Rocha, Elisabetta Giuffra, Marcel Amills, Alex Clop, Maria Ballester, Gwenola Tosser-Klopp, Jing Li, Chao Fang, Ming Fang, Qishan Wang, Zhuocheng Hou, Qin Wang, Fuping Zhao, Lin Jiang, Guiping Zhao, Zhengkui Zhou, Rong Zhou, Hehe Liu, Juan Deng, Long Jin, Mingzhou Li, Delin Mo, Xiaohong Liu, Yaosheng Chen, Xiaolong Yuan, Jiaqi Li, Shuhong Zhao, Yi Zhang, Xiangdong Ding, Dongxiao Sun, Hui-Zeng Sun, Cong Li, Yu Wang, Yu Jiang, Dongdong Wu, Wenwen Wang, Xinzhong Fan, Qin Zhang, Kui Li, Hao Zhang, Ning Yang, Xiaoxiang Hu, Wen Huang, Jiuzhou Song, Yang Wu, Jian Yang, Weiwei Wu, Claudia Kasper, Xinfeng Liu, Xiaofei Yu, Leilei Cui, Xiang Zhou, Seyoung Kim, Wei Li, Hae Kyung Im, Edward S. Buckler, Bing Ren, Michael C. Schatz, Jingyi Jessica Li, Abraham A. Palmer, Laurent Frantz, Huaijun Zhou, Zhe Zhang, George E. Liu","doi":"10.1038/s41588-025-02121-5","DOIUrl":"https://doi.org/10.1038/s41588-025-02121-5","url":null,"abstract":"<p>Genetic mutation and drift, coupled with natural and human-mediated selection and migration, have produced a wide variety of genotypes and phenotypes in farmed animals. We here introduce the Farm Animal Genotype–Tissue Expression (FarmGTEx) Project, which aims to elucidate the genetic determinants of gene expression across 16 terrestrial and aquatic domestic species under diverse biological and environmental contexts. For each species, we aim to collect multiomics data, particularly genomics and transcriptomics, from 50 tissues of 1,000 healthy adults and 200 additional animals representing a specific context. This Perspective provides an overview of the priorities of FarmGTEx and advocates for coordinated strategies of data analysis and resource-sharing initiatives. FarmGTEx aims to serve as a platform for investigating context-specific regulatory effects, which will deepen our understanding of molecular mechanisms underlying complex phenotypes. The knowledge and insights provided by FarmGTEx will contribute to improving sustainable agriculture-based food systems, comparative biology and eventual human biomedicine.</p>","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"19 1","pages":""},"PeriodicalIF":30.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143635167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genomic analysis of 1,325 Camellia accessions sheds light on agronomic and metabolic traits for tea plant improvement
IF 30.8 1区 生物学
Nature genetics Pub Date : 2025-03-17 DOI: 10.1038/s41588-025-02135-z
Weilong Kong, Xiangrui Kong, Zhongqiang Xia, Xiaofeng Li, Fang Wang, Ruiyang Shan, Zhihui Chen, Xiaomei You, Yuanyan Zhao, Yanping Hu, Shiqin Zheng, Sitong Zhong, Shengcheng Zhang, Yanbing Zhang, Kaixing Fang, Yinghao Wang, Hui Liu, Yazhen Zhang, Xinlei Li, Hualing Wu, Guo-Bo Chen, Xingtan Zhang, Changsong Chen
{"title":"Genomic analysis of 1,325 Camellia accessions sheds light on agronomic and metabolic traits for tea plant improvement","authors":"Weilong Kong, Xiangrui Kong, Zhongqiang Xia, Xiaofeng Li, Fang Wang, Ruiyang Shan, Zhihui Chen, Xiaomei You, Yuanyan Zhao, Yanping Hu, Shiqin Zheng, Sitong Zhong, Shengcheng Zhang, Yanbing Zhang, Kaixing Fang, Yinghao Wang, Hui Liu, Yazhen Zhang, Xinlei Li, Hualing Wu, Guo-Bo Chen, Xingtan Zhang, Changsong Chen","doi":"10.1038/s41588-025-02135-z","DOIUrl":"https://doi.org/10.1038/s41588-025-02135-z","url":null,"abstract":"<p>The tea plant stands as a globally cherished nonalcoholic beverage crop, but the genetic underpinnings of important agronomic and metabolomic traits remain largely unexplored. Here we de novo deep resequenced 802 tea plants and their relative accessions globally. By integrating public <i>Camellia</i> accessions, we constructed a comprehensive genome-wide genetic variation map and annotated deleterious mutations for 1,325 accessions. Population genetic analyses provided insights into genetic divergence from its relatives, different evolutionary bottlenecks, interspecific introgression and conservation of wild relatives. Our findings suggest the pivotal role of southwest China as the origin of tea plants, revealing the genetic diversity and domestication status of ancient tea plants. Genome-wide association studies herein identified thousands of substantial associations with leaf shape and metabolite traits, pinpointing candidate genes for crucial agronomic and flavor traits. This study illuminates the tea plant’s evolution and provides references for tea plant design breeding.</p>","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"55 1","pages":""},"PeriodicalIF":30.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143635166","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A telomere-to-telomere genome assembly of cotton provides insights into centromere evolution and short-season adaptation
IF 30.8 1区 生物学
Nature genetics Pub Date : 2025-03-17 DOI: 10.1038/s41588-025-02130-4
Guanjing Hu, Zhenyu Wang, Zunzhe Tian, Kai Wang, Gaoxiang Ji, Xingxing Wang, Xianliang Zhang, Zhaoen Yang, Xuan Liu, Ruoyu Niu, De Zhu, Yuzhi Zhang, Lian Duan, Xueyuan Ma, Xianpeng Xiong, Jiali Kong, Xianjia Zhao, Ya Zhang, Junjie Zhao, Shoupu He, Corrinne E. Grover, Junji Su, Keyun Feng, Guangrun Yu, Jinlei Han, Xinshan Zang, Zhiqiang Wu, Weihua Pan, Jonathan F. Wendel, Xiongfeng Ma
{"title":"A telomere-to-telomere genome assembly of cotton provides insights into centromere evolution and short-season adaptation","authors":"Guanjing Hu, Zhenyu Wang, Zunzhe Tian, Kai Wang, Gaoxiang Ji, Xingxing Wang, Xianliang Zhang, Zhaoen Yang, Xuan Liu, Ruoyu Niu, De Zhu, Yuzhi Zhang, Lian Duan, Xueyuan Ma, Xianpeng Xiong, Jiali Kong, Xianjia Zhao, Ya Zhang, Junjie Zhao, Shoupu He, Corrinne E. Grover, Junji Su, Keyun Feng, Guangrun Yu, Jinlei Han, Xinshan Zang, Zhiqiang Wu, Weihua Pan, Jonathan F. Wendel, Xiongfeng Ma","doi":"10.1038/s41588-025-02130-4","DOIUrl":"https://doi.org/10.1038/s41588-025-02130-4","url":null,"abstract":"<p>Cotton (<i>Gossypium hirsutum</i> L.) is a key allopolyploid crop with global economic importance. Here we present a telomere-to-telomere assembly of the elite variety Zhongmian 113. Leveraging technologies including PacBio HiFi, Oxford Nanopore Technology (ONT) ultralong-read sequencing and Hi-C, our assembly surpasses previous genomes in contiguity and completeness, resolving 26 centromeric and 52 telomeric regions, 5S rDNA clusters and nucleolar organizer regions. A phylogenetically recent centromere repositioning on chromosome D08 was discovered specific to <i>G. hirsutum</i>, involving deactivation of an ancestral centromere and the formation of a unique, satellite repeat-based centromere. Genomic analyses evaluated favorable allele aggregation for key agronomic traits and uncovered an early-maturing haplotype derived from an 11 Mb pericentric inversion that evolved early during <i>G. hirsutum</i> domestication. Our study sheds light on the genomic origins of short-season adaptation, potentially involving introgression of an inversion from primitively domesticated forms, followed by subsequent haplotype differentiation in modern breeding programs.</p>","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"24 1","pages":""},"PeriodicalIF":30.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143635164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cross-ancestry and sex-stratified genome-wide association analyses of amygdala and subnucleus volumes
IF 30.8 1区 生物学
Nature genetics Pub Date : 2025-03-17 DOI: 10.1038/s41588-025-02136-y
Yuan Ji, Nana Liu, Yunjun Yang, Meiyun Wang, Jingliang Cheng, Wenzhen Zhu, Shijun Qiu, Zuojun Geng, Guangbin Cui, Yongqiang Yu, Weihua Liao, Hui Zhang, Bo Gao, Xiaojun Xu, Tong Han, Zhenwei Yao, Quan Zhang, Wen Qin, Feng Liu, Meng Liang, Sijia Wang, Qiang Xu, Jiayuan Xu, Jilian Fu, Peng Zhang, Wei Li, Dapeng Shi, Caihong Wang, Su Lui, Zhihan Yan, Feng Chen, Jing Zhang, Wen Shen, Yanwei Miao, Dawei Wang, Jia-Hong Gao, Xiaochu Zhang, Kai Xu, Xi-Nian Zuo, Longjiang Zhang, Zhaoxiang Ye, Mulin Jun Li, Junfang Xian, Bing Zhang, Chunshui Yu
{"title":"Cross-ancestry and sex-stratified genome-wide association analyses of amygdala and subnucleus volumes","authors":"Yuan Ji, Nana Liu, Yunjun Yang, Meiyun Wang, Jingliang Cheng, Wenzhen Zhu, Shijun Qiu, Zuojun Geng, Guangbin Cui, Yongqiang Yu, Weihua Liao, Hui Zhang, Bo Gao, Xiaojun Xu, Tong Han, Zhenwei Yao, Quan Zhang, Wen Qin, Feng Liu, Meng Liang, Sijia Wang, Qiang Xu, Jiayuan Xu, Jilian Fu, Peng Zhang, Wei Li, Dapeng Shi, Caihong Wang, Su Lui, Zhihan Yan, Feng Chen, Jing Zhang, Wen Shen, Yanwei Miao, Dawei Wang, Jia-Hong Gao, Xiaochu Zhang, Kai Xu, Xi-Nian Zuo, Longjiang Zhang, Zhaoxiang Ye, Mulin Jun Li, Junfang Xian, Bing Zhang, Chunshui Yu","doi":"10.1038/s41588-025-02136-y","DOIUrl":"https://doi.org/10.1038/s41588-025-02136-y","url":null,"abstract":"<p>The amygdala is a small but critical multi-nucleus structure for emotion, cognition and neuropsychiatric disorders. Although genetic associations with amygdala volumetric traits have been investigated in sex-combined European populations, cross-ancestry and sex-stratified analyses are lacking. Here we conducted cross-ancestry and sex-stratified genome-wide association analyses for 21 amygdala volumetric traits in 6,923 Chinese and 48,634 European individuals. We identified 191 variant–trait associations (<i>P</i> &lt; 2.38 × 10<sup>−9</sup>), including 47 new associations (12 new loci) in sex-combined univariate analyses and seven additional new loci in sex-combined and sex-stratified multivariate analyses. We identified 12 ancestry-specific and two sex-specific associations. The identified genetic variants include 16 fine-mapped causal variants and regulate amygdala and fetal brain gene expression. The variants were enriched for brain development and colocalized with mood, cognition and neuropsychiatric disorders. These results indicate that cross-ancestry and sex-stratified genetic association analyses may provide insight into the genetic architectures of amygdala and subnucleus volumes.</p>","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"499 1","pages":""},"PeriodicalIF":30.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143635168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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