{"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":"10.1038/s41588-025-02135-z","url":null,"abstract":"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 Camellia 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. This study provides a de novo resequencing of 802 Camellia accessions and a genome-wide variation map. Genome-wide association study (GWAS) and metabolite GWAS identify genes responsible for crucial agronomic and flavor traits.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"57 4","pages":"997-1007"},"PeriodicalIF":31.7,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-025-02135-z.pdf","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":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature geneticsPub Date : 2025-03-17DOI: 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":"10.1038/s41588-025-02130-4","url":null,"abstract":"Cotton (Gossypium hirsutum 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 G. hirsutum, 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 G. hirsutum 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. A telomere-to-telomere genome assembly of the elite Gossypium hirsutum variety ZM113 provides insights into upland cotton short-season adaptation and identifies a repositioned, satellite repeat-rich centromere.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"57 4","pages":"1031-1043"},"PeriodicalIF":31.7,"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}
{"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, the CHIMGEN Consortium","doi":"10.1038/s41588-025-02136-y","DOIUrl":"10.1038/s41588-025-02136-y","url":null,"abstract":"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 (P < 2.38 × 10−9), 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. Cross-ancestry and sex-stratified genome-wide association analyses for 21 amygdala volumetric traits in East Asian and European individuals provide insight into the genetic architectures of amygdala and subnucleus volumes.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"57 4","pages":"839-850"},"PeriodicalIF":31.7,"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}
Nature geneticsPub Date : 2025-03-11DOI: 10.1038/s41588-025-02076-7
{"title":"Unraveling the role of succinyl-CoA in tumor immunity","authors":"","doi":"10.1038/s41588-025-02076-7","DOIUrl":"10.1038/s41588-025-02076-7","url":null,"abstract":"The study highlights the crucial role of succinyl-CoA in tumor immunity by inducing the succinylation of PD-L1. We identified the succinyltransferase CPT1A as a potential therapeutic target. CPT1A could be a valuable biomarker for evaluating the efficacy of anti-PD-1 therapy and suggests a promising treatment strategy.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"57 3","pages":"496-497"},"PeriodicalIF":31.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143589831","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}
Nature geneticsPub Date : 2025-03-11DOI: 10.1038/s41588-025-02114-4
{"title":"Revealing the distinct genomic features of Japanese soybeans","authors":"","doi":"10.1038/s41588-025-02114-4","DOIUrl":"10.1038/s41588-025-02114-4","url":null,"abstract":"Japanese soybeans have been bred for centuries for traditional soy-based food production. A pangenome study using genome data from 462 soybeans worldwide revealed distinct genomic features in Japanese soybeans, as well as several quantitative trait loci alleles that are important for breeding cultivars suited to traditional soy-based foods.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"57 4","pages":"784-785"},"PeriodicalIF":31.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143599060","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}
Nature geneticsPub Date : 2025-03-11DOI: 10.1038/s41588-025-02077-6
Long Liang, Xinwei Kuang, Yi He, Lin Zhu, Poyee Lau, Xin Li, Dingan Luo, Lan Gong, Wenbin Zhou, Fanglin Zhang, Xiaowei Liang, Zhuofeng Li, Bin Hu, Dandan Liu, Tao Ding, Hui Li, Shuang Zhao, Juan Su, Mien-Chie Hung, Jing Liu, Hong Liu, Xiang Chen
{"title":"Alterations in PD-L1 succinylation shape anti-tumor immune responses in melanoma","authors":"Long Liang, Xinwei Kuang, Yi He, Lin Zhu, Poyee Lau, Xin Li, Dingan Luo, Lan Gong, Wenbin Zhou, Fanglin Zhang, Xiaowei Liang, Zhuofeng Li, Bin Hu, Dandan Liu, Tao Ding, Hui Li, Shuang Zhao, Juan Su, Mien-Chie Hung, Jing Liu, Hong Liu, Xiang Chen","doi":"10.1038/s41588-025-02077-6","DOIUrl":"10.1038/s41588-025-02077-6","url":null,"abstract":"Tumors undergo metabolic reprogramming to meet the energetic, synthetic and redox demands essential for malignancy, often characterized by increased glycolysis and lactate production. However, the role of mitochondrial metabolism in tumor immunity remains unclear. The present study integrates spatial transcriptomics, bulk transcriptomics and proteomics, revealing a strong link between the metabolite succinyl-CoA and tumor immunity as well as the efficacy of anti-programmed cell death protein-1 (PD-1) therapy in patients with melanoma. Elevated succinyl-CoA levels, through α-ketoglutarate or succinate supplementation, enhanced T cell-mediated tumor elimination, both in vitro and in vivo. Mechanistically, succinylation of the ligand of PD-1 (PD-L1) at lysine 129 led to its degradation. Increased carnitine palmitoyltransferase 1A (CPT1A), identified as a succinyltransferase for PD-L1, boosted anti-tumor activity. Preclinically, bezafibrate, a hyperlipidemia drug, upregulated CPT1A and synergized with CTLA-4 monoclonal antibody to inhibit tumor growth. Clinically, higher PD-L1 and lower CPT1A levels in tumors correlated with better anti-PD-1 therapy responses, suggesting potential biomarkers for prediction of treatment efficacy. Succinylation of PD-L1 by carnitine palmitoyltransferase 1A (CPT1A) in melanoma leads to its degradation and enhanced T cell-dependent killing in vitro. Increasing CPT1A levels synergizes with anti-CTLA-4 treatment to suppress tumor growth in a mouse melanoma model.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"57 3","pages":"680-693"},"PeriodicalIF":31.7,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-025-02077-6.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143589833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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