Nature genetics最新文献_第2页

Toward clinical long-read genome sequencing for rare diseases 迈向罕见病临床长读基因组测序

IF 30.8 1区生物学

Nature genetics Pub Date : 2025-05-07 DOI: 10.1038/s41588-025-02160-y

Jesper Eisfeldt, Marlene Ek, Magnus Nordenskjöld, Anna Lindstrand

引用次数: 0

Middle Eastern genomes: new references for disease and population diversity studies 中东基因组：疾病和人口多样性研究的新参考文献

IF 31.7 1区生物学

Nature genetics Pub Date : 2025-05-05 DOI: 10.1038/s41588-025-02174-6

引用次数: 0

Near-complete Middle Eastern genomes refine autozygosity and enhance disease-causing and population-specific variant discovery 接近完整的中东基因组改进了自合子性，增强了致病和人群特异性变异的发现

IF 31.7 1区生物学

Nature genetics Pub Date : 2025-05-05 DOI: 10.1038/s41588-025-02173-7

Mohammadmersad Ghorbani, Shabir Moosa, Zenab Siddig, Radi Farhad, Haroon Naeem, William T. Harvey, Francesco Kumara Mastrorosa, Katherine M. Munson, Rozaimi Mohamad Razali, Elbay Aliyev, Ilhame Diboun, Rawan Abouelhassan, Melissa Tauro, Sondoss Hassan, Rebecca Mathew, Muna Al Hashmi, Lisa S. Mathew, Kun Wang, Abdul Rahman Salhab, Fazulur Rehaman Vempalli, Ahmed El Khouly, Qatar Genome Program Research Consortium, Iman Alazwani, Sara Tomei, Khalid A. Fakhro, Alia Satti, Ruba Benini, Arang Rhie, Evan E. Eichler, Younes Mokrab

{"title":"Near-complete Middle Eastern genomes refine autozygosity and enhance disease-causing and population-specific variant discovery","authors":"Mohammadmersad Ghorbani, Shabir Moosa, Zenab Siddig, Radi Farhad, Haroon Naeem, William T. Harvey, Francesco Kumara Mastrorosa, Katherine M. Munson, Rozaimi Mohamad Razali, Elbay Aliyev, Ilhame Diboun, Rawan Abouelhassan, Melissa Tauro, Sondoss Hassan, Rebecca Mathew, Muna Al Hashmi, Lisa S. Mathew, Kun Wang, Abdul Rahman Salhab, Fazulur Rehaman Vempalli, Ahmed El Khouly, Qatar Genome Program Research Consortium, Iman Alazwani, Sara Tomei, Khalid A. Fakhro, Alia Satti, Ruba Benini, Arang Rhie, Evan E. Eichler, Younes Mokrab","doi":"10.1038/s41588-025-02173-7","DOIUrl":"10.1038/s41588-025-02173-7","url":null,"abstract":"Advances in long-read sequencing have enabled routine complete assembly of human genomes, but much remains to be done to represent broader populations and show impact on disease-gene discovery. Here, we report highly accurate, near-complete and phased genomes from six Middle Eastern (ME) family trios (n = 18) with neurodevelopmental conditions, representing ancestries from Sudan, Jordan, Syria, Qatar and Afghanistan. These genomes revealed 42.2 Mb of new sequence (13.8% impacting known genes), 75 new HLA/KIR alleles and strong signals of inbreeding, with ROH covering up to one-third of chromosomes 6 and 12 in one individual. Using assembly-based variant calling, we identified 23 de novo and recessive variants as strong candidates for causing previously unresolved symptoms in the probands. The ME genomes revealed unique variation relative to existing references, showing enhanced mappability and variant calling. These results underscore the value of de novo assembly for disease variant discovery and the need for sampled ME-specific references to better characterize population-relevant variation. Generation and analysis of high-quality, genome assemblies from Middle Eastern trios demonstrate the utility of ancestry-matched data and assembly-based variation analysis.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"57 5","pages":"1119-1131"},"PeriodicalIF":31.7,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-025-02173-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143905440","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}

引用次数: 0

Genetic insights into infertility from large-scale analyses 从大规模分析中对不孕症的遗传见解

IF 31.7 1区生物学

Nature genetics Pub Date : 2025-04-30 DOI: 10.1038/s41588-025-02186-2

Katherine S. Ruth

引用次数: 0

Quantifying reproducible multivariate differential expression in genetic perturbation screens 基因干扰筛选中可重复多元差异表达的量化

IF 31.7 1区生物学

Nature genetics Pub Date : 2025-04-30 DOI: 10.1038/s41588-025-02177-3

Stefan Peidli

引用次数: 0

Insights into the evolution and genetic diversity of the Malus genus from pan-genome analysis 从泛基因组分析了解苹果属的进化和遗传多样性

IF 31.7 1区生物学

Nature genetics Pub Date : 2025-04-29 DOI: 10.1038/s41588-025-02171-9

引用次数: 0

Pangenome analysis reveals structural variation associated with seed size and weight traits in peanut 全基因组分析揭示了花生种子大小和重量性状的结构变异

IF 31.7 1区生物学

Nature genetics Pub Date : 2025-04-28 DOI: 10.1038/s41588-025-02170-w

Kunkun Zhao, Hongzhang Xue, Guowei Li, Annapurna Chitikineni, Yi Fan, Zenghui Cao, Xiaorui Dong, Huimin Lu, Kai Zhao, Lin Zhang, Ding Qiu, Rui Ren, Fangping Gong, Zhongfeng Li, Xingli Ma, Shubo Wan, Rajeev K. Varshney, Chaochun Wei, Dongmei Yin

{"title":"Pangenome analysis reveals structural variation associated with seed size and weight traits in peanut","authors":"Kunkun Zhao, Hongzhang Xue, Guowei Li, Annapurna Chitikineni, Yi Fan, Zenghui Cao, Xiaorui Dong, Huimin Lu, Kai Zhao, Lin Zhang, Ding Qiu, Rui Ren, Fangping Gong, Zhongfeng Li, Xingli Ma, Shubo Wan, Rajeev K. Varshney, Chaochun Wei, Dongmei Yin","doi":"10.1038/s41588-025-02170-w","DOIUrl":"10.1038/s41588-025-02170-w","url":null,"abstract":"Peanut (Arachis hypogaea L.) is an important oilseed and food legume crop, with seed size and weight being critical traits for domestication and breeding. However, genomic rearrangements like structural variations (SVs) underlying seed size and weight remain unclear. Here we present a comprehensive pangenome analysis utilizing eight high-quality genomes (two diploid wild, two tetraploid wild and four tetraploid cultivated peanuts) and resequencing data of 269 accessions with diverse seed sizes. We identified 22,222 core or soft-core, 22,232 distributed and 5,643 private gene families. The frequency of SVs in subgenome A is higher than in subgenome B. We identified 1,335 domestication-related SVs and 190 SVs associated with seed size or weight. Notably, a 275-bp deletion in gene AhARF2-2 results in loss of interaction with AhIAA13 and TOPLESS, reducing the inhibitory effect on AhGRF5 and promoting seed expansion. This high-quality pangenome serves as a fundamental resource for the genetic enhancement of peanuts and other legume crops. A graph-based peanut pangenome constructed using 6 newly assembled and 2 previously published genomes and 269 resequenced accessions highlights the contribution of structural variants to pod size.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"57 5","pages":"1250-1261"},"PeriodicalIF":31.7,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-025-02170-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143880419","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}

引用次数: 0

Oryza genome evolution through a tetraploid lens 水稻基因组通过四倍体透镜进化

IF 31.7 1区生物学

Nature genetics Pub Date : 2025-04-28 DOI: 10.1038/s41588-025-02183-5

Alice Fornasiero, Tao Feng, Noor Al-Bader, Aseel Alsantely, Saule Mussurova, Nam V. Hoang, Gopal Misra, Yong Zhou, Leonardo Fabbian, Nahed Mohammed, Luis Rivera Serna, Manjula Thimma, Victor Llaca, Praveena Parakkal, David Kudrna, Dario Copetti, Shanmugam Rajasekar, Seunghee Lee, Jayson Talag, Chandler Sobel-Sorenson, Marie-Christine Carpentier, Olivier Panaud, Kenneth L. McNally, Jianwei Zhang, Andrea Zuccolo, M. Eric Schranz, Rod A. Wing

{"title":"Oryza genome evolution through a tetraploid lens","authors":"Alice Fornasiero, Tao Feng, Noor Al-Bader, Aseel Alsantely, Saule Mussurova, Nam V. Hoang, Gopal Misra, Yong Zhou, Leonardo Fabbian, Nahed Mohammed, Luis Rivera Serna, Manjula Thimma, Victor Llaca, Praveena Parakkal, David Kudrna, Dario Copetti, Shanmugam Rajasekar, Seunghee Lee, Jayson Talag, Chandler Sobel-Sorenson, Marie-Christine Carpentier, Olivier Panaud, Kenneth L. McNally, Jianwei Zhang, Andrea Zuccolo, M. Eric Schranz, Rod A. Wing","doi":"10.1038/s41588-025-02183-5","DOIUrl":"10.1038/s41588-025-02183-5","url":null,"abstract":"Oryza is a remarkable genus comprising 27 species and 11 genome types, with ~3.4-fold genome size variation, that possesses a virtually untapped reservoir of genes that can be used for crop improvement and neodomestication. Here we present 11 chromosome-level assemblies (nine tetraploid, two diploid) in the context of ~15 million years of evolution and show that the core Oryza (sub)genome is only ~200 Mb and largely syntenic, whereas the remaining nuclear fractions (~80–600 Mb) are intermingled, plastic and rapidly evolving. For the halophyte Oryza coarctata, we found that despite detection of gene fractionation in the subgenomes, homoeologous genes were expressed at higher levels in one subgenome over the other in a mosaic form, demonstrating subgenome equivalence. The integration of these 11 new reference genomes with previously published genome datasets provides a nearly complete view of the consequences of evolution for genome diversification across the genus. Chromosome-level genome assemblies of nine tetraploid and two diploid wild Oryza species provide insights into genome evolution within the genus Oryza and the potential for crop improvement and neodomestication.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"57 5","pages":"1287-1297"},"PeriodicalIF":31.7,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-025-02183-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143880420","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}

引用次数: 0

A plant dual-kinase protein traps a pathogen effector to trigger immunity 植物双激酶蛋白捕获病原体效应物以触发免疫

IF 31.7 1区生物学

Nature genetics Pub Date : 2025-04-23 DOI: 10.1038/s41588-025-02176-4

引用次数: 0

Pan-genomic analysis highlights genes associated with agronomic traits and enhances genomics-assisted breeding in alfalfa 泛基因组分析突出了与苜蓿农艺性状相关的基因，增强了基因组学辅助育种

IF 31.7 1区生物学

Nature genetics Pub Date : 2025-04-23 DOI: 10.1038/s41588-025-02164-8

Fei He, Shuai Chen, Yangyang Zhang, Kun Chai, Qing Zhang, Weilong Kong, Shenyang Qu, Lin Chen, Fan Zhang, Mingna Li, Xue Wang, Huigang Lv, Tiejun Zhang, Xiaofan He, Xiao Li, Yajing Li, Xianyang Li, Xueqian Jiang, Ming Xu, Bilig Sod, Junmei Kang, Xingtan Zhang, Ruicai Long, Qingchuan Yang

{"title":"Pan-genomic analysis highlights genes associated with agronomic traits and enhances genomics-assisted breeding in alfalfa","authors":"Fei He, Shuai Chen, Yangyang Zhang, Kun Chai, Qing Zhang, Weilong Kong, Shenyang Qu, Lin Chen, Fan Zhang, Mingna Li, Xue Wang, Huigang Lv, Tiejun Zhang, Xiaofan He, Xiao Li, Yajing Li, Xianyang Li, Xueqian Jiang, Ming Xu, Bilig Sod, Junmei Kang, Xingtan Zhang, Ruicai Long, Qingchuan Yang","doi":"10.1038/s41588-025-02164-8","DOIUrl":"10.1038/s41588-025-02164-8","url":null,"abstract":"Alfalfa (Medicago sativa L.), a globally important forage crop, is valued for its high nutritional quality and nitrogen-fixing capacity. Here, we present a high-quality pan-genome constructed from 24 diverse alfalfa accessions, encompassing a wide range of genetic backgrounds. This comprehensive analysis identified 433,765 structural variations and characterized 54,002 pan-gene families, highlighting the pivotal role of genomic diversity in alfalfa domestication and adaptation. Key structural variations associated with salt tolerance and quality traits were discovered, with functional analysis implicating genes such as MsMAP65 and MsGA3ox1. Notably, overexpression of MsGA3ox1 led to a reduced stem–leaf ratio and enhanced forage quality. The integration of genomic selection and marker-assisted breeding strategies improved genomic estimated breeding values across multiple traits, offering valuable genomic resources for advancing alfalfa breeding. These findings provide insights into the genetic basis of important agronomic traits and establish a solid foundation for future crop improvement. Pan-genome analysis of 24 alfalfa accessions identifies key structural variations associated with salt tolerance and quality traits and provides resources for genomics-assisted breeding in alfalfa.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"57 5","pages":"1262-1273"},"PeriodicalIF":31.7,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143862802","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