Pub Date : 2025-12-15DOI: 10.1038/s41576-025-00917-z
Genomic approaches have transformed how we study microorganisms, which shape nearly every aspect of life on Earth. This Focus issue explores the methods and insights gained from the application of microbial genomics within ecological and evolutionary contexts. Microbial genomics has yielded transformative insights into the ecology and evolution of microorganisms. Nature Reviews Genetics presents a Focus issue that explores how genomic approaches reveal microbial dynamics across ecological and evolutionary contexts.
{"title":"Microbial ecology and evolution in the genomics era","authors":"","doi":"10.1038/s41576-025-00917-z","DOIUrl":"10.1038/s41576-025-00917-z","url":null,"abstract":"Genomic approaches have transformed how we study microorganisms, which shape nearly every aspect of life on Earth. This Focus issue explores the methods and insights gained from the application of microbial genomics within ecological and evolutionary contexts. Microbial genomics has yielded transformative insights into the ecology and evolution of microorganisms. Nature Reviews Genetics presents a Focus issue that explores how genomic approaches reveal microbial dynamics across ecological and evolutionary contexts.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"27 1","pages":"1-2"},"PeriodicalIF":52.0,"publicationDate":"2025-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41576-025-00917-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145754667","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}
Pub Date : 2025-12-03DOI: 10.1038/s41576-025-00912-4
Kelly E. Blevins, María C. Ávila-Arcos, Verena J. Schuenemann, Anne C. Stone
Pathogen emergence and adaptation are constant, but the mechanisms underlying pathogen success as well as host susceptibility and resistance are often only observable in time series data. Ancient DNA research of pathogens and their hosts provides unique insights into past occurrences, including the changes that led to pathogen jumps between animals and humans, pandemic outbreaks, the timing of such events and the genetic, cultural and ecological factors that affect pathogen success and human survival and recovery. Recent technological improvements and the increasing number of ancient samples analysed have enabled the unprecedented investigation of pathogen evolution. Such studies are poised to benefit from the increased diversity of sequenced ancient pathogens, adoption of a broader framework that considers the entire ecosystem of host–pathogen interactions and growing collaboration with related fields. Ancient DNA techniques are being applied to study increasingly diverse pathogens of the past. The authors review the latest insights into pathogen–host coevolution, zoonotic events and the spread of pathogens, all while highlighting the importance of a One Health approach to this research.
{"title":"Ancient DNA insights into diverse pathogens and their hosts","authors":"Kelly E. Blevins, María C. Ávila-Arcos, Verena J. Schuenemann, Anne C. Stone","doi":"10.1038/s41576-025-00912-4","DOIUrl":"10.1038/s41576-025-00912-4","url":null,"abstract":"Pathogen emergence and adaptation are constant, but the mechanisms underlying pathogen success as well as host susceptibility and resistance are often only observable in time series data. Ancient DNA research of pathogens and their hosts provides unique insights into past occurrences, including the changes that led to pathogen jumps between animals and humans, pandemic outbreaks, the timing of such events and the genetic, cultural and ecological factors that affect pathogen success and human survival and recovery. Recent technological improvements and the increasing number of ancient samples analysed have enabled the unprecedented investigation of pathogen evolution. Such studies are poised to benefit from the increased diversity of sequenced ancient pathogens, adoption of a broader framework that considers the entire ecosystem of host–pathogen interactions and growing collaboration with related fields. Ancient DNA techniques are being applied to study increasingly diverse pathogens of the past. The authors review the latest insights into pathogen–host coevolution, zoonotic events and the spread of pathogens, all while highlighting the importance of a One Health approach to this research.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"27 1","pages":"96-111"},"PeriodicalIF":52.0,"publicationDate":"2025-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145664343","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}
Pub Date : 2025-12-01DOI: 10.1038/s41576-025-00924-0
Shubham Khetan
In this Tools of the Trade article, Shubham Khetan presents PADIT-seq (protein affinity to DNA by in vitro transcription and RNA sequencing), which enables the reliable identification of low-affinity DNA binding sites for transcription factors.
{"title":"Detecting transcription factor binding sites with PADIT-seq","authors":"Shubham Khetan","doi":"10.1038/s41576-025-00924-0","DOIUrl":"10.1038/s41576-025-00924-0","url":null,"abstract":"In this Tools of the Trade article, Shubham Khetan presents PADIT-seq (protein affinity to DNA by in vitro transcription and RNA sequencing), which enables the reliable identification of low-affinity DNA binding sites for transcription factors.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"27 2","pages":"114-114"},"PeriodicalIF":52.0,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145644915","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}
Pub Date : 2025-11-28DOI: 10.1038/s41576-025-00918-y
J. Pamela Engelberts, Gene W. Tyson
Technical challenges and high costs remain barriers to the widespread application of microbial single-cell genomics. However, combining meta-omics approaches with single-cell genomics provides new opportunities to better understand microbial diversity, function and community dynamics. Engelberts and Tyson discuss the potential and challenges of microbial single-cell genomics, emphasizing the integration of single-cell omics and meta-omics data as a promising opportunity to reveal the ecological and evolutionary processes that shape microbial communities.
{"title":"Understanding microbial ecology and evolution with single-cell genomics","authors":"J. Pamela Engelberts, Gene W. Tyson","doi":"10.1038/s41576-025-00918-y","DOIUrl":"10.1038/s41576-025-00918-y","url":null,"abstract":"Technical challenges and high costs remain barriers to the widespread application of microbial single-cell genomics. However, combining meta-omics approaches with single-cell genomics provides new opportunities to better understand microbial diversity, function and community dynamics. Engelberts and Tyson discuss the potential and challenges of microbial single-cell genomics, emphasizing the integration of single-cell omics and meta-omics data as a promising opportunity to reveal the ecological and evolutionary processes that shape microbial communities.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"27 1","pages":"3-4"},"PeriodicalIF":52.0,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145611565","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}
Pub Date : 2025-11-28DOI: 10.1038/s41576-025-00908-0
Yon Ho Jee, Yixuan He, Wenhan Lu, Yue Shi, Daniel Lazarev, Mark J. Daly, Mary Pat Reeve, Alicia R. Martin
{"title":"Dissecting pleiotropy to gain mechanistic insights into human disease","authors":"Yon Ho Jee, Yixuan He, Wenhan Lu, Yue Shi, Daniel Lazarev, Mark J. Daly, Mary Pat Reeve, Alicia R. Martin","doi":"10.1038/s41576-025-00908-0","DOIUrl":"https://doi.org/10.1038/s41576-025-00908-0","url":null,"abstract":"","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"175 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145611566","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}
Pub Date : 2025-11-10DOI: 10.1038/s41576-025-00913-3
Shaoqian Ma
In this Tools of the Trade article, Shaoqian Ma discusses scFLUENT-seq, a method that enables quantitative, genome-wide analysis of nascent transcription in single cells.
{"title":"Nascent transcription quantification with scFLUENT-seq","authors":"Shaoqian Ma","doi":"10.1038/s41576-025-00913-3","DOIUrl":"10.1038/s41576-025-00913-3","url":null,"abstract":"In this Tools of the Trade article, Shaoqian Ma discusses scFLUENT-seq, a method that enables quantitative, genome-wide analysis of nascent transcription in single cells.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"27 2","pages":"113-113"},"PeriodicalIF":52.0,"publicationDate":"2025-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145478133","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}
Pub Date : 2025-11-06DOI: 10.1038/s41576-025-00904-4
Robert Chen, Áine Duffy, Ron Do
{"title":"Genomics of drug target prioritization for complex diseases","authors":"Robert Chen, Áine Duffy, Ron Do","doi":"10.1038/s41576-025-00904-4","DOIUrl":"https://doi.org/10.1038/s41576-025-00904-4","url":null,"abstract":"","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"230 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145447222","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}
Pub Date : 2025-11-04DOI: 10.1038/s41576-025-00903-5
Tomas Kay, Patrick K. Piekarski, Daniel J. C. Kronauer
{"title":"Convergent evolution of a conserved molecular network underlies parenting and sociality","authors":"Tomas Kay, Patrick K. Piekarski, Daniel J. C. Kronauer","doi":"10.1038/s41576-025-00903-5","DOIUrl":"https://doi.org/10.1038/s41576-025-00903-5","url":null,"abstract":"","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"88 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2025-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145434677","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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