Simon Snoeck, Oliver Johanndrees, Thorsten Nürnberger, Cyril Zipfel
{"title":"Plant pattern recognition receptors: from evolutionary insight to engineering","authors":"Simon Snoeck, Oliver Johanndrees, Thorsten Nürnberger, Cyril Zipfel","doi":"10.1038/s41576-024-00793-z","DOIUrl":"10.1038/s41576-024-00793-z","url":null,"abstract":"The plant immune system relies on germline-encoded pattern recognition receptors (PRRs) that sense foreign and plant-derived molecular patterns, and signal health threats. Genomic and pangenomic data sets provide valuable insights into the evolution of PRRs and their molecular triggers, which is furthering our understanding of plant–pathogen co-evolution and convergent evolution. Moreover, in silico and in vivo methods of PRR identification have accelerated the characterization of receptor–ligand complexes, and advances in protein structure prediction algorithms are revealing novel PRR sensor functions. Harnessing these recent advances to engineer PRRs presents an opportunity to enhance plant disease resistance against a broad spectrum of pathogens, enabling more sustainable agricultural practices. This Review summarizes both established and innovative approaches to leverage genomic data and translate resulting evolutionary insights into engineering PRR recognition specificities. Genomic and pangenomic data are yielding insights into the evolution of plant pattern recognition receptors (PRRs) and their molecular triggers. Recent advances in in silico and in vivo methods, alongside protein structure prediction, are helping to harness these insights for PRR engineering, offering sustainable solutions for broad-spectrum plant disease resistance.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 4","pages":"268-278"},"PeriodicalIF":39.1,"publicationDate":"2024-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142598302","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":"Genetic conflict and its resolution between the sexes","authors":"Abderrahman Khila","doi":"10.1038/s41576-024-00802-1","DOIUrl":"10.1038/s41576-024-00802-1","url":null,"abstract":"Abderrahman Khila highlights an important 2015 paper by Barson et al. that demonstrated how sexual conflict in Atlantic salmon affects genetic evolution.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 3","pages":"154-154"},"PeriodicalIF":39.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142588683","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":"Exploring biodiversity through museomics","authors":"Charles C. Davis, Sandra Knapp","doi":"10.1038/s41576-024-00801-2","DOIUrl":"10.1038/s41576-024-00801-2","url":null,"abstract":"Natural history collections are unparalleled resources for studying biodiversity across multiple dimensions. As multi-omic tools are being applied to museum specimens, the emerging field of museomics is undergoing a rapid and exciting transformation, with new opportunities, challenges and confrontations with past legacies. In this Comment, the authors showcase how the emerging field of museomics — the application of multi-omic tools to natural history collections — is undergoing a rapid and exciting transformation, with new opportunities, challenges and confrontations with past legacies.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 3","pages":"149-150"},"PeriodicalIF":39.1,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142588684","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}
Joshua S. James, Junbiao Dai, Wei Leong Chew, Yizhi Cai
{"title":"The design and engineering of synthetic genomes","authors":"Joshua S. James, Junbiao Dai, Wei Leong Chew, Yizhi Cai","doi":"10.1038/s41576-024-00786-y","DOIUrl":"https://doi.org/10.1038/s41576-024-00786-y","url":null,"abstract":"<p>Synthetic genomics seeks to design and construct entire genomes to mechanistically dissect fundamental questions of genome function and to engineer organisms for diverse applications, including bioproduction of high-value chemicals and biologics, advanced cell therapies, and stress-tolerant crops. Recent progress has been fuelled by advancements in DNA synthesis, assembly, delivery and editing. Computational innovations, such as the use of artificial intelligence to provide prediction of function, also provide increasing capabilities to guide synthetic genome design and construction. However, translating synthetic genome-scale projects from idea to implementation remains highly complex. Here, we aim to streamline this implementation process by comprehensively reviewing the strategies for design, construction, delivery, debugging and tailoring of synthetic genomes as well as their potential applications.</p>","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"36 1","pages":""},"PeriodicalIF":42.7,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142588685","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":"Slide-tags enables spatial single-nucleus sequencing","authors":"Andrew J. C. Russell","doi":"10.1038/s41576-024-00797-9","DOIUrl":"10.1038/s41576-024-00797-9","url":null,"abstract":"In this Tools of the Trade article, Andrew Russell describes Slide-tags, a method for scalable, spatially resolved single-nucleus sequencing.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 2","pages":"78-78"},"PeriodicalIF":39.1,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142574463","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":"The phenotypic consequences of enhancer evolution","authors":"Julie Jung, Thomas King","doi":"10.1038/s41576-024-00800-3","DOIUrl":"10.1038/s41576-024-00800-3","url":null,"abstract":"In this Journal Club, Julie Jung and Thomas King recount a paper by Chan et al. that identified the regulatory changes underlying recurrent phenotypic evolution in stickleback fish.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 2","pages":"79-79"},"PeriodicalIF":39.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142520169","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":"Context-specific regulatory variants in precision medicine and agriculture","authors":"Lingzhao Fang","doi":"10.1038/s41576-024-00798-8","DOIUrl":"10.1038/s41576-024-00798-8","url":null,"abstract":"Lingzhao Fang recalls how a 2002 paper by Brem et al., which investigated the genetic basis of natural variation in gene expression in budding yeast, and the GTEx atlas of genetic regulatory effects across human tissues inspired the FarmGTEx project to accelerate precision agriculture.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 2","pages":"81-81"},"PeriodicalIF":39.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142536895","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":"Causal inference for epigenetic ageing","authors":"Kejun Ying","doi":"10.1038/s41576-024-00799-7","DOIUrl":"10.1038/s41576-024-00799-7","url":null,"abstract":"In this Tools of the Trade article, Kejun Ying describes epigenome-wide Mendelian randomization, which integrates Mendelian randomization into a DNA-methylation-based epigenetic clock to identify CpG sites with potential causal links to lifespan and healthspan.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 1","pages":"3-3"},"PeriodicalIF":39.1,"publicationDate":"2024-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142520168","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":"Cohesin and CTCF emerge as building blocks of 3D genome structure","authors":"Julia Horsfield","doi":"10.1038/s41576-024-00795-x","DOIUrl":"10.1038/s41576-024-00795-x","url":null,"abstract":"In this Journal Club, Julia Horsfield recounts two papers that demonstrated how cohesin and CTCF together organize the genome and regulate gene expression.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 2","pages":"80-80"},"PeriodicalIF":39.1,"publicationDate":"2024-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142489503","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":"How the waxing and waning of a mutation determines HIV treatment success","authors":"Pleuni S. Pennings","doi":"10.1038/s41576-024-00791-1","DOIUrl":"10.1038/s41576-024-00791-1","url":null,"abstract":"In this Journal Club, Pleuni Pennings recalls two papers that connected the evolutionary dynamics of HIV variants with therapeutic outcomes, illustrating how evolutionary insights can inform public health decisions.","PeriodicalId":19067,"journal":{"name":"Nature Reviews Genetics","volume":"26 1","pages":"6-6"},"PeriodicalIF":39.1,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142451794","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}