{"title":"Detection and Annotation of Unique Regions in Mammalian Genomes.","authors":"Beatriz Vieira Mourato, Bernhard Haubold","doi":"10.1093/g3journal/jkae257","DOIUrl":null,"url":null,"abstract":"<p><p>Long unique genomic regions have been reported to be highly enriched for developmental genes in mice and humans. In this paper we identify unique genomic regions using an efficient method based on fast string matching. We quantify the resource consumption and accuracy of this method before applying it to the genomes of 18 mammals. We annotate their unique regions of at least 10 kb and find that they are strongly enriched for developmental genes across the board. We then investigated the subset of unique regions that lack annotations, which we call \"anonymous\". The longest anonymous unique region in the tasmanian devil spanned 83 kb and contained the gene encoding inositol polyphosphate-5-phosphatase A, which is an essential part of intracellular signaling. This discovery of an essential gene in a unique region implies that unique regions might be given priority when annotating mammalian genomes. Our documented pipeline for annotating unique regions in any mammalian genome is available from the repository github.com/evolbioinf/auger; additional data for this study is available from the dataverse at doi.org/10.17617/3.4IKQAG.</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":null,"pages":null},"PeriodicalIF":2.1000,"publicationDate":"2024-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"G3: Genes|Genomes|Genetics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/g3journal/jkae257","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0
Abstract
Long unique genomic regions have been reported to be highly enriched for developmental genes in mice and humans. In this paper we identify unique genomic regions using an efficient method based on fast string matching. We quantify the resource consumption and accuracy of this method before applying it to the genomes of 18 mammals. We annotate their unique regions of at least 10 kb and find that they are strongly enriched for developmental genes across the board. We then investigated the subset of unique regions that lack annotations, which we call "anonymous". The longest anonymous unique region in the tasmanian devil spanned 83 kb and contained the gene encoding inositol polyphosphate-5-phosphatase A, which is an essential part of intracellular signaling. This discovery of an essential gene in a unique region implies that unique regions might be given priority when annotating mammalian genomes. Our documented pipeline for annotating unique regions in any mammalian genome is available from the repository github.com/evolbioinf/auger; additional data for this study is available from the dataverse at doi.org/10.17617/3.4IKQAG.
期刊介绍:
G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights.
G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.