Detection and Annotation of Unique Regions in Mammalian Genomes.

IF 2.1 3区 生物学 Q3 GENETICS & HEREDITY
Beatriz Vieira Mourato, Bernhard Haubold
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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.

哺乳动物基因组中独特区域的检测与注释
据报道,在小鼠和人类中,长的独特基因组区域高度富集发育基因。在本文中,我们使用一种基于快速字符串匹配的高效方法来识别独特的基因组区域。在将该方法应用于 18 种哺乳动物的基因组之前,我们对其资源消耗和准确性进行了量化。我们对至少 10 kb 的独特区域进行了注释,发现这些区域强烈富集了所有发育基因。然后,我们研究了缺乏注释的独特区域子集,我们称其为 "匿名 "区域。塔斯马尼亚袋獾中最长的匿名独特区域横跨 83 kb,包含编码肌醇多磷酸-5-磷酸酶 A 的基因,该基因是细胞内信号转导的重要组成部分。在一个独特的区域发现了一个重要基因,这意味着在注释哺乳动物基因组时,可以优先考虑独特的区域。我们在任何哺乳动物基因组中注释独特区域的记录管道可从存储库 github.com/evolbioinf/auger 获取;本研究的其他数据可从 doi.org/10.17617/3.4IKQAG 的数据筐获取。
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来源期刊
G3: Genes|Genomes|Genetics
G3: Genes|Genomes|Genetics GENETICS & HEREDITY-
CiteScore
5.10
自引率
3.80%
发文量
305
审稿时长
3-8 weeks
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.
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