Vieira Mourato Beatriz, Haubold Bernhard
Research Group Bioinformatics, Max-Planck-Institute for Evolutionary Biology, August-Thienemann-Str. 2, Plön, Schleswig-Holstein 24306, Germany.
G3 (Bethesda). 2025 Jan 8;15(1). doi: 10.1093/g3journal/jkae257.
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 (URs) of at least 10 kb and find that they are strongly enriched for developmental genes across the board. We then investigated the subset of URs that lack annotations, which we call "anonymous." The longest anonymous UR 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 UR implies that URs might be given priority when annotating mammalian genomes. Our documented pipeline for annotating URs in any mammalian genome is available from the repository github.com/evolbioinf/auger; the additional data for this study are available from the dataverse at doi.org/10.17617/3.4IKQAG.
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有效方法来识别独特基因组区域。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。我们注释了它们至少10 kb的独特区域（URs），发现这些区域普遍强烈富集发育基因。然后，我们研究了缺乏注释的URs子集，我们将其称为“匿名”子集。袋獾中最长的匿名UR跨度为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传导的重要组成部分。在一个UR中发现一个必需基因意味着在注释哺乳动物基因组时，URs可能应被优先考虑。我们记录的用于注释任何哺乳动物基因组中URs的流程可从github.com/evolbioinf/auger存储库获取；本研究的其他数据可从doi.org/10.17617/3.4IKQAG的数据存储库获取。
