PDF(Sci-hub)
Abstract：
Understanding the evolutionary history and adaptive process depends on the knowledge that we can acquire from both ancient and modern genomic data. With the availability of a deluge of whole-genome sequencing data from ancient and modern goat samples, a user-friendly database making efficient reuse of these important resources is needed. Here, we use the genomes of 208 modern domestic goats, 24 bezoars, 46 wild ibexes, and 82 ancient goats to present a comprehensive goat genome variation database (GGVD). GGVD hosts a total of ∼41.44 million SNPs, ∼5.14 million indels, 6,193 selected loci, and 112 introgression regions. Users can freely visualize the frequency of genomic variations in geographical maps, selective sweeps in interactive tables, Manhattan plots, or line charts, as well as the heatmap patterns of the SNP genotype. Ancient data can be shown in haplotypes to track the state of genetic variants of selection and introgression events in the early, middle, and late stages. For facilitating access to sequence features, the UCSC Genome Browser, BLAT, BLAST, LiftOver, and pcadapt are also integrated into GGVD. GGVD will be a convenient tool for population genetic studies and molecular marker designing in goat breeding programs, and it is publicly available at http://animal.nwsuaf.edu.cn/GoatVar.
摘要：
了解进化史和适应过程取决于我们可以从古代和现代基因组数据中获得的知识。随着大量来自古代和现代山羊样本的全基因组测序数据的可用性，需要一个用户友好的数据库，使这些重要资源的有效重用。这里,我们使用208只现代家养山羊的基因组，24个牛黄，46个野生ibexes，和82只古代山羊提供了一个全面的山羊基因组变异数据库(GGVD)。GGVD总共托管了4144万个SNP，-514万indel,6,193个选定基因座，和112个渗入区域。用户可以自由地可视化地理图中基因组变异的频率，在交互式表格中进行选择性扫描，曼哈顿地块，或折线图，以及SNP基因型的热图模式。古代的数据可以在单倍型中显示，以跟踪早期选择和渗入事件的遗传变异状态，中间,和后期阶段。为了便于访问序列特征，UCSC基因组浏览器，BLAT,BLAST,LiftOver,和pcadapt也集成到GGVD中。GGVD将成为山羊育种计划中种群遗传研究和分子标记设计的便捷工具，它可以在http://animal上公开获得。nwsuaf.edu.cn/GoatVar.
