GGVD：一个山羊基因组变异数据库，用于追踪选择信号和古老渐渗的动态进化过程。

GGVD: A goat genome variation database for tracking the dynamic evolutionary process of selective signatures and ancient introgressions.

机构信息

Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.

College of Information Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China.

出版信息

J Genet Genomics. 2021 Mar 20;48(3):248-256. doi: 10.1016/j.jgg.2021.03.003. Epub 2021 Apr 9.

DOI:10.1016/j.jgg.2021.03.003

PMID:33965348

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

了解进化历史和适应过程取决于我们能够从古基因组和现代基因组数据中获取的知识。随着大量古现代山羊样本的全基因组测序数据的出现，需要一个用户友好的数据库来高效地重复利用这些重要资源。在这里，我们使用了 208 只现代家养山羊、24 只胃石、46 只野生盘羊和 82 只古代山羊的基因组，构建了一个全面的山羊基因组变异数据库（GGVD）。GGVD 共包含约 4144 万个 SNP、514 万个 indel、6193 个选择的基因座和 112 个渐渗区域。用户可以自由地在地理图谱上可视化基因组变异的频率、交互式表格中的选择扫描、曼哈顿图或折线图，以及 SNP 基因型的热图模式。古基因组数据可以以单倍型形式展示，以跟踪选择和渐渗事件在早期、中期和晚期的遗传变异状态。为了方便访问序列特征，UCSC 基因组浏览器、BLAT、BLAST、LiftOver 和 pcadapt 也集成到了 GGVD 中。GGVD 将成为山羊群体遗传学研究和分子标记设计的便捷工具，可在 http://animal.nwsuaf.edu.cn/GoatVar 上访问。