Next-generation sequencing has yielded a vast amount of cattle genomic data for global characterization of population genetic diversity and identification of genomic regions under natural and artificial selection. However, efficient storage, querying, and visualization of such large datasets remain challenging. Here, we developed a comprehensive database, the Bovine Genome Variation Database (BGVD). It provides six main functionalities: gene search, variation search, genomic signature search, Genome Browser, alignment search tools, and the genome coordinate conversion tool. BGVD contains information on genomic variations comprising ~60.44 M SNPs, ~6.86 M indels, 76,634 CNV regions, and signatures of selective sweeps in 432 samples from modern cattle worldwide. Users can quickly retrieve distribution patterns of these variations for 54 cattle breeds through an interactive source of breed origin map, using a given gene symbol or genomic region for any of the three versions of the bovine reference genomes (ARS-UCD1.2, UMD3.1.1, and Btau 5.0.1). Signals of selection sweep are displayed as Manhattan plots and Genome Browser tracks. To further investigate and visualize the relationships between variants and signatures of selection, the Genome Browser integrates all variations, selection data, and resources, from NCBI, the UCSC Genome Browser, and Animal QTLdb. Collectively, all these features make the BGVD a useful archive for in-depth data mining and analyses of cattle biology and cattle breeding on a global scale. BGVD is publicly available at http://animal.nwsuaf.edu.cn/BosVar.
为了研究世界家牛的遗传多样性和鉴定基因组受选择区域，通过高通量测序技术已经产生了大量的牛基因组重测序数据。然而，对如此庞大的数据集进行有效的存储、查询和可视化仍然具有挑战性。本研究中，我们利用全世界54个家牛品种432个样本的重测序数据开发了牛基因组变异数据库 (the Bovine Genome Variation Database，BGVD)。BGVD包括六个主要功能: 基因快速检索、变异检索、基因组选择信号检索、基因组浏览器、比对工具和基因组坐标转换。BGVD存储了~60.44 M SNPs、~6.86 M indels、76,634个CNV以及六大群体的选择信号信息。用户可以通过搜索基因名或位置，快速检索三个参考基因组中(ARS-UCD1.2、UMD3.1.1和Btau 5.0.1) 54个牛品种的遗传变异分布模式和六个群体的选择信号。选择信号通过曼哈顿图和基因组浏览器来展示。基因组浏览器不仅包括基因组遗传变异和选择信号的信息，还整合了NCBI、UCSC基因组浏览器、动物QTLdb的资源。综上所述，所有这些特性使BGVD成为一个非常实用的牛基因组遗传变异数据库，可用于深度挖掘和分析全球范围内的牛基因组数据。BGVD的网址是http://animal.nwsuaf.edu.cn/BosVar。





PDF全文下载地址:

http://gpb.big.ac.cn/articles/download/779