Database Construction Of Yak Genome

Yak (Bos grunniens) is a livestock endemic to the high-altitude regions of the Qinghai-Tibetan Plateau and adjacent areas ranging from3,000to5,500m above sea level. It provides the basic resources (food, transport, shelter and fuel) that are necessary for Tibetans and other nomadic pastoralists living at high altitudes. Due to the long adaptation to extreme conditions in high-altitude, where is cold, hypoxia and lack of grass, this species has become an ideal model for hypoxia adaptation research. With the advance of second-generation sequencing technologies, the yak genome sequencing project was initialized five years ago and a high-quality genomic sequence was produced. At the same time, we started to construct genome database, including reference gene set and genetic map. This database makes all related data easily accessible to researchers around the world for gene function studies and genetic improvement in yak and related animals.We collected and analyzed genomic data using various bioinformatics techniques, stored data in database and created the Yak Genome Database (YGD:http://me.lzu.edu.cn/yak). First, we collected repeat sequence and annotated gene function accurately. Second, we generated a three-way genome comparison between human, cattle and yak using Mercator and MAVID. Finally, we integrated the whole genome re-sequencing data and genetic variation analysis results from three domestic and three wild yaks, including SNPs, InDels and Structure Variations. The Yak Genome Database is running on Linux operation system, and using PostgreSQL database for data storage and queries. Apache web server and PHP are used to generate web pages dynamically in server side. On the client side, the web page is displayed using IFrame in HTML and JavaScript, which is mainly based on jQuery framework and jQuery UI user interface JavaScript library.The yak genome database contains all new data resources of yak genome and easy-to-use online tools. YGD use GBrowse as genome browser, which can visualize the genome of the yak, display GC contents, genes, repeats, SNVs, SNPs and multiple types of RNA sets. The database can be searched by keywords of gene annotations, gene names, gene ids and GO terms. Alternatively, user can use BLAST tool to search the genome or gene by sequence similarities. Another important function of this database is "gene functions description", by which user can view gene annotation, domain function, GO annotation, KEGG annotation and gene family annotation. Gene page also provides download link for users to download gene sequences. In addition, users can browse co-linear regions between human, cattle and yak, and inspect gene orthology relationships. The database for yak genome analysis will not only serve as a foundation to yak functional and comparative genomics but also as a tool to understand the yak unique adaptation and evolution, and reveal the underlying mechanism of adaptation to the extreme environment. In addition, the population genomic data of domestic and wild yaks will help researchers to discover genes that are important to agronomic traits and facilitate studies of genetic improvement in yak.All related contents have been published in BMC Genomics, Nature Genetics and other journals. This database has been visited and/or downloaded for more than2,000times.