Bovine Genome Database: new tools for gleaning function from the Bos taurus genome.

Christine G Elsik,Marianne L Emery,Aditi Tayal,Darren E Hagen,Deepak R Unni,Hung N Nguyen,Colin M Diesh

doi:10.1093/nar/gkv1077

Abstract

We report an update of the Bovine Genome Database (BGD) (http://BovineGenome.org). The goal of BGD is to support bovine genomics research by providing genome annotation and data mining tools. We have developed new genome and annotation browsers using JBrowse and WebApollo for two Bos taurus genome assemblies, the reference genome assembly (UMD3.1.1) and the alternate genome assembly (Btau_4.6.1). Annotation tools have been customized to highlight priority genes for annotation, and to aid annotators in selecting gene evidence tracks from 91 tissue specific RNAseq datasets. We have also developed BovineMine, based on the InterMine data warehousing system, to integrate the bovine genome, annotation, QTL, SNP and expression data with external sources of orthology, gene ontology, gene interaction and pathway information. BovineMine provides powerful query building tools, as well as customized query templates, and allows users to analyze and download genome-wide datasets. With BovineMine, bovine researchers can use orthology to leverage the curated gene pathways of model organisms, such as human, mouse and rat. BovineMine will be especially useful for gene ontology and pathway analyses in conjunction with GWAS and QTL studies.

Highlights

The bovine genome is used to address fundamental questions in ruminant biology and evolution and to identify genes associated with complex traits important to humans, such those related to meat and milk production, the environmental footprint of production, and animal health
We have recognized the need to integrate the bovine genome annotations with large genomic datasets, such as those generated in genome-wide association studies (GWAS), which have become common with the availability of efficient technologies for large-scale genotyping
To aid the interpretation of these genome-wide data sets, bovine genome annotations need to be accessible to researchers on a large scale and integrated with functional information in formats that can be used in statistical analyses, such as gene set enrichment analysis (GSEA)

Summary

Introduction

The Annotation Assembly Comparison Tool allows users to look up locations of genes on two bovine assemblies (UMD3.1.1 and Btau 4.6.1) to see if there are assembly differences at these loci. BGD currently provides tools to navigate between the UMD3.1.1 and Btau 4.6.1 assemblies to help researchers determine whether their regions of interest differ across assemblies.

Results

Conclusion