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

Area of Science:

• Genomics
• Bioinformatics
• Animal Science

Background:

• The Bovine Genome Database (BGD) is crucial for advancing bovine genomics research.
• Existing resources require updates to incorporate new genome assemblies and data integration capabilities.

Purpose of the Study:

• To update the Bovine Genome Database (BGD) with enhanced genome annotation and data mining tools.
• To provide researchers with improved access to bovine genomic data and analytical functionalities.

Main Methods:

• Developed new genome and annotation browsers using JBrowse and WebApollo for two Bos taurus genome assemblies (UMD3.1.1 and Btau_4.6.1).
• Customized annotation tools to prioritize genes and utilize 91 tissue-specific RNAseq datasets.
• Integrated bovine genome, annotation, QTL, SNP, and expression data with external sources using the InterMine system to create BovineMine.

Main Results:

• Introduced updated genome and annotation browsers for reference and alternate Bos taurus genome assemblies.
• Implemented enhanced annotation tools for prioritizing gene identification and evidence selection.
• Launched BovineMine, a data warehousing system integrating diverse bovine datasets with external biological information.

Conclusions:

• The updated BGD and BovineMine provide powerful tools for bovine genomics research.
• BovineMine facilitates comparative genomics and pathway analysis by leveraging orthology with model organisms.
• These advancements will aid in gene ontology, pathway analyses, and the interpretation of GWAS and QTL studies in cattle.