Bovine Genome Database: Resources for Re-Annotating the Bos taurus Genome

The Bovine Genome Database (BGD, http://bovinegenome.org) is a genome informatics resource for Bos taurus. Users may access data through genome browsers (GBrowse and JBrowse), BLAST searching, and gene query interfaces. Genome browsers, available for different assembly versions, display gene predictions, non-coding RNA, repeats, pseudogenes, SNPs, markers, QTL, and alignments of protein homologs and transcript sequences.

We are currently focused on re-annotating the Bos taurus UMD3.1 genome assembly, which was assembled from genome sequencing data generated by the BCM Human Genome Sequencing Center, with DNA originating from the Hereford cow, Dominette. RNAseq data from 88 tissues of Dominette and her close relatives, provided by the USDA ARS, serve as a valuable resource to identify new transcripts and to make corrections to computational gene predictions. We have created reference-based assemblies of each library, and are in the process of integrating them into gene predictions. The assemblies are available for viewing in JBrowse and searching with BLAST. 

We have deployed new community annotation tools using the WebApollo Annotation Editor, allowing registered users to submit manual annotations on an ongoing basis.  WebApollo is a significant improvement over the older annotation tools, because it allows users to edit annotations using a web browser. Edits to annotations are saved to the server as they are made, and are instantly visible to all other annotators. We invite bovine researchers to register for annotation on the BGD website, and to manually check and correct annotations in light of the new RNAseq data.