A goal of the Bovine Genome Database project is to support the efforts of bovine genomics researchers by providing navigation and annotation tools for the bovine genome.
Genomic sequence of the Hereford cow, L1 Dominette 01449, was initially generated and assembled by the Baylor College of Medicine Human Genome Sequencing Center. Similar to most genome projects, the Bos taurus genome assembly went through several iterations of improvement, which are summarized here. The work of the Bovine Genome Sequencing and Analysis Consortium to annotate and analyze assemblies Btau_3.1 and Btau_4.0 culminated in a publication in Science in 2009. At the same time, the Center for Bioinformatics and Computational Biology at the University of Maryland used the same genomic sequence data to generate an alternate assembly, UMD2, which was published in Genome Biology in 2009. Since then, both the Btau and UMD assemblies have been upgraded to the current versions, Btau_4.6.1 and UMD3.1.1. Note that the difference between UMD3.1.1 and its predecessor, UMD3.1, is the suppression of 173 contaminant contigs; however, the chromosome coordinate systems are identical between UMD3.1 and UMD3.1.1.
Both current assemblies are available for download at the NCBI ftp site for the Bos taurus genome, where UMD3.1.1 is designated the "reference" assembly and Btau_4.6.1 is designated the "alternate" assembly. The UCSC Genome Browser supports both UMD3.1.1 and Btau_4.6.1, and maintains most of the older versions. Ensembl currently supports only UMD3.1, with Btau_4.0 and Btau_3.1 available in the Ensembl archive.
BGD provides genome browsers (JBrowse) for both UMD3.1 and Btau_4.6.1, each with a track the allows users to navigate to the identical region in the other assembly. Although our browsers display the most recent NCBI annotation release, which used UMD3.1.1, we maintain the older assembly name (UMD3.1) because we also display the Ensembl gene set generated on that assembly. Since Ensembl does not provide annotation for Btau_4.6.1, we have used the UCSC LiftOver tool to transfer the Ensembl annotations. In addition to Ensembl and NCBI annotations, BGD provides the Bovine Official Gene Set version 2 (OGSv2), which includes the manual annotations created by members of the BGSAC and mapped to the newest assemblies using LiftOver.
The existence of two competing genome assembies is not an ideal situation for the bovine research community. Different researchers may find different advantages and disadvantages with each one. Btau_4.6.1 includes the Y chromosome, which was added using sequence from the Hereford bull, L1 Domino 99375, the sire of Dominette. UMD3.1.1 does not include the Y chromosome; it does include the mitochrondrial genome, a previously existing bovine mitochondrial chromosome accession that was tacked on to the Hereford reference assembly. Researchers should always be careful to note which assembly is used in a particular analysis.
Please cite the use of BGD, including BovineMine, JBrowse/WebApollo, BLAST and other BGD tools:
Elsik CG, Unni DR, Diesh CM, Tayal A, Emery ML, Nguyen HN, Hagen DE. Bovine Genome Database: new tools for gleaning function from the Bos taurus genome. Nucleic Acids Res. 2015 Oct 19. pii: gkv1077. [Epub ahead of print] PubMed PMID: 26481361.