The Bovine Genome Database
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. Both versions are available for download at the NCBI ftp site for the Bos taurus genome.
The existence of two competing versions of a genome assemby is not an ideal situation for the bovine research community. Different researchers will find different advantages and disadvantages with each version. The Btau_4.6.1 assembly includes the Y chromosome, which was added using sequence from the Hereford bull, L1 Domino 99375, the sire of Dominette. The UMD3.1 version does not include the Y chromosome; however, some researchers feel the the UMD3.1 assembly is the more contiguous version. NCBI now designates the UMD3.1 assembly as the "reference" assembly and the Btau_4.6.1 assembly as the "alternate" assembly. Ensembl currently supports only the UMD3.1 assembly, with Btau_4.0 and Btau_3.1 availlable in the Ensembl archive. The UCSC Genome Browser supports both assemblies. To best leverage the bovine genome data, researchers should note which genome assembly was used to generate a particular dataset, and be sure to cite the particular assembly they use in their manuscripts.
At BGD, we are working to provide tools to navigate across the Btau_4.6.1 and UMD3.1 assemblies, to leverage both assemblies to identify difficult-to-assemble regions that may be areas of focus in a new bovine genome-upgrade project, and to re-annotate the bovine genome using RNASeq data that was generated from 87 tissues of Dominette and her relatives. We have created new manual annotation tools using Web Apollo, and will be seeking input from the research community after we complete computational annotation. The Dominette RNASeq data is available for viewing with the UMD3.1 Jbrowse. Users may notice that some older tools, such as the Bovine QTL viewer, are not currently provided, as we work to integrate them with the latest assemblies. These will be available in the near future. Our work to re-annotate the bovine genome is supported by Agriculture and Food Research Initiative Competitive grant no. 2010-65205-20647 from the USDA National Institute of Food and Agriculture.
Please cite the use of BGD:
Reese JT, Childers CP, Sundaram JP, Dickens CM, Childs KL, Vile DC, Elsik CG. 2010. Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome. BMC Genomics. 11:645. PMID: 21092105.
Childers CP, Reese JT, Sundaram JP, Vile DC, Dickens CM, Childs KL, Salih H, Bennett AK, Hagen DE, Adelson DL, Elsik CG. 2011. Bovine Genome Database: integrated tools for genome annotation and discovery. Nucleic Acids Res. 39:D830-4. PMID:21123190