Reference Genome History

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. Both the Btau and UMD assemblies were upgraded in series of releases, ending with Btau_5.0.1 and UMD3.1.1, respectively. 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.
The newest bovine genome reference assembly is ARS-UCD1.2, which is available for download at NCBI. NCBI continutes to provide ftp access to older bovine reference genome assemblies for researchers who are completing projects with those assemblies.
BGD provides genome browsers (JBrowse) and BovineMine for both ARS-UCD1.2 and UMD3.1.  Users should pay close attention to assembly versions when using various other bovine genome resources. The UCSC Genome Browser and Ensembl do not yet support ARS-UCD1.2.