2012 Annual Report
1a.Objectives (from AD-416):
The objective of this cooperative research project is to produce a high quality draft, annotated genome sequence for the American plains bison (Bison bison) that will facilitate comparative studies on genomic variability in bison and allow comparisons to genomes of other ruminant and non-ruminant species.
1b.Approach (from AD-416):
Liver and other tissues will be obtained from 5 to 10 bison bulls that exit Yellowstone National Park. DNA samples from the bulls will be screened at our collaborator's laboratory at Texas A&M for any evidence of cattle genes and with microsatellite assays to select the single animal for sequencing that is most representative of the Yellowstone herd. Previous work by our collaborator has not found any evidence of cattle genes in bison from the Yellowstone herd. DNA will be extracted from hepatic tissue and used to prepare libraries for:.
1)unmated shotgun reads on the 454 sequencer to 3-4X coverage;.
2)a 20kB library for mated pair reads on the 454 sequencer to 1 X coverage,.
3)a 3kB mated pair library for 1X coverage on the 454 sequencer; and.
4)a library for short reads on the Illumina Hi-seek to achieve 25-30X coverage. Commercially available kits for the two sequencers will be obtained and procedures will be in accordance with manufacturer’s recommendations. The sequence data will be assembled using the cattle genome as a scaffold.
Bison in Yellowstone National Park are endemically infected with Brucella abortus (B. abortus). Data collected in the project document that the pathophysiology of brucellosis in bison differs from cattle, and that bison are more susceptible to infection with B. abortus. In an effort to gain basic knowledge of the interactions between host and pathogen, we are collaborating with Iowa State University, Texas A&M University, and the University of Maryland on obtaining and annotating the genomic sequence of bison. This will allow detailed understanding of gene expression and regulation in the host and pathogen during natural infections. Greater knowledge of these interactions will allow identification of host and pathogen genes that regulate or modulate infection. In these studies, we used new generation sequencing technology to develop the sequence of the bison genome. Shotgun and mated pair sequencing has been completed and the genome is currently being assembled and annotated. Advances in basic molecular knowledge of host and pathogen gene expression will be of benefit in developing new species-specific approaches for advancement of vaccines and diagnostics.