Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 1/8/2016
Publication Date: 1/8/2016
Citation: Bickhart, D.M., Rosen, B.D., Schroeder, S.G., Van Tassell, C.P. 2016. Comparative ruminant genomics highlights segmental duplication and mobile element insertion diversity. Plant and Animal Genome Conference Proceedings. San Diego, CA, Jan. 9–13, W109.
Technical Abstract: We have expanded upon a previously reported comparative genomics approach using a read-depth (JaRMs) and a hybrid read-pair, split-read (RAPTR-SV) copy number variation (CNV) detection method that uses read alignments to the cattle reference genome in order to identify species-specific genomic rearrangements. By using a common reference genome, we were able to interrogate alignment discrepancies that were shared by individuals of different species in order to find putative functional differences such as mobile element insertion (MEI) within transcriptional start sites. Illumina platform sequence reads from four Goat, 14 Water Buffalo and 20 Bos taurus Indicus individuals were aligned to the Bos taurus UMD3.1 reference assembly. In order to filter misassembled regions and Cattle-specific segmental duplications (SD), we used CNV calls from 40 Bos taurus individuals of 5 different breeds as a background. We were able to confirm previously identified deletions of the Bos taurus bitter taste receptor (T2R65A) and the neuropeptide FF-amid peptide precursor (NPFF) genes in Buffalo with JaRMs and RAPTR-SV results. In just the Buffalo samples, we identified 41 genes that had MEIs within promoter regions after being filtered against our background dataset. The MEI-affected genes showed a DAVID functional enrichment for genes involved in cytoskeletal structure and actin filament organization, suggesting that MEI may be responsible for some of the external phenotypic differences between Buffalo and Cattle. By examining the full spectrum of genomic differences among Cattle, Goat and Buffalo, we will uncover additional species-specific differences that may underlie the unique phenotypes of domesticated ruminant livestock.