ARS | Publication request: Sequence analysis for a de novo genome assembly of Bos indicus (Nelore) cattle

Submitted to: Animal Genetics International Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: May 27, 2010
Publication Date: July 25, 2010
Citation: Sonstegard, T.S., Schroeder, S.G., Smith, T.P., Zimin, A., Matukumalli, L.K., Ajmone-Marsan, P., Wiedmann, R.T., Negrini, R., Yorke, J., Van Tassell, C.P., Garcia, J.F. 2010. Sequence analysis for a de novo genome assembly of Bos indicus (Nelore) cattle. Animal Genetics International Conference Proceedings.

Technical Abstract: A second draft sequence assembly of the bovine genome based on the sub-species, Bos indicus, is essential to better evaluate the genetic variation underlying the prototypical beef and dairy cattle in tropical and sub-tropical production environments. A linebred bull (Futuro), two generations removed from the 1962 Brazilian importation of Nelore, was selected for genome sequencing based on validation of indicine lineage from mtDNA sequence analysis, and a relatively low BovineSNP50 cumulative heterozygosity index of 0.16 (max = 0.40). Sequence data was produced from both Roche FLX454 and Illumina GAIIx platforms using paired end reads from long (5 and 20 kb) and short (300 and 500 bp) insert libraries and single end shotgun reads. Total sequence produced was greater than 120 gb. After trimming for redundancy and chimerism, long insert mate pair reads yielded 175X clone coverage, while short libraries yielded 27X sequence coverage. An additional 1X and 3X sequence coverage was generated 350 and 80 bp reads shotgun reads, respectively. Sequence data is being assembled de novo using Celera Assembler, and the final assembly will be submitted to NCBI for annotation. Two different SNP discovery analyses of Futuro’s GA-derived sequence, alone or combined with that of ten additional Nelore bulls (1X sequence depth per animal), each produced approximately 15 million SNP. For draft sequence alone, SNP were uniformly distributed across Futuro’s genome suggesting heterogeneity. These SNP resources were used to develop high and low density SNP assays that will be used to better characterize all breeds.