Multi-platform Next Generation Sequencing of a High Quality Genome Assembly for the Goat

The goat is adapted to most of the environmental conditions found around the world.  The species has evolved to be tolerant to diseases, productive in tropical or arid regions, and culturally and economically important in developing countries.  Characterization of genetic adaptations and development of SNP-based tools for genetic improvement in indigenous goats requires a high quality reference genome sequence.  Male goats from breeds or populations expected to have a high level of inbreeding were screened with the Illumina GoatSNP50.  Fifteen male goats from four breeds (San Clemente, Boer, Myotonic, Kiko) were evaluated for genomic coefficients of inbreeding (FROH) using runs of homozygosity.  This analysis identified "Papadom", a San Clemente buck, as the most inbred male goat for deep sequencing (FROH=0.46).  Paired end reads from long (5 and 20 kb) and short (300 and 500 bp) insert libraries and single end shotgun reads were sequenced using Roche FLX454 and Illumina MiSeq and HiSeq platforms.  A de novo assembly of the sequence data will be completed with the University of Maryland short read assembler.  The goat genome sequence will be used for SNP discovery in African and European goat populations and genome comparison to the bezoar, which is a potential source species of domestication.