Sequencing multiple genomes of the pig and other suids: Insights in speciation and selection

M.A.M. Groenen, H.J.Megens, R.P.M.A. Crooijmans, O. Madsen, M. Bosse, Y. Paudel, L. Frantz, J. Ma, R. Cunningham, L. B. Schook
Plant and Animal Genome XIX Conference, January 15-19, 2011, San Diego, CA


The recent completion of a draft genome sequence of the pig (Sus scrofa) is a landmark for genetic studies of this important agricultural species. In addition, the pig also offers a number of characteristics that makes it an important model species for biomedical applications and to address questions related to evolution and domestication. In particular, the multiple independent domestication events in the past, the existence of a large variety of breeds and wild populations in Europe and Asia, and the existence of a large number of closely related species contribute to the importance of this species as a model in population genomics. The Suidae family consists of over 12 different species that have survived to date and that have evolved over a relative short time span of 1-10 million years. We have initiated sequencing of several members of the suidea family including Sus verrucosus, Sus barbatus, Sus celebensis and Phacochoerus africanus. The genomes of these species were sequenced using Illumina sequencing technology at a depth that varied from 12-25x. Detailed analysis of these genomes is being done by a combination of de novo genome assembly and alignment against the porcine reference genome (build 10). To further address questions related to speciation and selection we also sequenced the genomes of 32 individual pigs. These included Wild Boars from Europe, China and Japan, the Chinese Meishan breed and individuals of the major European commercial breeds like Large White, Landrace, Duroc and Pietrain. Preliminary results of the analysis of these genome sequences will be presented at the meeting.