Objective:
To develop a pre-finish level (>6-X coverage) quality assembly of the porcine genome sequence. The genome sequence assembly will be an invaluable.

Approach:
This project contributes to the International Swine Genome Sequencing Consortium (ISGSC, www.piggenome.org) effort to generate a draft sequence assembly of the porcine genome, based on 3-fold sequence depth generated from a minimal tile path of BAC clones across approximately 95% of the genome coupled with directed whole-genome shotgun (WGS) sequencing to bring the level of genome coverage to greater than 6-fold. Funding from the USDA-NRI to the University of Illinois at Urbana-Champaign, on behalf of the ISGSC, supports the BAC-skim sequencing activities at The Wellcome Trust Sanger Institute (WTSI). This project will contribute WGS sequence reads to the effort. The WTSI has already constructed several small insert libraries suitable for WG-shotgun sequencing from the Duroc 2-14 genome that was selected by the ISGSC for the porcine genome project. Additional supplemental funding has been obtained from other industry and international governmental sources to contribute additional WGS-generated sequence. The strategy is a clone-by-clone approach that is based on a fully mature sequence-ready BAC physical map of the genome that was recently completed by the ISGSC. The overall aim is to use a hybrid (3X clone-by-clone combined with 3X whole genome shotgun, WGS) approach to produce a 6X draft sequence of the complete porcine genome. Three chromosomes (17% of the genome), chromosomes 4, 7 and 14, will be sequenced to a depth of 6X with funding from Netherlands IPG and the European Union, respectively. The sequence quality of the remainder of the genome will be brought to a similar level by assembling the physically anchored sequence generated by BAC-skim with WGS data generated by this project, together with individual ISGSC members and other international collaborators. Furthermore, the bioinformatic capabilities of Ensembl, a program based at the WTSI and European Bioinformatics Institute will be used to provide a complete annotation for the sequence generated.