Swine in Biomedical Research Conference 2005, Chicago, IL. Abstract S7.
A reference sequence for the swine genome will provide an invaluable resource for swine genetics and genomics, as well as for comparative studies with other mammals. A programme to obtain a reference sequence that will be publicly available is being developed by a consortium of laboratories from ten countries. The project is being developed in two phases. The first phase has focused on the production of a physical map of the swine genome in mapped, bacterial large insert clones. The map is based principally on a BAC library generated from a single female pig (CHORI-242), which has been end-sequenced and fingerprinted in Illinois and at the Sanger Institute, but also draws in additional end-sequences and fingerprints from three other libraries (CHORI-44, pigEBAC and INRA). The physical map is being assembled on the basis of overlapping fingerprints, using alignment of end sequences to the human genome sequence to help orient and order contigs and the radiation hybrid map of the swine genome generated at the University of Illinois, to position contigs on the swine genome. To date, the map contains around 1500 contigs and we hope to reduce this number to a few hundred, by summer 2005. Views of the BAC end sequences mapped to the human genome are displayed in Ensembl (http://www.ensembl.org) and provide a useful resource for researchers to identify clones containing genes of interest by homology with human genes.
The strategy that will be used to sequence the swine genome is a combined whole genome sequencing and mapped clone sequencing approach. The majority of the sequence data will be derived from the single animal used to generate the CHORI-242 BAC library. Data will be deposited in the GenBank and Ensembl trace archives as they are generated and sequence assemblies, display and automated annotation will be made available by the Sanger Institute and Ensembl.