Click on a chromosome for a closer view
This release features the preliminary assemblies for chromosomes
1, 2, 4, 5, 6, 7, 8, 11, 10, 12, 13, 14, 15, 17 and X of the pig genome,Sus scrofa.
Using the integrated highly contiguous physical map of the pig genome
(Humphray et al, Genome Biology 2007,8:R139) as a template for sequencing, the
International Swine Genome Sequencing Consortium
(1,
2)
has secured first phase funding
from the USDA to achieve a draft 4x sequence depth across the genome
through a minimal tilepath BAC-by-BAC approach. The
map is localised to the genome through the integration of
the UIUC RH markers, the tilepath is being selected from the
CH-242 library
generated from a single Duroc sow.
Sequencing of chromosomes 7 and 14 to a depth of 6-8x is supported by the EU SABRE project, in order to improve the quality and utility of the sequence for functional genomics and sequencing of chromosome 4 to a similar depth is supported by the Institute for Pig Genetics in the Netherlands. The assembled sequence in this release was generated following the clone positioning dictated by the physical map. Sequence clones are typically represented by a number of contigs (average 4 contigs per clone), where overlaps with the neighbouring clones have been trimmed. Gaps between contigs in clones in this assembly are indicated by 100-base spacers. As a way of minimising the number of clones required to cover the genome, sequence clones are identified in a series of iterative rounds, as a consequence there are gaps where clones have yet to be sequenced, these gaps between sequenced clones are represented by spacers of 5,000 bases in the assembly.
The major histocompatibility complex of the pig, which resides on either side of the centromere on chromosome 7 has been completely sequenced previously in BACs from the library PigI (INRA Porcine BAC library) and this has been incorporated into this release. CHORI-242 clones have been selected for these regions and will be incorporated in future releases.
Preliminary annotation of the chromosome sequences has been generated by alignments of the sequence to several public databases (eg Uniprot). Ab-initio gene predictions and e-PCR based marker annotation can also be viewed at this site. A new addition in this release is the alignment of human peptides to the pig sequence to generate putative gene models. These feature provide links to the corresponding GeneView pages in the Ensembl human site.
© 2008 WTSI / EBI. Ensembl is available to download for public use - please see the code licence for details.
