GNAS2009 Abstract #9 - Reecy, James

Porcine Gene Annotation

James Reecy, Alan Archibald.

Department of Animal Science, Iowa State University, Ames, IA USA
The Roslin Instituteand the Royal (Dick) School of Veterinary Studies University of Edinburgh Roslin Midlothian EH25 9PS Scotland, UK

The Swine Genome Sequencing Consortium (http://piggenome.org/), TheWellcome Trust Sanger Institute (http://www.sanger.ac.uk/Projects/S_scrofa/) and the Ensembl team (http://www.ensembl.org) recently announced the release of an annotated assembly and gene set for the pig genome (http://www.ensembl.org/Sus_scrofa/Info/Index).  The current genome annotation started with 9,277 pig proteins from RefSeq (excluding all the predictedmodels, i.e. XP_) and UniProt sequences of which 7,144 aligned uniquely.  Similarly, 11,930 swine cDNAs and 898,859 pig ESTs that aligned with > 97% identify and > 90% coverage were mapped to the genome.  This resource was complemented this with ~130,000 additional proteins, mostly from other mammals and ~20,000 human Ensembl models of which around 50% aligned with >90% coverage.  All the gene predictions were merged giving priority to pig specific proteins to give a final gene set of 17,493 genes and 520 pseudogenes.