Plant and Animal Genome XIII, San Diego, CA. Abstract P559.
We have developed a BAC based physical map across the pig genome. Representing over 15x complexity, the database is a useful starting point for gene cloning experiments and acts as a template for the identification of a minimum tile path of clones across the genome as a prerequisite for clone-based genome sequencing and functional experiments. HindIII fingerprint data have been generated mainly from 4 BAC libraries, the largest proportion deriving from CHORI-242 (Pieter deJong) and Roslin PigEBAC libraries. In total over 267,000 fingerprints have been produced. The initial genome assembly was generated with a fixed tolerance of 7 and a cutoff of 1x10-10 and contained 14,000 contigs. BACs were also end sequenced to generate around 650 bp of sequence from each end of the clones. A total of 468,078 reads were generated and have been submitted to the trace repository (http://trace.ensembl.org/), representing approximately 10% of sequence coverage of the genome. This enables not only positional cloning experiments but also informs the contiguation of fingerprint contigs, exploiting the large blocks of homology that exist between the human and pig genomes. We are now using reduced stringency fingerprint matches in the context of human alignment information to produce a more continuous physical map. To date we have reduced the total contig number to 5607. The FPC database and BAC end sequence searches to human are available via the web from at: http://www.sanger.ac.uk/Projects/S_scrofa/, and BAC end sequences matched to latest assembly (NCBI35) of the human genome which are visible through Ensembl