Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Regional Genome Sequence Assembly For A Targeted Segment On Porcine Chromosome 17

Zhi-liang Hu¹ , Sean Humphray ² , Carol Scott ² , Jane Rogers ² , Antonio M. Ramos ¹ , James M. Reecy ¹ , Max F. Rothschild ¹

¹  Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 2255 Kildee Hall, Ames, IA 50011

²  2 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

Previously, the Sanger Institute, UIUC, Roslin and INRA collaborated to develop a 16-fold complexity BAC fingerprint physical map of the swine genome. This library has very good coverage of the entire pig genome. We have used this library to target a specific region on porcine chromosome 17 by developing a list of ordered BACs from overlapping tile path. This region corresponds to an 8.5 Mbp segment on human chromosome 20. Since the sequence from individual clones is 200 Kbp or greater, the current publicly available software is not capable of handling the task of assembling those long sequences. We have taken an alternative approach to assemble the sequences based on available minimum tiling path (MTL) and blast overlaps. Programs were developed to order the clones, check the sequence overlaps, calculate the coordinates, and produce the alignment maps. With 70 selected clones, we were able to assemble their sequences into a 5.713 Mbp contig. Our tools will be useful for a quick targeted regional genome assembling with the minimal genome-wide sequences and tile path available. The results may be improved with more sequences from the porcine genome-sequencing project.