Plant & Animal Genomes XIV Conference

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

An In-Depth Analysis Of A Large Contig From The Atlantic Salmon Physical BAC Map

Krzysztof P. Lubieniecki¹ , Siemon H.S. Ng¹ , Glenn A. Cooper² , Marianne Beetz-Sargent² , Jacquie E. Schein³ , Ben F. Koop² , William S. Davidson¹

¹  Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada

²  Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, Canada

³  Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia

An Atlantic salmon physical map was built based on HindIII digestion patterns of 200,640 BAC clones. Using FPC and a cut-off Sulton score of e-12, the map comprises 3,454 contigs and 37,285 singletons. We investigated the reliability of the contig generation by carrying out an in-depth analysis of one particular contig that contains ~450 BACs. Four BACs that did not appear to overlap one another from the contig build were selected for shot-gun sequencing and assembly. The remaining BACs in the contig were end sequenced. Sequence comparisons of the fully sequenced BACs revealed that three clones do indeed overlap one other giving an orientation of 64I05 -- 424M18 -- 189M17, whereas the fourth BAC does not belong to this group. The BAC end sequences were used to orient many of the remaining BACs relative to the overlapping composite sequence. Primers were then designed from sequences at the ends of BACs that did not fall into the composite sequence, and these were used to group and orient additional BACs relative to one another and the composite sequence. This allowed us to identify the BACs at the extremities of the contig. We have designed probes corresponding to these sequences and are screening the BAC library for clones that may allow the extension of this large contig. The data generated are yielding a more precise depth of coverage and spatial view of the contig. This work lays the foundation for future contig characterizations and the generation of minimum tiling paths for sequencing the Atlantic salmon genome.