Plant & Animal Genomes XVI Conference

January 12-16, 2008
Town & Country Convention Center
San Diego, CA

A BAC-Based Physical Map Of The Channel Catfish Genome

Shaolin Wang¹ , Peng Xu¹ , Hong Liu ¹ , Lei Liu² , Jim Thorsen³ , Huseyin Kucuktas¹ , Zhanjiang Liu¹

¹  The FISH Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA

²   The W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL 61801

³  Aquaculture Protein Centre, Norwegian School of Veterinary Science, Institute of Basic Science and Aquatic medicine, Section for Aquatic medicine and nutrition, PB 8146 Dep, N-0033 Oslo, Norway

Catfish is the major aquaculture species in the United States. To enhance its genome studies involving genetic linkage and comparative mapping, a bacterial artificial chromosome (BAC) contig-based physical map of the channel catfish (Ictalurus punctatus) genome was generated using four color fluorescence-based fingerprints. A total of 40,416 BAC clones (6.5X genome coverage) was processed from the channel catfish BAC library CHORI-212, and 34,580 (85.6% success, 5.6X genome coverage) fingerprints were validated and used in the final FPC assembly. Each BAC clone contains, on average, 95.2 restriction fragments. A total of 3,307 contigs was assembled using a cutoff value of 1e-20. Trial assemblies were conducted with stringency of 1e-15-1e-40, and such assemblies are made available in a web site such that they can be merged upon as additional information becomes available. Each contig contains an average of 9.25 clones with an average size of 291 kb. The combined contig size for all contigs was 0.965 Gb, approximately the genome size of channel catfish. The reliability of the contig assembly was assessed by both hybridization of gene probes to BAC clones contained in the fingerprinted assembly, and by validation of randomly selected contigs using overgo probes designed from BAC end sequences. The presented physical map should greatly enhance genome research in catfish, particularly aiding in the identification of genomic regions containing genes underlying important performance traits. Along with this BAC contig-based physical map, a large number of BAC end sequences have been generated to facilitate the integration of the genetic linkage and physical maps.