Physical Map Construction and Physical Characterization of Channel Catfish Genome

Abstract

Catfish is the major aquaculture species in the United States. To enhance genome studies involving linkage mapping, comparative mapping and linkage map and physical map integration, over 20,000 Bacterial Artificial Chromosome (BAC) end sequences were generated and a BAC-based physical map of the channel catfish (Ictalurus punctatus Rafinesque) genome was constructed using four color fluorescence-based fingerprinting. A total of 25,195 BAC ends were sequenced, generating 20,366 clean BAC end sequences (BES) with an average reading length of 557 bp. The total reading length of 11,414,601 bp represented approximately 1.2% of the catfish genome. Based on this survey, the catfish genome was found to be highly AT-rich with 60.7% A/T. Approximately 12% of the catfish genome consisted of dispersed repetitive elements with the TC1 transposons making up the largest percentage by base pair (4.57%). Microsatellites were detected in 17.5% of BAC end sequences, providing valuable resources for marker development and map integration. BAC end sequences were anchored to the zebrafish and Tetraodon genome by Basic Local Alignment Search Tool (BLAST) search, revealing 16% and 8.2% significant hits (E < e-5), respectively. The mate-paired BAC end sequences were used to compare with zebrafish and Tetraodon genome and identified 23 conserved syntenies. A total of 40,416 BAC clones were fingerprinted, generating 34,580 (84.3% success rate, 5.6X genome coverage) validated fingerprints for the FPC (Fingerprinted Contig) assembly. A total of 3,307 contigs were assembled using a cutoff value of 1e-20 and size deviation tolerance of 0.4 bp. Each contig contained an average of 9.25 clones, with an average size of 292 kb. The combined contig size for all contigs represents approximately 1X genome size of the channel catfish. The accuracy of the contig assembly was assessed by hybridizations on BAC library high-density filters using overgo probes from a set of genes, followed by determination of positive clones in comparison with their locations in the assembly. The constructed physical map should provide an important and powerful tool for genomic studies in catfish, including comparative mapping among various fish species.