Genome-Wide Comparative Mapping of Channel Catfish with Zebrafish

Comparative mapping is a powerful tool to study evolution of genomes.  In addition, comparative genome analysis of an aquaculture species, for which genome resources are less rich, can also allow transfer of genome information from the well-studied model species.  Catfish is an economically important aquaculture species in United States.  A large number of genome resources have been developed in channel catfish including genetic linkage maps, physical maps, BAC end sequences (BES), integrated linkage and physical maps using BES-derived markers, physical-contig specific sequences which generated from the next-generation sequencing technology, and the draft genome sequences. In this study, whole genome comparative analysis was conducted between channel catfish and zebrafish utilizing all currently available catfish genome resources. A total of 486Mb draft genome sequences were mapped to the linkage map, and 12,892 unique genes were annotated through analysis of conserved syntenies.  The homologous chromosomes of zebrafish to catfish linkage groups were identified based on the sets of genes on the zebrafish chromosomes and the catfish linkage groups. A large number of conserved syntenies were identified although the exact order and orientation of genes within each physical contig is unknown at present due to low resolution of the catfish linkage map (only ~2500 markers).  Detailed analysis of the conserved syntenies at chromosome level indicated extensive inter-chromosomal and intra-chromosomal rearrangements during genome evolution.  The whole genome comparative map of catfish and zebrafish should facilitate the assembly and annotation of the catfish genome, and perhaps also facilitate further validation of the zebrafish genome assembly.