Identification and Characterization of Full-Length cDNAs in Channel Catfish (Ictalurus punctatus) and Blue Catfish (Ictalurus furcatus).

Fei Chen; Yoona Lee; Yanliang Jiang; Shaolin Wang; Peatman, Eric; Abernathy, Jason; Hong Liu; Shikai Liu; Kucuktas, Huseyin; Caihuan Ke; Zhanjiang Liu

Background: Genome annotation projects, gene functional studies, and phylogenetic analyses for a given organism all greatly benefit from access to a validated full-length cDNA resource. While increasingly common in model species, fulllength cDNA resources in aquaculture species are scarce. Methodology and Principal Findings: Through in silico analysis of catfish (Ictalurus spp.) ESTs, a total of 10,037 channel catfish and 7,382 blue catfish cDNA clones were identified as potentially encoding full-length cDNAs. Of this set, a total of 1,169 channel catfish and 933 blue catfish full-length cDNA clones were selected for re-sequencing to provide additional coverage and ensure sequence accuracy. A total of 1,745 unique gene transcripts were identified from the full-length cDNA set, including 1,064 gene transcripts from channel catfish and 681gene transcripts from blue catfish, with 416 transcripts shared between the two closely related species. Full-length sequence characteristics (ortholog conservation, UTR length, Kozak sequence, and conserved motifs) of the channel and blue catfish were examined in detail. Comparison of gene ontology composition between full-length cDNAs and all catfish ESTs revealed that the full-length cDNA set is representative of the gene diversity encoded in the catfish transcriptome. Conclusions: This study describes the first catfish full-length cDNA set constructed from several cDNA libraries. The catfish full-length cDNA sequences, and data gleaned from sequence characteristics analysis, will be a valuable resource for ongoing catfish whole-genome sequencing and future gene-based studies of function and evolution in teleost fishes.

ANTISENSE DNA; CATFISHES; CHANNEL catfish; ICTALURUS furcatus; ANIMAL genome mapping; GENETIC transcription; GENETIC regulation; PHYLOGENY; CHROMATOGRAMS; CLONING

PLoS ONE, 2010, Vol 5, Issue 7, p1

1932-6203

Academic Journal

10.1371/journal.pone.0011546