Identification and characterization of full-length cDNAs in channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus)

• Published in: PloS one Vol. 5; no. 7; p. e11546
• Main Authors: Chen, Fei, Lee, Yoona, Jiang, Yanliang, Wang, Shaolin, Peatman, Eric, Abernathy, Jason, Liu, Hong, Liu, Shikai, Kucuktas, Huseyin, Ke, Caihuan, Liu, Zhanjiang
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 12.07.2010; Public Library of Science (PLoS)
• Subjects: 3' Untranslated Regions - genetics; Animals; Annotations; Aquaculture; Biotechnology; Catfish; Cloning; Conservation; Conserved sequence; DNA, Complementary - genetics; Environmental science; Expressed Sequence Tags; Fish; Fisheries; Gene expression; Gene sequencing; Genetics and Genomics/Animal Genetics; Genetics and Genomics/Gene Discovery; Genetics and Genomics/Genome Projects; Genomes; Genomics; Ictaluridae - classification; Ictaluridae - genetics; Ictalurus furcatus; Ictalurus punctatus; Identification; Laboratories; Library collections; Oceanography; Phylogenetics; Phylogeny; Proteins; Selenium; Studies; Wildlife conservation; Alabama; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0011546

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, full-length cDNA resources in aquaculture species are scarce. 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 681 gene 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. 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.