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, Eric Peatman, Jason Abernathy, Hong Liu, Shikai Liu, Huseyin Kucuktas, Caihuan Ke, Zhanjiang Liu

Research output: Contribution to journalArticle

36 Scopus citations

Abstract

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.

Original languageEnglish (US)
Article numbere11546
JournalPloS one
Volume5
Issue number7
DOIs
StatePublished - 2010

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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    Chen, F., Lee, Y., Jiang, Y., Wang, S., Peatman, E., Abernathy, J., Liu, H., Liu, S., Kucuktas, H., Ke, C., & Liu, Z. (2010). Identification and characterization of full-length cDNAs in channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus). PloS one, 5(7), [e11546]. https://doi.org/10.1371/journal.pone.0011546