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

Chen F, Lee Y, Jiang Y, Wang S, Peatman E, Abernathy J, Liu H, Liu S, Kucuktas H, Ke C, Liu Z - PLoS ONE (2010)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America.

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, full-length 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 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.

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.

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Comparison of the ORF length distribution between channel catfish and blue catfish full-length cDNAs.
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pone-0011546-g001: Comparison of the ORF length distribution between channel catfish and blue catfish full-length cDNAs.

Mentions: As shown in Table 1, the average length of the full-length cDNAs from channel catfish was 1,135 bp and 1,070 bp from blue catfish. The length of ORFs from channel catfish ranged from 114 bp to 1,416 bp, with an average ORF length of 689 bp. The range of ORF lengths from blue catfish was from 156 bp to 1,371 bp, with an average length of 702 bp. The average length of 3′UTRs from channel catfish was 243 bp, while the average length was 250 bp from blue catfish. Channel catfish and blue catfish full-length cDNAs exhibited similar patterns of distribution of ORF and 3′UTR length (Figures 1 and 2). The majority of ORF lengths ranged from 300 bp to 999 bp, while most of the 3′UTRs had lengths less than 400 bp. The analysis through the identification of ORFs and UTRs had the strength of detecting protein coding capacity and provided valuable information allowing comparisons of the distribution pattern between the two ictalurid catfish species. However, given the bias of cDNA library creation and our selection process towards smaller transcripts, the results likely do not represent comprehensive ORF and UTR distributions in the catfish transcriptome.


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

Chen F, Lee Y, Jiang Y, Wang S, Peatman E, Abernathy J, Liu H, Liu S, Kucuktas H, Ke C, Liu Z - PLoS ONE (2010)

Comparison of the ORF length distribution between channel catfish and blue catfish full-length cDNAs.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2902525&req=5

pone-0011546-g001: Comparison of the ORF length distribution between channel catfish and blue catfish full-length cDNAs.
Mentions: As shown in Table 1, the average length of the full-length cDNAs from channel catfish was 1,135 bp and 1,070 bp from blue catfish. The length of ORFs from channel catfish ranged from 114 bp to 1,416 bp, with an average ORF length of 689 bp. The range of ORF lengths from blue catfish was from 156 bp to 1,371 bp, with an average length of 702 bp. The average length of 3′UTRs from channel catfish was 243 bp, while the average length was 250 bp from blue catfish. Channel catfish and blue catfish full-length cDNAs exhibited similar patterns of distribution of ORF and 3′UTR length (Figures 1 and 2). The majority of ORF lengths ranged from 300 bp to 999 bp, while most of the 3′UTRs had lengths less than 400 bp. The analysis through the identification of ORFs and UTRs had the strength of detecting protein coding capacity and provided valuable information allowing comparisons of the distribution pattern between the two ictalurid catfish species. However, given the bias of cDNA library creation and our selection process towards smaller transcripts, the results likely do not represent comprehensive ORF and UTR distributions in the catfish transcriptome.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America.

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, full-length 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 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.

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.

Show MeSH