Limits...
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.

Show MeSH
Phylogenetic analysis of putative catfish paralogues.Highly similar channel catfish sequences (Channel) and one blue catfish sequence (Blue) sharing the same BLAST identity, or two highly similar blue catfish sequences with one channel catfish sequence sharing the same BLAST identity, were subjected to phylogenetic analysis. The phylogenetic tree was drawn by using the neighbor-joining method in MEGA 4.0 package. The topological stability of the tree was evaluated by 1,000 bootstrap replications. Data were analyzed using Poisson correction and gaps were removed by complete deletion.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC2902525&req=5

pone-0011546-g006: Phylogenetic analysis of putative catfish paralogues.Highly similar channel catfish sequences (Channel) and one blue catfish sequence (Blue) sharing the same BLAST identity, or two highly similar blue catfish sequences with one channel catfish sequence sharing the same BLAST identity, were subjected to phylogenetic analysis. The phylogenetic tree was drawn by using the neighbor-joining method in MEGA 4.0 package. The topological stability of the tree was evaluated by 1,000 bootstrap replications. Data were analyzed using Poisson correction and gaps were removed by complete deletion.

Mentions: In the absence of a catfish whole genome sequence, full-length cDNAs may provide valuable information in the analysis of gene duplication events. Consensus sequences are often constructed from partial fragments of allelic variants and/or paralogous sequences, complicating analyses of gene copy numbers and gene families. Based on sequence similarity, shared UniProt BLASTX identity and GO annotation, there were several catfish full-length transcripts, with high sequence identity, from 79% to 99%, likely representing paralogues. However, it was difficult to differentiate between gene duplication and allelic variation if only comparing highly similar transcripts from a given species. Using a two species (channel catfish and blue catfish) approach with full-length cDNA sequences may help to distinguish gene duplication from allelic variants [28]. Using the rationale that allelic variation within the same species should be smaller than the variation present between orthologues from different species [29], two potentially paralogous sequences from either channel catfish or blue catfish and a putatively orthologous sequence with the same UniProt BLASTX identity from the other species (channel or blue) were subjected to phylogenetic analysis. When channel catfish and blue catfish orthologues were more tightly grouped on the resulting tree than the additional, highly similar sequence from blue or channel catfish, the two sequences from the same species likely represented paralogues rather than allelic variants. Assuming that the evolutionary distance of allelic variants should be closer than that of orthologues from a closely related species, there were two channel catfish paralogs and three blue catfish paralogs identified from the full-length cDNA set (Figure 6). Additional expansion of full-length cDNA sets from both blue catfish and channel catfish in the future should allow validation and extension of this approach to gene duplication analysis.


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)

Phylogenetic analysis of putative catfish paralogues.Highly similar channel catfish sequences (Channel) and one blue catfish sequence (Blue) sharing the same BLAST identity, or two highly similar blue catfish sequences with one channel catfish sequence sharing the same BLAST identity, were subjected to phylogenetic analysis. The phylogenetic tree was drawn by using the neighbor-joining method in MEGA 4.0 package. The topological stability of the tree was evaluated by 1,000 bootstrap replications. Data were analyzed using Poisson correction and gaps were removed by complete deletion.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0011546-g006: Phylogenetic analysis of putative catfish paralogues.Highly similar channel catfish sequences (Channel) and one blue catfish sequence (Blue) sharing the same BLAST identity, or two highly similar blue catfish sequences with one channel catfish sequence sharing the same BLAST identity, were subjected to phylogenetic analysis. The phylogenetic tree was drawn by using the neighbor-joining method in MEGA 4.0 package. The topological stability of the tree was evaluated by 1,000 bootstrap replications. Data were analyzed using Poisson correction and gaps were removed by complete deletion.
Mentions: In the absence of a catfish whole genome sequence, full-length cDNAs may provide valuable information in the analysis of gene duplication events. Consensus sequences are often constructed from partial fragments of allelic variants and/or paralogous sequences, complicating analyses of gene copy numbers and gene families. Based on sequence similarity, shared UniProt BLASTX identity and GO annotation, there were several catfish full-length transcripts, with high sequence identity, from 79% to 99%, likely representing paralogues. However, it was difficult to differentiate between gene duplication and allelic variation if only comparing highly similar transcripts from a given species. Using a two species (channel catfish and blue catfish) approach with full-length cDNA sequences may help to distinguish gene duplication from allelic variants [28]. Using the rationale that allelic variation within the same species should be smaller than the variation present between orthologues from different species [29], two potentially paralogous sequences from either channel catfish or blue catfish and a putatively orthologous sequence with the same UniProt BLASTX identity from the other species (channel or blue) were subjected to phylogenetic analysis. When channel catfish and blue catfish orthologues were more tightly grouped on the resulting tree than the additional, highly similar sequence from blue or channel catfish, the two sequences from the same species likely represented paralogues rather than allelic variants. Assuming that the evolutionary distance of allelic variants should be closer than that of orthologues from a closely related species, there were two channel catfish paralogs and three blue catfish paralogs identified from the full-length cDNA set (Figure 6). Additional expansion of full-length cDNA sets from both blue catfish and channel catfish in the future should allow validation and extension of this approach to gene duplication analysis.

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