Identification and characterization of full-length cDNAs in channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus).
<h4>Background</h4>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 a...
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Public Library of Science (PLoS)
2010
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oai:doaj.org-article:1b012ab38ad0424d8f02a068f2a09ca52021-12-02T20:20:09ZIdentification and characterization of full-length cDNAs in channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus).1932-620310.1371/journal.pone.0011546https://doaj.org/article/1b012ab38ad0424d8f02a068f2a09ca52010-07-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/20634964/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>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.<h4>Methodology and principal findings</h4>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.<h4>Conclusions</h4>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.Fei ChenYoona LeeYanliang JiangShaolin WangEric PeatmanJason AbernathyHong LiuShikai LiuHuseyin KucuktasCaihuan KeZhanjiang LiuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 5, Iss 7, p e11546 (2010) |
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Medicine R Science Q Fei Chen Yoona Lee Yanliang Jiang Shaolin Wang Eric Peatman Jason Abernathy Hong Liu Shikai Liu Huseyin Kucuktas Caihuan Ke Zhanjiang Liu Identification and characterization of full-length cDNAs in channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus). |
| description |
<h4>Background</h4>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.<h4>Methodology and principal findings</h4>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.<h4>Conclusions</h4>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. |
| format |
article |
| author |
Fei Chen Yoona Lee Yanliang Jiang Shaolin Wang Eric Peatman Jason Abernathy Hong Liu Shikai Liu Huseyin Kucuktas Caihuan Ke Zhanjiang Liu |
| author_facet |
Fei Chen Yoona Lee Yanliang Jiang Shaolin Wang Eric Peatman Jason Abernathy Hong Liu Shikai Liu Huseyin Kucuktas Caihuan Ke Zhanjiang Liu |
| author_sort |
Fei Chen |
| title |
Identification and characterization of full-length cDNAs in channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus). |
| title_short |
Identification and characterization of full-length cDNAs in channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus). |
| title_full |
Identification and characterization of full-length cDNAs in channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus). |
| title_fullStr |
Identification and characterization of full-length cDNAs in channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus). |
| title_full_unstemmed |
Identification and characterization of full-length cDNAs in channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus). |
| title_sort |
identification and characterization of full-length cdnas in channel catfish (ictalurus punctatus) and blue catfish (ictalurus furcatus). |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2010 |
| url |
https://doaj.org/article/1b012ab38ad0424d8f02a068f2a09ca5 |
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