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Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs

BACKGROUND: EST sequencing is one of the most efficient means for gene discovery and molecular marker development, and can be additionally utilized in both comparative genome analysis and evaluation of gene duplications. While much progress has been made in catfish genomics, large-scale EST resource...

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Autores principales: Li, Ping, Peatman, Eric, Wang, Shaolin, Feng, Jinian, He, Chongbo, Baoprasertkul, Puttharat, Xu, Peng, Kucuktas, Huseyin, Nandi, Samiran, Somridhivej, Benjaporn, Serapion, Jerry, Simmons, Micah, Turan, Cemal, Liu, Lei, Muir, William, Dunham, Rex, Brady, Yolanda, Grizzle, John, Liu, Zhanjiang
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1906771/
https://www.ncbi.nlm.nih.gov/pubmed/17577415
http://dx.doi.org/10.1186/1471-2164-8-177
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author Li, Ping
Peatman, Eric
Wang, Shaolin
Feng, Jinian
He, Chongbo
Baoprasertkul, Puttharat
Xu, Peng
Kucuktas, Huseyin
Nandi, Samiran
Somridhivej, Benjaporn
Serapion, Jerry
Simmons, Micah
Turan, Cemal
Liu, Lei
Muir, William
Dunham, Rex
Brady, Yolanda
Grizzle, John
Liu, Zhanjiang
author_facet Li, Ping
Peatman, Eric
Wang, Shaolin
Feng, Jinian
He, Chongbo
Baoprasertkul, Puttharat
Xu, Peng
Kucuktas, Huseyin
Nandi, Samiran
Somridhivej, Benjaporn
Serapion, Jerry
Simmons, Micah
Turan, Cemal
Liu, Lei
Muir, William
Dunham, Rex
Brady, Yolanda
Grizzle, John
Liu, Zhanjiang
author_sort Li, Ping
collection PubMed
description BACKGROUND: EST sequencing is one of the most efficient means for gene discovery and molecular marker development, and can be additionally utilized in both comparative genome analysis and evaluation of gene duplications. While much progress has been made in catfish genomics, large-scale EST resources have been lacking. The objectives of this project were to construct primary cDNA libraries, to conduct initial EST sequencing to generate catfish EST resources, and to obtain baseline information about highly expressed genes in various catfish organs to provide a guide for the production of normalized and subtracted cDNA libraries for large-scale transcriptome analysis in catfish. RESULTS: A total of 17 cDNA libraries were constructed including 12 from channel catfish (Ictalurus punctatus) and 5 from blue catfish (I. furcatus). A total of 31,215 ESTs, with average length of 778 bp, were generated including 20,451 from the channel catfish and 10,764 from blue catfish. Cluster analysis indicated that 73% of channel catfish and 67% of blue catfish ESTs were unique within the project. Over 53% and 50% of the channel catfish and blue catfish ESTs, respectively, had significant similarities to known genes. All ESTs have been deposited in GenBank. Evaluation of the catfish EST resources demonstrated their potential for molecular marker development, comparative genome analysis, and evaluation of ancient and recent gene duplications. Subtraction of abundantly expressed genes in a variety of catfish tissues, identified here, will allow the production of low-redundancy libraries for in-depth sequencing. CONCLUSION: The sequencing of 31,215 ESTs from channel catfish and blue catfish has significantly increased the EST resources in catfish. The EST resources should provide the potential for microarray development, polymorphic marker identification, mapping, and comparative genome analysis.
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spelling pubmed-19067712007-07-04 Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs Li, Ping Peatman, Eric Wang, Shaolin Feng, Jinian He, Chongbo Baoprasertkul, Puttharat Xu, Peng Kucuktas, Huseyin Nandi, Samiran Somridhivej, Benjaporn Serapion, Jerry Simmons, Micah Turan, Cemal Liu, Lei Muir, William Dunham, Rex Brady, Yolanda Grizzle, John Liu, Zhanjiang BMC Genomics Research Article BACKGROUND: EST sequencing is one of the most efficient means for gene discovery and molecular marker development, and can be additionally utilized in both comparative genome analysis and evaluation of gene duplications. While much progress has been made in catfish genomics, large-scale EST resources have been lacking. The objectives of this project were to construct primary cDNA libraries, to conduct initial EST sequencing to generate catfish EST resources, and to obtain baseline information about highly expressed genes in various catfish organs to provide a guide for the production of normalized and subtracted cDNA libraries for large-scale transcriptome analysis in catfish. RESULTS: A total of 17 cDNA libraries were constructed including 12 from channel catfish (Ictalurus punctatus) and 5 from blue catfish (I. furcatus). A total of 31,215 ESTs, with average length of 778 bp, were generated including 20,451 from the channel catfish and 10,764 from blue catfish. Cluster analysis indicated that 73% of channel catfish and 67% of blue catfish ESTs were unique within the project. Over 53% and 50% of the channel catfish and blue catfish ESTs, respectively, had significant similarities to known genes. All ESTs have been deposited in GenBank. Evaluation of the catfish EST resources demonstrated their potential for molecular marker development, comparative genome analysis, and evaluation of ancient and recent gene duplications. Subtraction of abundantly expressed genes in a variety of catfish tissues, identified here, will allow the production of low-redundancy libraries for in-depth sequencing. CONCLUSION: The sequencing of 31,215 ESTs from channel catfish and blue catfish has significantly increased the EST resources in catfish. The EST resources should provide the potential for microarray development, polymorphic marker identification, mapping, and comparative genome analysis. BioMed Central 2007-06-18 /pmc/articles/PMC1906771/ /pubmed/17577415 http://dx.doi.org/10.1186/1471-2164-8-177 Text en Copyright © 2007 Li et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Li, Ping
Peatman, Eric
Wang, Shaolin
Feng, Jinian
He, Chongbo
Baoprasertkul, Puttharat
Xu, Peng
Kucuktas, Huseyin
Nandi, Samiran
Somridhivej, Benjaporn
Serapion, Jerry
Simmons, Micah
Turan, Cemal
Liu, Lei
Muir, William
Dunham, Rex
Brady, Yolanda
Grizzle, John
Liu, Zhanjiang
Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs
title Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs
title_full Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs
title_fullStr Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs
title_full_unstemmed Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs
title_short Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs
title_sort towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ests
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1906771/
https://www.ncbi.nlm.nih.gov/pubmed/17577415
http://dx.doi.org/10.1186/1471-2164-8-177
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