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Open Access Research article

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

Ping Li1, Eric Peatman1, Shaolin Wang1, Jinian Feng1, Chongbo He1, Puttharat Baoprasertkul1, Peng Xu1, Huseyin Kucuktas1, Samiran Nandi1, Benjaporn Somridhivej1, Jerry Serapion1, Micah Simmons1, Cemal Turan1, Lei Liu2, William Muir3, Rex Dunham1, Yolanda Brady1, John Grizzle1 and Zhanjiang Liu1*

Author Affiliations

1 The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA

2 The W. M. Keck Center for Comparative and Functional Genomics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

3 Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA

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BMC Genomics 2007, 8:177  doi:10.1186/1471-2164-8-177

Published: 18 June 2007

Abstract

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.