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Utilization of microarray technology for functional genomics in ictalurid catfish

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Abstract:

The channel catfish, Ictalurus punctatus, and the closely related blue catfish, Ictalurus furcatus, are important species in aquaculture and serve as biological models for immunology, neurobiology and environmental monitoring. Directed and high-throughput sequencing technologies have produced 44 767 channel catfish expressed sequence tags (ESTs) and 10 764 blue catfish ESTs to date. Experiments incorporating large-scale gene expression analyses have utilized a 660 cDNA macroarray, a 1900 cDNA spotted microarray and in situ synthesized oligonucleotide microarrays covering 19 000 and 28 000 genes. These experiments have revealed numerous transcripts that are differentially expressed in response to environmental stressors, immunostimulation and exposure to viral and bacterial pathogens. A current collaboration with the U.S. Department of Energy’s Community Sequencing Programme will soon provide a much larger resource of ESTs for both catfish species. This will enhance the coverage of the catfish transcriptome and lead to the production of more comprehensive microarrays for future investigations. Functional characterization of the catfish genome will improve the understanding of genetic variation in catfish populations and their responses to environmental variation and enhance the role of the channel catfish as a model species and source of dietary protein.

Keywords: catfish; gene expression; genome; microarray

Document Type: Regular Paper

DOI: https://doi.org/10.1111/j.1095-8649.2008.01898.x

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, U.S.A. 2: USDA-ARS, Bovine Functional Genomics Laboratory, Beltsville, MD 20705, U.S.A.

Publication date: 2008-06-01

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