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Bioinformatic Mining of Type I Microsatellites from Expressed Sequence Tags of Channel Catfish (Ictalurus punctatus)

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Abstract

Gene-derived markers are pivotal to the analysis of genome structure, organization, and evolution and necessary for comparative genomics. However, gene-derived markers are relatively difficult to develop. This project utilized the genomic resources of channel catfish expressed sequence tags (ESTs) to identify simple sequence repeats (SSRs), or microsatellites. It took the advantage of ESTs for the establishment of gene identities, and of microsatellites for the acquisition of high polymorphism. When microsatellites are tagged to genes, the microsatellites can then be used as gene markers. A bioinformatic analysis of 43,033 ESTs identified 4855 ESTs containing microsatellites. Cluster analysis indicated that 1312 of these ESTs fell into 569 contigs, and the remaining 3534 ESTs were singletons. A total of 4103 unique microsatellite-containing genes were identified. The dinucleotide CA/TG and GA/TC pairs were the most abundant microsatellites. AT-rich microsatellite types were predominant among trinucleotide and tetranucleotide microsatellites, consistent with our earlier estimation that the catfish genome is highly AT-rich. Our preliminary results indicated that the majority of the identified microsatellites were polymorphic and, therefore, useful for genetic linkage mapping of catfish. Mapping of these gene-derived markers is under way, which will set the foundation for comparative genome analysis in catfish.

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Acknowledgments

We thank all the laboratories that deposited channel catfish EST sequences to the dbEST database at NCBI, which made this project possible. This project was supported by a grant from USDA NRI Animal Genome Basic Genome Reagents and Tools Program (USDA/NRICGP 2003-35205-12827). We appreciate the support of Auburn University AAES Foundation Grant and Biogrant from the Office of the Vice President for Research.

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Authors and Affiliations

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

    Jerry Serapion, Huseyin Kucuktas, Jinian Feng & Zhanjiang Liu

  2. Northwest Sci-Tech University of Agriculture and Forestry, Yangling, Shaanxi, China

    Jinian Feng

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  1. Jerry Serapion
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  2. Huseyin Kucuktas
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  3. Jinian Feng
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  4. Zhanjiang Liu
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Correspondence to Zhanjiang Liu.

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Serapion, J., Kucuktas, H., Feng, J. et al. Bioinformatic Mining of Type I Microsatellites from Expressed Sequence Tags of Channel Catfish (Ictalurus punctatus) . Mar. Biotechnol. 6, 364–377 (2004). https://doi.org/10.1007/s10126-003-0039-z

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