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

Bioinformatic Mining of Type I Microsatellites from Expressed Sequence Tags of Channel Catfish... 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. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Marine Biotechnology Springer Journals

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

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Publisher
Springer Journals
Copyright
Copyright © 2004 by Springer-Verlag
Subject
Life Sciences; Freshwater & Marine Ecology; Microbiology; Zoology; Engineering, general
ISSN
1436-2228
eISSN
1436-2236
D.O.I.
10.1007/s10126-003-0039-z
Publisher site
See Article on Publisher Site

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.

Journal

Marine BiotechnologySpringer Journals

Published: May 13, 2004

References

  • Simultaneous analysis of six microsatellite markers in Atlantic cod (Gadus morhua): a novel multiplex assay system for use in selective breeding studies.
    Delghandi, M.; Mortensen, A.; Westgaard, J.I.

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