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Use of Comparative Genomics to Develop EST-SSRs for Red Drum (Sciaenops ocellatus)

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Abstract

Microsatellites physically linked to expressed sequence tags (EST-SSRs) are an important resource for linkage mapping and comparative genomics, and data mining in publicly available EST databases is a common strategy for EST-SSR discovery. At present, many species lack species-specific EST sequence data needed for the efficient characterization of EST-SSRs. This paper describes the discovery and development of EST-SSRs for red drum (Sciaenops ocellatus), an estuarine-dependent sciaenid species of economic importance in the USA and elsewhere, using a phylogenetically informed, comparative genomics approach to primer design. The approach entailed comparing existing genomic resources from species closely allied phylogenetically to red drum, with resources from more distantly related outgroup species. By taking into account the degree to which flanking regions are conserved across taxa, the efficiency of PCR primer design was increased greatly. The amplification success rate for primers designed for red drum was 100 % when using EST libraries from confamilial species and 92 % when using an EST library from a species in the same suborder. The primers developed also amplified EST-SSRs in a wide range of perciform fishes, suggesting potential use in comparative genomics. This study demonstrates that EST-SSRs can be efficiently developed for an organism when limited species-specific data are available by exploiting genomic resources from well-studied species, even those at extended phylogenetic distances.

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Acknowledgments

We thank M. Renshaw for technical assistance in the laboratory and for providing tissues for cross-amplifications. Funding was provided by the Saltonstall-Kennedy Program (Award NA10NMF4270199) of the National Marine Fisheries Service (U.S. Department of Commerce) and by Texas AgriLife Research (Project H-6703). This paper is no. 86 in the series “Genetic Studies in Marine Fishes” and contribution no. 211 of the Center for Biosystematics and Biodiversity at Texas A&M University.

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  1. Department of Wildlife and Fisheries Sciences, Center for Biosystematics and Biodiversity, Texas A&M University, TAMU 2258, College Station, TX, 77843-2258, USA

    Christopher M. Hollenbeck, David S. Portnoy & John R. Gold

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  1. Christopher M. Hollenbeck
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  2. David S. Portnoy
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  3. John R. Gold
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Correspondence to Christopher M. Hollenbeck.

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Hollenbeck, C.M., Portnoy, D.S. & Gold, J.R. Use of Comparative Genomics to Develop EST-SSRs for Red Drum (Sciaenops ocellatus). Mar Biotechnol 14, 672–680 (2012). https://doi.org/10.1007/s10126-012-9449-0

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