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Sci Rep. 2013 Dec 3;3:3376. doi: 10.1038/srep03376.

Combining next-generation sequencing and online databases for microsatellite development in non-model organisms.

Author information

1] Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (EBD, CSIC), C/Américo Vespucio s/n, 41092 Sevilla, Spain [2] School of Marine Studies, University of the South Pacific, Lower Laucala Campus, Suva, Fiji Islands [3] Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, Pavillon Charles-Eugène-Marchand, Québec G1V 0A6, Canada.


Next-generation sequencing (NGS) is revolutionising marker development and the rapidly increasing amount of transcriptomes published across a wide variety of taxa is providing valuable sequence databases for the identification of genetic markers without the need to generate new sequences. Microsatellites are still the most important source of polymorphic markers in ecology and evolution. Motivated by our long-term interest in the adaptive radiation of a non-model species complex of whitefishes (Coregonus spp.), in this study, we focus on microsatellite characterisation and multiplex optimisation using transcriptome sequences generated by Illumina® and Roche-454, as well as online databases of Expressed Sequence Tags (EST) for the study of whitefish evolution and demographic history. We identified and optimised 40 polymorphic loci in multiplex PCR reactions and validated the robustness of our analyses by testing several population genetics and phylogeographic predictions using 494 fish from five lakes and 2 distinct ecotypes.

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