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

Rico, Ciro and Normandeau, E. and Dion-Coˆte´, A-M. and Rico, M.I. and Coˆte´, G. and Bernatchez, L. (2013) Combining next - generation sequencing and online databases for microsatellite development in non - model organisms. Scientific Reports, 3 (3376). pp. 1-8. ISSN NA

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    Abstract

    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 IlluminaH 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.

    Item Type: Journal Article
    Additional Information: Published online only
    Subjects: Q Science > QH Natural history > QH301 Biology
    Q Science > QH Natural history > QH426 Genetics
    Divisions: Faculty of Science, Technology and Environment (FSTE) > School of Marine Studies
    Depositing User: Generic Account
    Date Deposited: 24 Jul 2014 16:39
    Last Modified: 06 Jul 2016 13:02
    URI: http://repository.usp.ac.fj/id/eprint/7549
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