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MICROSATELLITE DEVELOPMENT IN RHODOPHYTA USING HIGH-THROUGHPUT SEQUENCE DATA

Authors

  • Lucía Couceiro,

    1. Área de Ecoloxía, Facultade de Ciencias, Universidade da Coruña, Campus de A Zapateira s/n, 1571-A Coruña, Spain
      CNRS-UPMC, UMR 7144, Équipe BEDIM, Station Biologique de Roscoff, Place Georges Teissier, F-29682 Roscoff Cedex, France
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  • Isabel Maneiro,

    1. Área de Ecoloxía, Facultade de Ciencias, Universidade da Coruña, Campus de A Zapateira s/n, 1571-A Coruña, Spain
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  • Stéphane Mauger,

    1. CNRS-UPMC, UMR 7144, Équipe BEDIM, Station Biologique de Roscoff, Place Georges Teissier, F-29682 Roscoff Cedex, France
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  • Myriam Valero,

    1. CNRS-UPMC, UMR 7144, Équipe BEDIM, Station Biologique de Roscoff, Place Georges Teissier, F-29682 Roscoff Cedex, France
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  • José Miguel Ruiz,

    1. Área de Ecoloxía, Facultade de Ciencias, Universidade da Coruña, Campus de A Zapateira s/n, 1571-A Coruña, Spain
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  • Rodolfo Barreiro

    1. Área de Ecoloxía, Facultade de Ciencias, Universidade da Coruña, Campus de A Zapateira s/n, 1571-A Coruña, Spain
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  • Received 29 July 2010. Accepted 20 April 2011.

Abstract

Shotgun genome sequencing is rapidly emerging as the method of choice for the identification of microsatellite loci in nonmodel organisms. However, to the best of our knowledge, this approach has not been applied to marine algae so far. Herein, we report the results of using the 454 next-generation sequencing (NGS) platform to randomly sample 36.0 and 40.9 Mbp (139,786 and 139,795 reads, respectively) of the genome of two red algae from the northwest Iberian Peninsula [Grateloupia lanceola (J. Agardh) J. Agardh and a still undescribed new member of the family Cruoriaceae]. Using data mining tools, we identified 4,766 and 5,174 perfect microsatellite loci in 4,344 and 4,504 sequences/contigs from G. lanceola and the Cruoriaceae, respectively. After conservative removal of potentially problematic loci (redundant sequences, mobile elements), primer design was possible for 1,371 and 1,366 loci, respectively. A survey of the literature indicates that microsatellite density in our Rhodophyta is at the low end of the values reported for other organisms investigated with the same technology (land plants and animals). A limited number of loci were successfully tested for PCR amplification and polymorphism finding that they may be suitable for population genetic studies. This study demonstrates that random genome sequencing is a rapid, effective alternative to develop useful microsatellite loci in previously unstudied red algae.

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