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Development and characterization of microsatellite markers in two agarophyte species, Gracilaria birdiae and Gracilaria caudata (Gracilariaceae, Rhodophyta), using next-generation sequencing

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Abstract

The two red algal species, Gracilaria birdiae Plastino and E.C. Oliveira and Gracilaria caudata J. Agardh, are the most important natural sources of agar in Brazil. Using the 454 sequencing system, we identified 464 and 487 perfect microsatellite loci in 6908 and 9602 sequences/contigs from G. birdiae and G. caudata, respectively. After a conservative removal of potentially problematic loci, 144 loci were tested (72 from each species). A total of 25 polymorphic microsatellite loci were defined (13 loci for G. birdiae and 17 loci for G. caudata, including 5 loci common to both species). The five microsatellite loci that cross-amplified in both species showed species-specific differences in allele size. Polymorphic microsatellite loci were used to assess the genetic diversity of both species in their main harvest and cultivation areas on the Brazilian coast. Gene diversity was similar in G. birdiae and G. caudata. However, significant heterozygote deficiency was observed in G. birdiae, whereas heterozygote excess occurred in G. caudata, suggesting that these two related species differ in their mating system. These results also raised new questions on their biology in the field and on their patterns of genetic structure across their geographical ranges. In addition, the 20 loci developed in this study proved successful in identifying each individual in the field as a unique multilocus genotype, and will be useful for studying lineage sorting, breeding programs, or conservation issues.

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Acknowledgments

This research was supported by the São Paulo Research Foundation (FAPESP: 2010/50175-3; 2011/10189-8), the Brazilian National Council for Scientific and Technological Development (CNPq: 300148/93-3; 301491/2013-5), the program of international cooperation USP/COFECUB between the University of São Paulo and the Comité Français d’Evaluation de la Coopération Universitaire avec le Brésil, and the International Research Network “Diversity, Evolution and Biotechnology of Marine Algae” (GDRI CNRS 0803). We are also most grateful to the Biogenouest Genomics core facility for its technical support and to Carolyn Engel-Gautier for the English review of this manuscript.

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Authors and Affiliations

  1. Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, CEP: 05508-090, São Paulo, SP, Brazil

    L. M. Ayres-Ostrock, E. M. Plastino & M. C. Oliveira

  2. Sorbonne Universités, UPMC Univ. Paris 06, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France

    S. Mauger, M. Valero & C. Destombe

  3. Centre National de la Recherche Scientifique, CNRS, UMI 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France

    S. Mauger, M. Valero & C. Destombe

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  1. L. M. Ayres-Ostrock
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  2. S. Mauger
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  3. E. M. Plastino
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  4. M. C. Oliveira
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  5. M. Valero
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  6. C. Destombe
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Correspondence to C. Destombe.

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Ayres-Ostrock, L.M., Mauger, S., Plastino, E.M. et al. Development and characterization of microsatellite markers in two agarophyte species, Gracilaria birdiae and Gracilaria caudata (Gracilariaceae, Rhodophyta), using next-generation sequencing. J Appl Phycol 28, 653–662 (2016). https://doi.org/10.1007/s10811-015-0592-7

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  • DOI: https://doi.org/10.1007/s10811-015-0592-7

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