Highly efficient identification of thousands of microsatellite loci in the pearl oyster (Pinctada martensii) from RNA-Seq |
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| Institution: | 1. Nuclear and Energy Research Institute, National Nuclear Energy Commission, Avenida Professor Lineu Prestes 2242, Cidade Universitária, CEP 05508-000 São Paulo, SP, Brazil;2. Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes 748, Cidade Universitária, CEP 05508-000 São Paulo, SP, Brazil;3. Department of Chemistry, Pontifical Catholic University of Rio de Janeiro, Rua Marquês de São Vicente 225, Gávea, CEP 22451-900 Rio de Janeiro, RJ, Brazil;1. Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, José Gutiérrez Abascal 2, 28006 Madrid, Spain;2. CRARC, Catalonian Reptile and Amphibian Recovery Center, 08783 Masquefa, Barcelona, Spain;3. Cabildo Insular de El Hierro, Centro de Reproducción e Investigación del lagarto gigante de El Hierro, El Hierro, Canary Islands, Spain;1. Institute of Biology of Inland Waters, Russian Academy of Sciences, 152742 Borok, Yaroslavl Province, Russia;2. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Prospect, 33, 119071 Moscow, Russia;1. Department of Chemistry, Villanova University, Villanova, PA 19085, USA;2. Department of Food Science, Cornell University, Ithaca, NY 14853, USA;3. Department of Biodiversity Earth and Environmental Sciences, Drexel University, Philadelphia, PA 19104, USA;4. Department of Botany, Academy of Natural Sciences of Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USA |
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| Abstract: | High-throughput RNA-Seq affords a cost and time effective means of obtaining large numbers of genetic markers for aquatic genomics. Here, we present thousands of novel microsatellite loci developed for the pearl oyster, Pinctada martensii from the Illumina HiSeq? 2000 library of the pearl sac. Free user-friendly bioinformatics tools were employed to screen for microsatellite loci and design appropriate primers in 102,762 unigenes with 7216 microsatellite loci identified in total, 4862 of which had flanking sequences suitable for polymerase chain reaction primer design. The 50 randomly chosen primer pairs were tested in two populations of pearl oyster (base population (POP1) and selected population (POP2), with 30 individuals of each population). All the primer pairs were amplified successfully in two populations. All loci were polymorphic in POP1, while there were 3 loci showing monomorphism in POP2. In POP1 and POP2, observed heterozygosity from 0.033 to 1.000 and 0.000 to 1.000, 19 and 16 microsatellite loci deviated significantly from Hardy–Weinberg expectations including a Bonferroni correction (P < 0.001). Thirteen loci were highly informative content (PIC ≥ 0.5) in both populations. These identified loci will be useful for potential application for evolutionary, population genetic and chromosome linkage mapping research on pearl oyster. |
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| Keywords: | Aquatic genomics High-throughput marker identification Microsatellite DNA |
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