ABSTRACT. Next-generation sequencing provides large-scale sequencing data with relative ease and at a reasonable cost, making it possible to identify a large amount of SSR markers in a timely and cost-effective manner. On the basis of the transcriptome database of Sinonovacula constricta obtained by Illumina/Solexa pyrosequencing, 60 polymorphic SSR markers were developed and characterized in 30 individuals. The number of alleles per polymorphic locus ranged from 2 to 7 with an average of 3.75 alleles. The observed and expected heterozygosities varied from 0.050 to 1.000 and from 0.050 to 0.836, respectively. Nineteen loci significantly deviated from Hardy-Weinberg equilibrium (P < 0.01) after Bonferroni's correction for multiple tests. In addition, interspecific transferability revealed that 20 polymorphic loci in Solen linearis were first characterized in this study. To the best of our knowledge, this is the highest number of SSRs in S. constricta and the first report of cross-species amplification. These novel polymorphic SSR markers will be particularly useful for conservation genetics, evolutionary studies, genetic trait mapping, and marker assisted selection in the species.
ABSTRACT. Large amounts of expressed sequence tags (ESTs) generated using next-generation sequencing technologies provide a cost-effective and valuable genomic resource for the development of microsatellite markers. In this study, we isolated 115 novel polymorphic microsatellite markers for the blood clam Tegillarca granosa from ESTs in 454 sequencing data. All the loci were characterized in 30 individual clams from a natural population in Xiangshan (Zhejiang Province, China). The number of alleles per locus varied from 2 to 10, with an average of 3.78. The observed and expected heterozygosities ranged from 0 to 1 and from 0.040 to 0.799, respectively. The polymorphic information content (PIC) ranged from 0.038 to 0.825, and 29 highly polymorphic loci (PIC ≥ 0.5) and 42 moderately polymorphic loci (0.25 < PIC < 0.5) were identified. Thirty-eight of the 115 loci deviated significantly from the Hardy-Weinberg equilibrium (P < 0.01) after a Bonferroni correction. A BlastX search revealed that 46 (40%) of the polymorphic loci identified were from transcript regions of known genes. The microsatellite markers developed in the present study 8977-8987 (2015) will greatly enrich the microsatellite resources of T. granosa, and are available for further population genetic analysis, genetic trait mapping, and molecular-assisted selection.
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