Characterization of polymorphic microsatellite markers and genetic diversity in the Hong Kong oyster Crassostrea hongkongensis using paired-end Illumina shotgun sequencing

We isolated and characterized a total of 41 polymorphic microsatellite loci in Crassostrea hongkongensis, an oyster restricted to southern China. Loci were screened in 30 wild individuals from southern coastal region in China. The number of alleles per locus ranged from 2 to 18, observed heterozygosity and expected heterozygosity ranged from 0.000-0.867 to 0.066-0.926, respectively. To study the genetic diversity and population structure of this species form 3 locations, such as Xiamen, Zhuhai and Qinzhou, 12 loci were chosen from the 41 loci. The three sample sets displayed different diversity levels and observed heterozygosity ranged from 0 to 0.867. Significant genotype heterogeneity (P < 0.001) over most loci indicated that the samples are not drawn from the same gene pool. The pairwise F (ST) values between XM and ZH, and QZ and ZH indicate that there were significant deviations in genetic differentiations for the Hongkong oyster populations from these locations. These new microsatellite loci will facilitate future studies of population structure and investigation of conservation genetics in this species.