Intraspecific genetic variation in mitochondrial 16S rRNA and COI genes in domestic and wild populations of Huaguizhikong scallop Chlamys nobilis Reeve

A 468 base-pair fragment of the mitochondrial 16S rRNA gene and a 481 base-pair fragment of the mitochondrial COI gene were used to study the geographic structure and genetic diversity within Huaguizhikong scallop Chlamys nobilis Reeve. The samples were collected from one Thailand population (TH) which sequences were obtained from the GenBank database, five domestic stocks [Fujian (FJ), Guangxi (GX), Hainan (HN), Daya Bay (DW), and Zhanjiang (ZJ)] and two wild populations [Guangxi (GY) and Daya Bay (DY)]. Sixty polymorphic sites were found in COI gene, and thirty-nine haplotypes were detected in all samples. In addition, twenty-four polymorphic sites were found, and twenty-seven haplotypes were detected in all samples of 16S rRNA gene. The analysis of haplotype frequency distribution and molecular variation indicated that genetic variation and geographic structure were significant. To COI gene and combined data set, the majority (COI: 78.7%, combined data set: 78.5%) of the genetic variation was distributed within populations, furthermore, less than 37.0% genetic variation of 16S rRNA could be distributed within populations. Variance of 16S rRNA gene (4.3%), COI gene (26.1%), and combined data set (23.4%) could be attributed among different geographic regions. The richest variation of 16S rRNA was observed in TH population among the eight populations supported the fact that TH has richer genetic polymorphism than Chinese population, which may sustain the idea of stock introduction. Otherwise, in the present study, we found that the gene diversity (Hd) level of wild population was higher than cultured populations of C. nobilis in three data sets. Our results indicated that genetic composition of cultured C. nobilis populations in southern China have been significantly affected by hatchery performance. Besides, the FJ stock which was the center seed stock of scallop C. nobilis cultured populations has been preliminarily confirmed in our research.