Genetic Diversity In The Atrina Pectinata Based On The Ribosome And Mitochondrial Gene Sequences

Widely distributed in the tropical and subtropical regions of the Indian and westernPacific oceans, Atrina pectinata, is a kind of large fan-shaped bivalve. It is aneconomically important shellfish, belonged to Mollusca, Lamellibranchia, Pterimorphia,Mytiloida, Pinnidae. In this paper, we studied the ITS and genetic diversity based ongene fragments of mitochondrial16S rRNA and COI, then we also research thecomplete mitochondrial genome by primer-waiking method. The main contents consistof the following parts.The internal transcribed spacers (ITS-1and ITS-2) of rRNA from A. pectinta wereamplified and sequenced.The results showed that the size of ITS-1was570bp andITS-2was618bp. The contents of T, C, A and G were20.2%,30.0%,22.3%, and27.5%in ITS-1;22.3%,27.3%,23.5%and26.9%in ITS-2, respectively. We compared the twoparts with other kinds of shellfishes (Chlamys farreri, Scapharca broughtonii,Crassostrea virginica, Ruditapes philippinarum) and found their identity in ITS-1wasbetween25.6%and38.1%, while in ITS-2was from24.5%to38.9%. The resultsshowed that the A. pectinata was highly divergent in genetic distance with the other fourshellfishes. As ITS was highly divergent, it could be used for genetic diversity study at A.pectinta’s population level.Mitochondrial16S rRNA gene fragments of A. pectinta sampled from5locations(Changdao, Wendeng, Rizhao, Zhanjiang and Hainan) were amplified with universalprimer. The PCR products were sequenced, and441bp nucleotide sequences wereobtained. The T, C, A, G and A+T contents in this fragment were29.91%,17.41%,25.74%,26.94%and55.65%, respectively. The A+T content was higher than the G+Ccontent. The diversity of the population analysis showed that the population of Wendenghad higher level of genetic diversity. Nine haplotypes were defined among fivepopulations, which were from26segregating sites. The fixation indices (Fst) analyzedby AMOVA totaled to Fst=0.5007(P<0.001), showing that the genetic fixationinter-populations is little larger than that intra-populations, and indicating significantgenetic fixation among the five populations. The Neighbor-joining (NJ) phylogenetictree and UPGMA phylogenetic tree were made from the five populations of A. pectinta.The result showed that the population of WD, CD and RZ might haveoriginated from one clade; While population of HN and ZJ from another.Mitochondrial COI gene fragments and ribosomal28S rRNA of A. pectintasampled from5locations including3Shandong populations (Changdao, Wendeng,Rizhao), a Guangdong population (Zhanjiang) and a Hainan population (Hainan) wereamplified with universal primers, and623bp,983bp nucleotide sequences wereobtained, respectively. Phylogenetic studies of Pinnidae based on28S rRNA partialsequences showed that A. pectinta had a close genetic relationship with Atrinavexillumju. The genetic diversity of5populations based on COI partial sequencesshowed the population of Wendeng had the highest level of genetic diversity. Thefixation indices (Fst) analyzed by AMOVA was0.1323(P<0.001), showed that thegenetic variation of A. pectinta was mainly from genetic fixation inter-populations.Cluster analysis based on28SrRNA and COI showed A. pectinta in our motherlandmight have differentiated into different subspecies.Bivalves exhibit an extraordinary degree of mitochondrial gene order variationwhen compared with other molluscs. In this study, we described the completemitochondrial genome of the pen shell A. pectinata. It is16,811bp in length, andcontains35genes including12protein-coding genes, two ribosomal RNAs, and21transfer RNAs (trnS and atp8lacked). All genes are encoded on the same strand. In geneorder, it shares none completely identical blocks with others in Bivalve. It may be aground pattern of pinnidae mitochondrial genomes. In addition, we also performed thecomparisons of gene arrangements with other bivalve species.We expected these findings could provide important molecular information for theprotection and utilization of A. pectinta resources in China. We also expect that thosefindings provide reference materials for the A. pectinata breeding industry furtherdevelopment.