| Rock scallop(Crassadoma gigantea),which belongs to Mollusca,Lamellibranchia,Pterioida,was native to North America Pacific coast.There are several valuable characteristics making C.gigantea favored in the international market,including fast growth,strong resistance and delicious meat.The C.gigantea was introduced to China to solve the problem of lacking varieties,low production and High mortality in scallop aquaculture.To date,the studies on C.gigantea are mainly focused on physiology,ecology,production and aquaculture,while the genetics background was rarely reported.In this study,the complete mitochondrial genome of C.gigantea was obtained by high-throughput sequencing using an Illumina.The genetic variation and relationship among C.gigantea,Chlamys farreri,Mizuhopecten yessoensis and Argopecten irradians were analyzed by useing the technology of PCR amplification,cloning and sequencing,and using the molecular marker of mitochondrial gene and nuclear gene.The main results drawn from this study are as follows:1.The mitochondrial genome of C.gigantea was a circular molecule with 18,495 bp in length and had been deposited in GenBank with accession number(MH016739).It contained 12 protein-coding genes(PCGs),2 rRNAs,23 tRNAs and non-coding regions(NCRs).Like most mitochondrial genomes of marine bivalve molluscs,the protein-coding gene ATP8 had not been identified in C.Gigantea.The base compositions of the C.gigantea mitochondrial genome were A = 21.19%,C = 15.24%,G = 28.75%,and T = 34.82%,with an overall A+T content of 56.02%.To investigate the nucleotide bias,the AT and GC skews were-0.243 and 0.309,respectively,indicating the occurrence of more G and T than C and A.The size of the coding regions in C.gigantea mtDNA was 11412 nts in length accounting for 61.70% of the whole genome.Different start codons of protein-coding genes were identified by careful manual inspection,though they were highly biased towards ATG.For most genes,the stop codons(TAG)were identified relatively completely.The gene order result showed that the gene order of C.gigantea was obviously different from A.irradians,but there were many similarities with M.yessoensis.To our surprise,it was showed almost identical gene junctions between C.gigantea and C.farreri.The phylogenetic trees which were constructed based on the 12 protein-coding genes have different results: one indicating a closer relationship between C.gigantea and C.Farreri,while another one indicating a closer relationship between C.gigantea and M.yessoensis.2.The sequences of Cytb gene and 12 S rRNA gene from four scallops were amplified byPCR and sequenced,10 individuals were sampled randomly from each scallop,and the related analysis of sequence characterization,genetic diversity,genetic distance and phylogenetic evolution were determined by using a suite of biology software.The results are as follows:(1)The A+T content of the sequences of Cytb gene among four scallops ranged from 57.12% to 59.64%,which higher than G+C content.The number of haplotype and polymorphic sites,haplotype diversities,nucleotide diversities and average nucleotide differences were ranged from 3 to 4,2 to 15,0.0.545 to 0.800,0.00100 to 0.00572 and 0.788 to 6.545,respectively.The four scallops all showed low diversity levels(PI <0.01).The both results of genetic distance and phylogenetic tree showed a closer relationship between C.gigantea and M.yessoensis.(2)The A+T content of the sequences of 12 S rRNA gene among four scallops ranged from 50.57% to 56.77%,which higher than G+C content.The number of haplotype and polymorphic sites,haplotype diversities,nucleotide diversities and average nucleotide differences were ranged from 2 to 3,2 to 3,0.264 to 0.623,0.00075 to 0.00207 and 0.427 to 1.882,respectively.The four scallops all showed low diversity levels(PI <0.01).The both results of genetic distance and phylogenetic tree showed a closer relationship between C.Farreri and M.yessoensis.3.The sequences of ITS1 and 5S rDNA from four scallops were amplified by PCR and sequenced,10 individuals were sampled randomly from each scallop,and the related analysis of sequence characterization,genetic diversity,genetic distance and phylogenetic evolution were determined by using a suite of biology software.The results are as follows:(1)The A+T content of the sequences of ITS1 among four scallops ranged from54.48% to 58.10%,which higher than G+C content.The number of haplotype and polymorphic sites,haplotype diversities,nucleotide diversities and average nucleotide differences were ranged from 2 to 6,1 to 12,0.425 to 0.800,0.00081 to 0.00486 and 0.366 to 2.44,respectively.The four scallops all showed low diversity levels(PI <0.01).The both results of genetic distance and phylogenetic tree showed a closer relationship between C.gigantea and M.yessoensis.(2)The A+T content of the sequences of 5S rDNA among four scallops ranged from 57.50% to 63.70%,which higher than G+C content.The number of haplotype and polymorphic sites,haplotype diversities,nucleotide diversities and average nucleotide differences were ranged from 2 to 5,1 to 14,0.533 to 0.841,0.00108 to 0.1058 and 0.533 to 5.726,respectively.The four scallops all showed low diversity levels(PI <0.01).The both results of genetic distance and phylogenetic tree showed a closer relationship between C.gigantea and M.yessoensis.In summary,our studies showed that the four scallops in the sampling area with a low level of genetic variation.From the phylogenetic tree,we can conclude that a closer relationship between C.gigantea and M.yessoensis,and there is also a close relationship among C.gigantea,M.yessoensis and C.Farreri. |
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