Complete Mitochondrial Genome,Phylogeography And Seascape Genetics Of Macridiscus Multifarius On The Southeast Coastal Areas Of China

Macridiscus multifarius belongs to Macridiscus,Veneridae,Venerida,Bivalvia,Mollusca.It is ecologically and economically important in the coastal regions of China.However,in recent years,global climate change,intensified marine pollution and overfishing have caused its resources to decline.In this study,the entire mitochondrial genome sequence analysis was used to analyze the evolutionary relationship of M.multifarius in the Veneridae.The mitochondrial 16S rRNA gene,Cytb gene and COX3gene,were used to analyze the genetic structure and genetic diversity of seven M.multifarius populations along the coast of China,and to analyze the genetic characteristics of seascape genetics of their populations in combination with environmental factors.Further provide some basic scientific data for the protection,development and utilization of M.multifarius resources,as well as the selection of high-quality broodstock during shellfish breeding.The results of the study are as followings:1.In this study,the full length of the mitochondrial genome of M.multifarius was obtained by second-generation high-throughput sequencing.It has 13 protein-coding genes encoded in the heavy chain,22 tRNA genes and 2 rRNA genes.Both the mitochondrial genome and protein-coding genes are AT-preferred.The phylogenetic tree of the 16Veneridae species and Sinonovacula constricta as an outgroup showed that the closest relationship between the M.multifarius is the Ruditapes philippinarum,followed by the Paratapes,once again the Dosinia,and the Meretrix is more closely related to the Cyclina sinensis and the Saxidomus purpuratus.2.In this study,16S rRNA,Cytb and COX3 genes were used as DNA molecular markers to analyze the genetic diversity and genetic structure of M.multifarius.Results showed that a total of 28 haplotypes and 24 mutation sites were obtained using the 16S rRNA gene.The haplotype diversity?Hd?was 0.7698 and the nucleotide diversity?Pi?was0.00206.For Cytb gene,a total of 32 haplotypes and 18 mutation sites were obtained.The haplotype diversity?Hd?was 0.90132 and the nucleotide diversity?Pi?was 0.00520.For COX3 gene,a total of 22 haplotypes and 10 mutation sites were obtained.The haplotype diversity?Hd?was 0.73775 and the nucleotide diversity?Pi?was 0.00444.Overall,it showed a moderately high level of haplotype diversity and a lower level of nucleotide diversity.The genetic differentiation coefficient(F_ST),STRUCTURE and Network results show that seven populations of M.multifarius are mainly divided into two lineages,of which the South China Sea population Beihai?BH?and Fangchenggang?FCG?are one lineage.The East China Sea population Zhangpu?ZP?,Changle?CL?,Mazhan?MZ?,Nanji?NJ?,Zhoushan?ZS?are one pedigree.The formation of lineages was mainly influenced by the pleistocene glaciation.The results of AMOVA analysis consistently showed that the mutation mainly occurred in the population.The results of the neutrality test are consistent with the neutral evolution.The results of the three molecular markers are not exactly the same.After comparison,it is found that the Cytb gene is more sensitive as a molecular marker and the results are more reliable.3.Five environmental factors:average temperature?SKT?,total precipitation?TOP?,average sea level pressure?SLP?,net surface solar radiation?SSR?,S?salinity?and hours of sunshine?SUND?,CCA analysis with haplotype distribution of M.multifarius,and PCA analysis with population distribution,the results show that temperature and precipitation are the main factors affecting the haplotype and population distribution.The formation of genetic structure of M.multifarius is mainly influenced by the geographical environment the ocean current and the characteristics of planktonic larval stage.Based on the above experimental results,the M.multifarius has the closest relationship with the R.philippinarum in the Veneridae,and the mitochondrial genome has AT-preference.The genetic diversity of M.multifarius in species was medium,and low nucleotide diversity.There are two main lineages:FCG and BH in the South China Sea are lineage,and ZS,NJ,CL,MZ and ZP in the East China Sea lineage.Among the six environmental factors,temperature and precipitation have the greatest influence on haplotype and population distribution,and some haplotype is more likely to be produced in high temperature and high precipitation areas.This study provides important reference value for the germplasm conservation and shellfish culture of M.multifarius.