基于COI和16S rRNA的库页岛马珂蛤遗传多样性和分子系统进化研究

Genetic diversity and phylogeny of Pseudocardium sachalinense based on COI and 16S r RNA barcoding

本研究以库页岛马珂蛤(Pseudocardium sachalinense)为研究对象,讨论COI和16S rRNA两种DNA条形码在贝类的遗传多样性、分子进化和种类鉴定的适用性,并利用两种条形码评估库页岛马珂蛤的遗传多样性。本文在获得库页岛马珂蛤线粒体全基因组的基础上,测序获得库页岛马珂蛤群体的COI和16S rRNA序列,发现COI基因核苷酸多样性为0.00195,高于16S rRNA核苷酸多样性(0.00073)。基于COI基因的单倍型多样性为0.76,大于16S rRNA的单倍型多样性(0.318)。其次,用全线粒体基因组构建8种贝类的系统进化树为参考,发现基于COI和16S rRNA的系统进化树与参考一致,提示这两种条形码片段可用于推断贝类的分子进化关系。最后,分别对马珂蛤科和帘蛤科15属17种贝类的COI基因和16Sr DNA进行序列比较,发现COI基因和16S rRNA的种间遗传距离均是种内距离的62倍。以上结果说明,16S rRNA与COI基因一样,能有效地构建马珂蛤科和帘蛤科的系统发育关系和物种鉴定,但在分析库页岛马珂蛤的遗传多样性时利用COI基因比16S rRNA能发现更多的遗传变异。

This study analyzed the phylogeny,genetic diversity,and species identification of Pseudocardium sachalinense using the COI gene and 16S rRNA.Firstly,we obtained the complete mitochondrial genome of P.sachalinense using Illumina sequencing.Compared with the mitochondrial genomes of the other close species,ATP8 was missing and tRNAMet was duplicated in this genome.Based on the sequences of COI and 16S rRNA from the P.sachalinense population,the nucleotide diversities of the COI gene and 16S rRNA were 0.00195 and 0.00073,respectively.The haplotype diversity of the COI gene was 0.76,larger than that of 16S rRNA(0.318).Secondly,a phylogenetic tree based on the mitochondrial proteins of species in Mactridae and Veneridae were constructed using the maximum likelihood(ML)method.Using this tree as a reference,we also constructed the ML phylogenetic trees using COI and 16S rRNA genes,respectively.These two trees were consistent with the reference,suggesting that these two DNA barcodes could be applied to the phylogenetic analysis.Thirdly,we analyzed the genetic distances based on sequences of the COI gene and 16S rRNA from 17 species in Mactridae and Veneridae.The average inter-and intra-species Kimura-2-parameter(K2P)distances based on COI sequences were 1.17 and 0.019,respectively.The average inter-and intra-species Kimura-2-parameter(K2P)distances based on 16S rRNA sequences were 1.117 and 0.018,respectively.The results suggested that for both the COI gene and 16S rRNA,the average inter-species genetic distances were 62 times larger than the intra-species distances.These results indicated that 16S rRNA could function as the COI gene to efficiently construct the phylogenetic tree and species identification.However,the COI gene could be used more effectively than 16S rRNA to analyze the genetic diversity of P.sachalinense.