日本囊对虾两种表型差异类型线粒体的全基因组比较

Comparative analysis of mitochondrial complete genomes between two phenotypic variants of Marsupenaeus japonicus

为了分析日本囊对虾两种表型差异类型的系统发育关系,实验系统比较了两种类型线粒体全基因组的基因结构、遗传距离和密码子偏好性等特征。结果显示,两种类型线粒体基因组的基因重叠区、基因间隔和密码子等方面均存在差异。两种类型的线粒体蛋白编码基因核苷酸序列的相似度为91.10%~95.00%,氨基酸序列的相似度为96.15%~100%。两种类型的A+T富集区的同源性只有82.60%,分歧度为15.40%,呈现高度遗传分化。日本囊对虾两种类型蛋白编码基因的核苷酸序列分歧度大于明对虾属和叉肢螯虾属,但氨基酸序列的分歧度小于后者。研究发现,基于cytb基因的种间遗传距离大于种内遗传距离的10倍;基于cox1基因的种间遗传距离分别为类型Ⅰ和类型Ⅱ的种内遗传距离的14.6倍和5.2倍。两种类型的nd1、nd4和nd5基因的Ka/Ks值大于1,表明受到正向选择。基于20种隶属9属的对虾线粒体基因组蛋白编码序列构建系统发育树,结果显示能有效区分各属对虾,其中日本囊对虾的两种类型首先聚类,再与宽沟对虾聚类。研究表明,日本囊对虾的两种表型差异类型基本达到物种水平,有必要进一步评估更多的性状差异,以提高两种囊对虾的特异性养殖技术。

The kuruma shrimp(Marsupenaeus japonicus)includes two morphologically similar varieties,which are distributed mostly allopatrically but coexist in the northern South China Sea.In order to further analyze the phylogenetic relationship between the two phenotypic varieties of M.japonicus,the gene structure,genetic distance and codon preference of their mitochondrial whole genomes.The results showed that there were differences in gene overlap region,gene spacing and codon preference between the two genomes.The similarity of the nucleotide sequences of the mitochondrial protein-encoding genes was between 91.10% and 95%,and the similarity of amino acid sequences was between 96.15% and 100%.The sequence homology of A+T rich regions was only82.60% and the divergence was 15.40%,indicating a high degree of genetic differentiation.The nucleotide sequence divergence of protein-coding genes between the two varieties was higher than that between Fenneropenaeus and Orconectes,while the divergence of amino acid sequence was smaller than that between the latter.The study found that the interspecific genetic distance based on cytb gene was more than 10 times the intraspecific genetic distance.The interspecific genetic distance based on cox1 gene was 14.6 times and 5.2 times of the intraspecific genetic distance for variety Ⅰ and variety Ⅱ,respectively.The Ka/Ks values of nd1,nd4 and nd5genes were greater than 1,indicating positive selection.Phylogenetic trees were constructed based on the protein coding sequence of 20 Penaeus species belonging to 9 genera,and the result showed that each genus could be effectively differentiated.In the phylogenetic tree,the two varieties of M.japonicus were clustered first,and then clustered with Melicertus latisulcatus.In view of these differences between the two Marsupenaeus species,we believe that it is essential and urgent to establish a genetic database for each and reevaluate their suitable ecological conditions in order to improve species-specific culturing techniques.