对虾科物种线粒体基因组特征和系统发育分析

Characteristics and phylogenetic analysis of mitochondrial genome in the Penaeidae

摘要:

综合分析对虾科(Penaeidae)21个物种线粒体基因组的全序列,发现其线粒体基因组的长度为15 893~16 071 bp,A+T含量为64.59%~70.61%。K_a/K_s分析表明,对虾科物种线粒体13个蛋白质编码基因(protein-coding genes, PCGs)中,atp8基因的K_a/K_s最高,表明在对虾科中atp8基因受到了较弱的选择压力;在差异位点的分析中,发现nd5和rrnL基因的差异位点比例较高,是理想的分子标记,可用于分析对虾不同群体之间的遗传多样性;在密码子的使用中,被编码的氨基酸均体现相似的偏好性。同时,采用ML(Maximum likelihood)和BI(Bayesian inference)方法构建系统发育树,结果显示,这两种方法构建的系统发育树拓扑结构完全一致,且同属物种也都归为一类或者单独归为一支。本研究为快速鉴定对虾科生物提供了可靠的分子标记,为分析对虾科物种遗传多样性提供理论依据。

Abstract:

The complete sequence of the mitochondrial genomes of 21 species in the Penaeidae were comprehensively analyzed, and the results showed that the length of the mitochondrial genome is 15 893 to 16 071 bp, A+T content is from 64.59% to 70.61%. The K_a/K_s analysis showed that among 13 protein-coding genes (PCGs) in the mitochondria of Penaeidae species, the K_a/K_s of atp8 gene was the highest, indicating that the atp8 gene may have subjected to relatively weak selection pressure in Penaeidae. In the analysis of the different sites, it was found that the nd5 and rrnL genes were ideal molecular markers. And the codon usage analysis showed that the encoded amino acid preferences were similar. At the same time, more systematic and comprehensive ML (Maximum likelihood) and BI (Bayesian inference) methods were adopted to construct a phylogenetic tree. The results showed that the topological structure of the phylogenetic tree constructed by these two methods was completely the same, and the species of the same genus were also classified into one category or separated into a branch. This study provides reliable molecular markers for the rapid identification of Penaeidae species, and provides a theoretical basis for analyzing the genetic diversity of Penaeidae species.