基于线粒体基因组的27种蜒螺进化分析

Phylogenetic analysis of 27 species of Neritidae based on mitochondrial genomes

  • 摘要:
    目的 通过对蜒螺科27种蜒螺线粒体基因组的系统发育分析,探讨其进化关系、遗传距离及选择压力,为蜒螺科的系统进化和起源提供理论依据。
    方法 采用生物信息学方法分析蜒螺科27个物种的碱基组成、蛋白质编码基因选择压力和遗传距离等,并利用13个蛋白质编码基因分别使用Astral法、贝叶斯(BI)法和最大似然(ML)法重建系统发育树。
    结果 27种蜒螺线粒体基因组全长为15 261~15 975 bp。碱基信息显示明显的AT偏性。Ka/Ks分析表明蜒螺科线粒体蛋白质编码基因在进化中受到纯化选择。13个蛋白质编码基因中,ATP8进化速率最快,COX2最慢。3种建树方法均获得相同的结果,蜒螺科分为3个主要分支,其中蜒螺属与其他属形成明显不同的进化支。
    结论 27种蜒螺线粒体基因组在结构和基因排序上具有高度保守性,但生活环境和生活方式的差异导致其进化关系不同。本研究为蜒螺的系统发育和进化提供了详细的分子生物学基础。

     

    Abstract: The family Neritidae is one of the most diverse groups within the subclass Neritimorpha, attracting widespread attention for its phylogenetic relationships. This study aims to explore the evolutionary relationships, genetic distances, and selection pressures of 27 species of Neritidae through a phylogenetic analysis of their mitochondrial genomes, to provide a theoretical basis for the systematic evolution and origin of Neritidae. Using bioinformatics methods, we analyzed the sequence base composition, selection pressure on protein-coding genes, and genetic distances of 27 Neritidae species. We reconstructed the phylogenetic tree using three different methods (Astral, Bayesian inference, and maximum likelihood) based on protein-coding genes. Results revealed that the mitochondrial genomes of 27 Neritidae species were all double-stranded closed circular DNA molecules, containing 37 genes (13 protein-coding genes, 2 ribosomal rRNA genes, 22 transfer RNA genes, and a non-coding control region). There was no gene rearrangement among species. The full length of the mitochondrial genomes involved in this study ranged from 15 261 to 15 975 bp, displaying a noticeable AT bias in base composition. The results of relative synonymous codon usage (RSCU) indicated that the usage frequencies of UUA, CCU, CGA and UCU were high, while that of CCG was the lowest. Ka/Ks analysis indicated purifying selection on mitochondrial protein-coding genes in the evolutionary process. Among the 13 protein-coding genes, ATP8 exhibited the fastest evolutionary rate, while COX2 showed the slowest. All three tree construction methods yielded consistent results, revealing the average genetic distances of each protein-coding gene ranged from 0.16 to 0.29. Among them, the gene with the largest average genetic distance was ND6 and the one with the smallest average genetic distance was COX1. The 27 Neritidae species were grouped into three evolutionary branches. The first branch consisted of 15 species of genus Nerita, with a distinct evolutionary relationship compared to other genera. The second branch comprised 6 species of genus Clithon and one species of genus Vitta. Species of the genera Neritina, Neripteron and Septaria formed the third branch. This study indicates that the mitochondrial genomes of the 27 Neritidae species exhibit high conservation in structure and gene arrangement but differ in evolutionary relationships due to variations in living environments and lifestyles. This research provides a detailed molecular biology foundation for understanding the systematic evolution of Neritidae.

     

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