Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda
Relation between mitochondrial DNA hyperdiversity, mutation rate and mitochondrial genome evolution in Melarhaphe neritoides (Gastropoda: Littorinidae) and other Caenogastropoda
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DOI：
10.1038/s41598-018-36428-7
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发表时间：
2018-12-19
影响因子：
4.6
通讯作者：
Backeljau, Thierry
中科院分区：
文献类型：
--
作者：
Fourdrilis, Severine;Martins, Antonio M. de Frias;Backeljau, Thierry
线粒体DNA高度多样性主要是由高突变率（mu）引起的，并对线粒体基因组结构和进化具有潜在的影响。在高度多样性的黑缝鱼（Melarhaphe neritoides）mtDNA中，高突变压力会产生异常大量的同义变异，预计这将（1）促进同义密码子使用的变化，（2）反映同义位点的选择，（3）增加mtDNA重组和基因重排，（4）与高mtDNA取代率相关。M.将neritoides进行测序，与密切相关的littorinids进行比较，并将其置于新腹足纲的系统发育背景中，以评估mtDNA超多样性和高mu对基因含量和基因顺序的影响。大多数有丝分裂基因组特征与软体动物中的趋势一致，除了缺乏T Psi C环的甲硫氨酸转移RNA的非典型二级结构。因此，M. Neritoides似乎不影响其有丝分裂基因组结构。同义位点处于正选择之下，这增加了同义位点非中性进化的证据。在这种非中性的情况下，置换率包括中性和非中性置换，高mu不一定与高置换率相关，因此解释了与高mu不同，高置换率与基因顺序重排相关。
Mitochondrial DNA hyperdiversity is primarily caused by high mutation rates (mu) and has potential implications for mitogenome architecture and evolution. In the hyperdiverse mtDNA of Melarhaphe neritoides (Gastropoda: Littorinidae), high mutational pressure generates unusually large amounts of synonymous variation, which is expected to (1) promote changes in synonymous codon usage, (2) reflect selection at synonymous sites, (3) increase mtDNA recombination and gene rearrangement, and (4) be correlated with high mtDNA substitution rates. The mitogenome of M. neritoides was sequenced, compared to closely related littorinids and put in the phylogenetic context of Caenogastropoda, to assess the influence of mtDNA hyperdiversity and high mu on gene content and gene order. Most mitogenome features are in line with the trend in Mollusca, except for the atypical secondary structure of the methionine transfer RNA lacking the T Psi C-loop. Therefore, mtDNA hyperdiversity and high mu in M. neritoides do not seem to affect its mitogenome architecture. Synonymous sites are under positive selection, which adds to the growing evidence of non-neutral evolution at synonymous sites. Under such non-neutrality, substitution rate involves neutral and non-neutral substitutions, and high mu is not necessarily associated with high substitution rate, thus explaining that, unlike high mu, a high substitution rate is associated with gene order rearrangement.