Molecular evolution of mitochondrial coding genes in the oxidative phosphorylation pathway in malacostraca: purifying selection or accelerated evolution?

Abstract

The mitochondrion is the energy-producing factory of eukaryotic cells, in which oxidative phosphorylation (OXPHOS) is the main pathway for the production of adenosine triphosphate (ATP) by cellular respiration. Because of their vital role in metabolism, mitochondrial proteins are predicted to evolve primarily under constant purifying selection. However, all mitochondrial coding genes of malacostraca had a significantly higher synonymous nt divergence (Ks) in this study. Complex I (NADH dehydrogenase) and complex V (ATP synthase) had a much higher ratio of non-synonymous to synonymous nt divergence (Ka/Ks) and non-synonymous diversity (πNS), whereas complex III (cytochrome bc₁ complex) and complex IV (cytochrome c oxidase) had a significantly lower Ka/Ks and non-synonymous diversity (πNS). The Ka/Ks, πNS, πS, and Ka results revealed that two types of mitochondrial genes, NADH dehydrogenase and ATP synthase, in malacostraca were consistent with accelerated evolution. Furthermore, two other types of mitochondrial genes, cytochrome bc₁ complex and cytochrome c oxidase, were consistent with purifying selection. Generally, the evolutionary pattern of all mitochondrial proteins of the OXPHOS pathway in malacostraca was not entirely consistent with purifying selection.

Keywords:

• Accelerated evolution
• malacostraca
• mitochondrion
• oxidative phosphorylation
• purifying selection

Disclosure statement

The project was designed by all authors of the paper and there was no conflict of interest with other people or organizations. All authors were working in jiangsu provincial key laboratory of coastal wetland bioresources and environmental protection, Iiangsu Synthetic Innovation Center for Coastal Bio-agriculture of Yancheng Teachers University.

Funding information

This work was funded by the National Natural Science Foundation of China (41301050) and the Natural Science Foundation of Jiangsu Province (12KJA180009) and was sponsored by the “Qing Lan Project” and the “333 Project” of Jiangsu province to Daizhen Zhang and the Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection (JLCBE12002).