Limited locomotive ability relaxed selective constraints on molluscs mitochondrial genomes

Shao’E Sun,Lingfeng Kong,Hong Yu,Qi Li

doi:10.1038/s41598-017-11117-z

Abstract

Mollusca are the second largest phylum in the animal kingdom with different types of locomotion. Some molluscs are poor-migrating, while others are free-moving or fast-swimming. Most of the energy required for locomotion is provided by mitochondria via oxidative phosphorylation. Here, we conduct a comparative genomic analysis of 256 molluscs complete mitochondrial genomes and evaluate the role of energetic functional constraints on the protein-coding genes, providing a new insight into mitochondrial DNA (mtDNA) evolution. The weakly locomotive molluscs, compared to strongly locomotive molluscs, show significantly higher Ka/Ks ratio, which suggest they accumulated more nonsynonymous mutations in mtDNA and have experienced more relaxed evolutionary constraints. Eleven protein-coding genes (CoxI, CoxII, ATP6, Cytb, ND1-6, ND4L) show significant difference for Ka/Ks ratios between the strongly and weakly locomotive groups. The relaxation of selective constraints on Atp8 arise in the common ancestor of bivalves, and the further relaxation occurred in marine bivalves lineage. Our study thus demonstrates that selective constraints relevant to locomotive ability play an essential role in evolution of molluscs mtDNA.

Highlights

In all eukaryotic taxa, mitochondria play a vital role as the power sources of cells by providing up to 95% cell energy through oxidative phosphorylation (OXPHOS)[1]
If the substitution rate are varied in the mitochondrial DNA (mtDNA) of strongly and weakly locomotive molluscs? Second, do all the mtDNA-encoding genes experience the same selection pressure? To address these questions, we conduct a comparative genomic analysis of 256 molluscs complete mitochondrial genomes and test the roles of the evolutionary constraints acted on mitochondria to provided a more complete view of mtDNA evolution
We analyzed 256 molluscs mitochondrial genomes to determine whether the mtDNA of different groups of molluscs experienced different strength of selective pressures during the evolution through calculating the ratio of rates of nonsynonymous substitution over synonymous substitutions (Ka/Ks), a traditional measure of the strength of selection on proteins[21]

Summary

Introduction

Mitochondria play a vital role as the power sources of cells by providing up to 95% cell energy through oxidative phosphorylation (OXPHOS)[1]. Shen et al identified that the mitochondrial encoded OXPHOS genes were targets of natural selection and allowed for adaptation to the huge change in energy demand that was required during the origin of flight in bats[11]. These studies provide important insight toward exploring how the metabolic requirement would impact selective constraints acting on the mitochondrial genome in vertebrates lineages; the full range of metabolic demands that characterize invertebrates lineages remains largely unexplored. Gastropoda is the largest molluscan class, comprising over 80% of all living molluscs They are present in every marine environment and have successfully invaded a vast array of freshwater habitats.

Methods

Results

Conclusion