Understanding the adaptive evolution of mitochondrial genomes in intertidal chitons

Abstract

Mitochondria are the centre of energy metabolism in eukaryotic cells and its genes are thus key to the evolution of molecular mechanisms that metabolize cellular energy. Intertidal zone is one of the most stressful environments with extreme shifts in temperature, salinity, pH and oxygen concentrations. Marine molluscs, particularly chitons belong to the ecologically dominant organisms in this extreme environment, symbolizing an ideal model to understand mitochondrial stress adaptation. Here, we used concatenated mitochondrial genetic components separately from seven chitons of the intertidal zone to reconstruct phylogenetic relationships among these species. We performed selection analyses considering sites and branches of individual proteincoding genes to identify potentially adaptive residues and localize them in the protein structures of mt subunits. Our results exhibited significant amino acid changes in sites under diversifying selection of all the protein-coding genes, indicative of the adaptive evolution of mitochondrial genome in chitons. Furthermore, we obtained sites in the transmembrane helices lining the proton translocation channel as well as in surrounding loop regions, providing implication towards functional modification of the OXPHOS proteins essential for survival in dynamic environment of the intertidal zone.

Characteristics of the completed chloroplast genome sequence of Xanthium spinosum: Comparative analyses, identification of mutational hotspots and phylogenetic implications

“…Moreover, this is the rst report of the development of genetic markers based on these regions and their use to distinguish among Xanthium species. In addition, the nucleotide substitution rate and BEB analyses revealed that the accD gene may be under positive selection, and other positively selected sites detected in the present study may drive the accD PCG, supporting the occupation of diverse habitats [46,47].…”

Characteristics of the Completed Chloroplast Genome Sequence of Xanthium Spinosum: Comparative Analyses, Identification of Mutational Hotspots and Phylogenetic Implications

“…The 2ΔLnL value of the accD gene is 25.91159 with a p-value of LRT is 0.0000024. The positively selected sites detected in the present study may drive the accD protein-coding gene allowing the occupation of diverse habitats [34,35].…”

Comparative analysis of plastid genomes within the Campanulaceae and phylogenetic implications

“…Besides, the positive selection is concerned with the shift of function and environment [109,111]. Therefore, positively selected sites detected in this study may drive the protein-coding genes allowing occupation of diverse habitats [48,109].…”

“…We took three main lineages of Cyanantheae, Campanuleae and outgroup as the foreground branch separately and calculated the positive selection occurred on the aboved branches by using 76 protein-coding genes individually. If the LRT p-values were significant (<0.05), Bayes Empirical Bayes (BEB) method [47] was implemented to calculate posterior probabilities for finding sites under positive selection on the three branches [48].…”

“…There existed limitation in the study of natural selection by using branch and site modes separately because for the majority of genes in a specified branch, only few sites were under positive selection, however, branch-site model allowed us to detect the various selective pressure on the labeled foreground lineage against the remanent background branches [48]. After the analysis of BEB, we found 96 sites under potentially positive selection in the 76 protein-coding genes with posterior probabilities more than 0.95 and 10 sites greater than 0.99 (S9 Table).…”