Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes

Abstract

We sequenced the mitochondrial genome of six colonial volvocine algae, namely: Pandorina morum, Pandorina colemaniae, Volvulina compacta, Colemanosphaera angeleri, Colemanosphaera charkowiensi, and Yamagishiella unicocca. Previous studies have typically reconstructed the phylogenetic relationship between colonial volvocine algae based on chloroplast or nuclear genes. Here, we explore the validity of phylogenetic analysis based on mitochondrial protein-coding genes. We found phylogenetic incongruence of the genera Yamagishiella and Colemanosphaera. In Yamagishiella, the stochastic error and linkage group formed by the mitochondrial protein-coding genes prevent phylogenetic analyses from reflecting the true relationship. In Colemanosphaera, a different reconstruction approach revealed a different phylogenetic relationship. This incongruence may be because of the influence of biological factors, such as incomplete lineage sorting or horizontal gene transfer. We also analyzed the substitution rates in the mitochondrial and chloroplast genomes between colonial volvocine algae. Our results showed that all volvocine species showed significantly higher substitution rates for the mitochondrial genome compared with the chloroplast genome. The nonsynonymous substitution (dN)/synonymous substitution (dS) ratio is similar in the genomes of both organelles in most volvocine species, suggesting that the two counterparts are under a similar selection pressure. We also identified a few chloroplast protein-coding genes that showed high dN/dS ratios in some species, resulting in a significant dN/dS ratio difference between the mitochondrial and chloroplast genomes.

Reassessment of suitable markers for taxonomy of Chaetophorales (Chlorophyceae, Chlorophyta) based on chloroplast genomes

“…The different substitution rates may be associated with the nature and accuracy of organelle-targeted DNA maintenance machineries (Sloan & Taylor, 2012). Furthermore, phylogenetic incongruence was observed between seven genes (rpl2, atpF, atpI, ccsA, cemA, chlB, and psbB) and four genes (atpB, psaB, rpl5, and ycf4) or others, which could be owing to systematic error, stochastic error, and biological factors (Hu et al, 2020). The variable sites, substitution rate (Ka/Ks), and gene evolution rate did not significantly differ between genes that supported Topology I and Topology II.…”

The organellar genomes of Silvetia siliquosa (Fucales, Phaeophyceae) and comparative analyses of the brown algae

“…The higher substitution rate observed in mitochondrial protein-coding genes is the result of the high mutation rate caused by the presence of oxygen free radicals in mitochondria [ 51 ]. Previous studies have also found that the substitution rates of mitochondrial genes in green algae Volvulina compacta and the red algal genus Porphyra are greater than those of chloroplast genes [ 52 , 53 ]. By contrast, the opposite result is observed in most seed plants, in which the mitochondrial substitution rate is estimated to be lower than that of the chloroplast [ 51 ].…”

Organellar genome comparisons of Sargassum polycystum and S. plagiophyllum (Fucales, Phaeophyceae) with other Sargassum species

“…The model was run with the following settings in the codeml.ctl files: runmode = − 2 and CodonFreq = 2. To ensure the accuracy and reliability of the data, synonymous substitution values > 5 were discarded from the subsequent analysis [41]. Bar plots and scatter plots of the values of dN, dS and dN/dS were generated for comparing mutation rates and screening of the selected genes.…”