Abstract
This study is the first determination of six chloroplast genomes of colonial volvocine algae, Colemanosphaera charkowiensis, Volvulina compacta, Pandorina colemaniae, Pandorina morum, Colemanosphaera angeleri, and Yamagishiella unicocca. Based on 55 chloroplast protein-coding genes, we compared the nonsynonymous (dN) and synonymous (dS) substitution rates between colonial volvocine algae and the other unicellular Chlamydomonadales species. When refer to the dN, we found 27 genes were significantly different, among them, 19 genes were significant higher in unicellular species (FDR-adjusted P < 0.05). When refer to the dS, we found 10 genes were significantly different, among them, 6 genes were significant higher in unicellular species (FDR-adjusted P < 0.05). Then we identified 14 putative fast-evolving genes and 11 putative positively selected genes of unicellular species, we analyzed the function of positively selected sites of the overlap genes of putative fast-evolving and positively selected genes, and found some sites were close to the important functional region of the proteins. Photosynthesis is the process to transform and store solar energy by chloroplast, it plays a vital role in the survival of algae, this study is the first to use the chloroplast genomes to analysis the evolutionary relationship between colonial and unicellular species in Chlamydomonadales. We found more genes have higher substitution rates in unicellular species and proposed that the fast-evolving and positively selected two genes, psbA and psbC, may help to improve the photosynthetic efficiency of unicellular species in Chlamydomonadales.
Highlights
The volvocine algae belong to Chlamydomonadales (Chlorophyta, Chlorophyceae)
Based on the chloroplast protein-coding genes, we examined the nucleotide substitution rates of Chlamydomonadales species and found that more genes have higher substitution rates in unicellular species when compared with colonial species
Our analysis was based on the protein-coding genes of 12 colonial volvocine algae and 16 unicellular species, we used the maximum likelihood (ML) method to calculate the value of dN and dS of each gene and each species
Summary
The volvocine algae belong to Chlamydomonadales (Chlorophyta, Chlorophyceae). This group of algae span the full range of organizational complexity, from unicellular species to colonial species, these algae are ideal model organisms to study the fundamental issues related to the transition to multicellularity. Evolutionary Analysis of Chlamydomonadales Species been sequenced using the application of generation sequencing technology, this provided massive data for us to study the nucleotide substitution rates based on the chloroplast protein-coding genes data sets (Smith and Lee, 2009; Smith and Lee, 2010; Hamaji et al, 2013; Smith et al, 2013; Del et al, 2015; Lemieux et al, 2015; Featherston et al, 2016; Hu et al, 2019). A relatively high dN/dS ratio could be interpreted as the positive or relaxed selection (Guisinger et al, 2008), the evolutionary analysis can reveal how species adaptive under selection pressure. Guisinger et al (2008) calculated the nucleotide substitution rates of chloroplast protein-coding genes of angiosperm, and found unprecedented accumulation of nucleotide substitutions in Geraniaceae, a model was proposed to illustrate this phenomenon. Zhang et al (2018) studied the molecular evolution of chloroplast protein-coding genes of an Antarctic sea ice alga Chlamydomonas sp. and revealed the adaptive mechanism of sed-ice environment
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