Evolution of organellar genes of chlorophyte algae: Relevance to phylogenetic inference

Nuttapong Mekvipad,Anchittha Satjarak,Tzen-Yuh Chiang

doi:10.1371/journal.pone.0216608

Abstract

Protein-coding genes in organellar genomes have been widely used to resolve relationships of chlorophyte algae. The mode of evolution of these protein-coding genes affects relationship estimations, yet selection effects on genes commonly used as markers in phylogenetic analyses are insufficiently well understood. To gain more understanding about the effects of green algal organelle protein-coding genes on phylogenies, more information is needed about the mode of gene evolution. We used phylogenetic frameworks to examine evolutionary relationships of 58 protein-coding genes present in the organellar genomes of chlorophyte and streptophyte algae at multiple levels: organelle, biological function, and individual gene, and calculated pairwise dN/dS ratios of algal organellar protein-coding genes to investigate mode of evolution. Results indicate that mitochondrial genes have evolved at a higher rate than have chloroplast genes. Low dN/dS ratios indicating relatively high level of conservation indicate that nad2, nad5, atpA, atpE, psbC, and psbD might be particularly good candidates for use as markers in chlorophyte phylogenies. Chlorophycean atp6, nad2, atpF, clpP, rps2, rps3, rps4, and rps7 protein-coding sequences exhibited selective mutations, suggesting that changes in proteins encoded by these genes might have increased fitness in Chlorophyceae.

Highlights

Land plants, closely-related streptophyte green algae, and chlorophyte green algae together form the Viridiplantae [1]
The chlorophyte algae, representing the majority of known green algal species, include three major algal classes (Chlorophyceae, Trebouxiophyceae, and Ulvophyceae), some smaller classes (e.g. Chlorodendrophyceae), and a paraphyletic assemblage of prasinophytes having traits considered to represent those of the last common Viridiplantae ancestor[3,4]
We examined whether individual organellar genes or concatenations of such genes provided sufficient information to resolve monophyletic relationships of known green algal class-level clades and investigated gene mode of evolution

Summary

Introduction

Land plants (embryophytes), closely-related streptophyte green algae, and chlorophyte green algae together form the Viridiplantae [1]. The modern Viridiplantae are (mostly) oxygenic photosynthetic eukaryotes hypothesized to have descended from a single common ancestor after the acquisition of primary plastids[2]. The chlorophyte algae, representing the majority of known green algal species, include three major algal classes (Chlorophyceae, Trebouxiophyceae, and Ulvophyceae), some smaller classes (e.g. Chlorodendrophyceae), and a paraphyletic assemblage of prasinophytes having traits considered to represent those of the last common Viridiplantae ancestor[3,4]. Molecular data available to date indicate that the class Chlorophyceae is probably a monophyletic group, monophyly of Ulvophyceae and Trebouxiophyceae has been questioned[5,6,7], and chloroplast genome data have increasingly been used to explore this issue[3]. Studies based upon chloroplast protein-coding gene sequence comparisons have supported a concept of monophyly for both Ulvophyceae and Chlorophyceae and indicated their sister.

Methods

Results

Discussion

Conclusion