The GC-rich mitochondrial and plastid genomes of the green alga Coccomyxa give insight into the evolution of organelle DNA nucleotide landscape.

David Roy Smith,Fabien Burki,James L Van Etten,Takashi Yamada,Patrick J Keeling,Igor V Grigoriev,Jane Grimwood,Juergen Kroymann

doi:10.1371/journal.pone.0023624

Abstract

Most of the available mitochondrial and plastid genome sequences are biased towards adenine and thymine (AT) over guanine and cytosine (GC). Examples of GC-rich organelle DNAs are limited to a small but eclectic list of species, including certain green algae. Here, to gain insight in the evolution of organelle nucleotide landscape, we present the GC-rich mitochondrial and plastid DNAs from the trebouxiophyte green alga Coccomyxa sp. C-169. We compare these sequences with other GC-rich organelle DNAs and argue that the forces biasing them towards G and C are nonadaptive and linked to the metabolic and/or life history features of this species. The Coccomyxa organelle genomes are also used for phylogenetic analyses, which highlight the complexities in trying to resolve the interrelationships among the core chlorophyte green algae, but ultimately favour a sister relationship between the Ulvophyceae and Chlorophyceae, with the Trebouxiophyceae branching at the base of the chlorophyte crown.

Highlights

Some of the most diverse and unusual mitochondrial and plastid DNAs from all eukaryotes come from the Chlorophyta — a lineage comprising the majority of known green algal species [1]
With respective sizes of 65 and 175 kilobases and noncoding DNA contents of 52 and 56%, the Coccomyxa mitochondrial and plastid genomes are among the most inflated organelle DNAs observed from the Trebouxiophyceae, and are more akin to the prodigious organelles genomes often found within the Chlorophyceae and Ulvophyceae
Apart from the ptDNA of L. terrestris, which is 195 kb and 55% noncoding, most of the trebouxiophyte organelle genomes studied heretofore are relatively condensed (Table 1), as exemplified by the P. minor mtDNA, which is 25 kb and contains only 22 genes, and the Helicosporidium ptDNA, which is 37.4 kb and 95% coding, making it the most streamlined plastid genome observed from the Viridiplantae

Summary

Introduction

Some of the most diverse and unusual mitochondrial and plastid DNAs (mtDNAs and ptDNAs) from all eukaryotes come from the Chlorophyta — a lineage comprising the majority of known green algal species [1]. Annotation of the Coccomyxa organelle genomes revealed 59 (mtDNA) and 115 (ptDNA) putative genes, which are listed, along with the genes from the other sequenced trebouxiophyte organelle DNAs, in Supplementary Tables S1 and S2.

Results

Conclusion