Comparative DNA Sequence Analyses of Pyramimonas parkeae Chloroplast and Mitochondrial Genomes

Prasinophytes form a paraphyletic assemblage of early diverging green algae. The heterogeneity in their morphologies and the results of phylogenetic analyses of some marker genes suggest that prasinophytes have the potential to reveal the traits of the last common ancestor of the main two green lineages: 1) chlorophyte algae, the putative clade that includes the majority of the modern green algal species, and 2) streptophyte algae, a smaller paraphyletic assemblage known to be closely related to land plants. Therefore, understanding the genetic composition of prasinophyte algae is fundamental to understanding the diversification and evolutionary process that may have occurred in both green lineages. In this study, we constructed chloroplast genome and mitochondrial genome of a prasinophyte, Pyramimonas parkeae NIES254. The chloroplast genome obtained in this study is 104,809 bp showing quadripartite structure. Comparison between the newly constructed chloroplast of Pyramimonas parkeae NIES254 to the reported strain CCMP726 showed high variability at the intra-specific level. We found four large hotspot regions, evidence for expansion/contraction of IRA-SSC-IRB boundaries, and differences in ycf20, psaC, and ndhE copy number. The de novo mitochondrial genome obtained shows similarity in gene content to that of other prasinophyte mitochondrial genomes. However, this de novo mitochondrial genome differs in gene arrangement showing evolutionary diversification of mitochondrial genomes of early diverging green algae.