The complete chloroplast DNA sequence of the green alga <i>Nephroselmis olivacea</i> : Insights into the architecture of ancestral chloroplast genomes

<jats:p> Green plants seem to form two sister lineages: Chlorophyta, comprising the green algal classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae, and Chlorophyceae, and Streptophyta, comprising the Charophyceae and land plants. We have determined the complete chloroplast DNA (cpDNA) sequence (200,799 bp) of <jats:italic>Nephroselmis olivacea</jats:italic> , a member of the class (Prasinophyceae) thought to include descendants of the earliest-diverging green algae. The 127 genes identified in this genome represent the largest gene repertoire among the green algal and land plant cpDNAs completely sequenced to date. Of the <jats:italic>Nephroselmis</jats:italic> genes, 2 ( <jats:italic>ycf81</jats:italic> and <jats:italic>ftsI</jats:italic> , a gene involved in peptidoglycan synthesis) have not been identified in any previously investigated cpDNA; 5 genes [ <jats:italic>ftsW</jats:italic> , <jats:italic>rnE</jats:italic> , <jats:italic>ycf62</jats:italic> , <jats:italic>rnpB</jats:italic> , and <jats:italic>trnS(cga)</jats:italic> ] have been found only in cpDNAs of nongreen algae; and 10 others ( <jats:italic>ndh</jats:italic> genes) have been described only in land plant cpDNAs. <jats:italic>Nephroselmis</jats:italic> and land plant cpDNAs share the same quadripartite structure—which is characterized by the presence of a large rRNA-encoding inverted repeat and two unequal single-copy regions—and very similar sets of genes in corresponding genomic regions. Given that our phylogenetic analyses place <jats:italic>Nephroselmis</jats:italic> within the Chlorophyta, these structural characteristics were most likely present in the cpDNA of the common ancestor of chlorophytes and streptophytes. Comparative analyses of chloroplast genomes indicate that the typical quadripartite architecture and gene-partitioning pattern of land plant cpDNAs are ancient features that may have been derived from the genome of the cyanobacterial progenitor of chloroplasts. Our phylogenetic data also offer insight into the chlorophyte ancestor of euglenophyte chloroplasts. </jats:p>