| Summary: | <p>Abstract</p> <p>Background</p> <p>The phylum Chlorophyta contains the majority of the green algae and is divided into four classes. The basal position of the Prasinophyceae has been well documented, but the divergence order of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae is currently debated. The four complete chloroplast DNA (cpDNA) sequences presently available for representatives of these classes have revealed extensive variability in overall structure, gene content, intron composition and gene order. The chloroplast genome of <it>Pseudendoclonium </it>(Ulvophyceae), in particular, is characterized by an atypical quadripartite architecture that deviates from the ancestral type by a large inverted repeat (IR) featuring an inverted rRNA operon and a small single-copy (SSC) region containing 14 genes normally found in the large single-copy (LSC) region. To gain insights into the nature of the events that led to the reorganization of the chloroplast genome in the Ulvophyceae, we have determined the complete cpDNA sequence of <it>Oltmannsiellopsis viridis</it>, a representative of a distinct, early diverging lineage.</p> <p>Results</p> <p>The 151,933 bp IR-containing genome of <it>Oltmannsiellopsis </it>differs considerably from <it>Pseudendoclonium </it>and other chlorophyte cpDNAs in intron content and gene order, but shares close similarities with its ulvophyte homologue at the levels of quadripartite architecture, gene content and gene density. <it>Oltmannsiellopsis </it>cpDNA encodes 105 genes, contains five group I introns, and features many short dispersed repeats. As in <it>Pseudendoclonium </it>cpDNA, the rRNA genes in the IR are transcribed toward the single copy region featuring the genes typically found in the ancestral LSC region, and the opposite single copy region harbours genes characteristic of both the ancestral SSC and LSC regions. The 52 genes that were transferred from the ancestral LSC to SSC region include 12 of those observed in <it>Pseudendoclonium </it>cpDNA. Surprisingly, the overall gene organization of <it>Oltmannsiellopsis </it>cpDNA more closely resembles that of <it>Chlorella </it>(Trebouxiophyceae) cpDNA.</p> <p>Conclusion</p> <p>The chloroplast genome of the last common ancestor of <it>Oltmannsiellopsis </it>and <it>Pseudendoclonium </it>contained a minimum of 108 genes, carried only a few group I introns, and featured a distinctive quadripartite architecture. Numerous changes were experienced by the chloroplast genome in the lineages leading to <it>Oltmannsiellopsis </it>and <it>Pseudendoclonium</it>. Our comparative analyses of chlorophyte cpDNAs support the notion that the Ulvophyceae is sister to the Chlorophyceae.</p>
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