The green algae are divided into the phyla Streptophyta and Chlorophyta. The Streptophyta (sensu Bremer ) encompasses the algae from the class Charophyceae and all land plants, whereas the Chlorophyta (sensu Sluiman ) contains algae from the classes Prasinophyceae, Ulvophyceae, Trebouxiophyceae and Chlorophyceae . The basal position of the Prasinophyceae in the Chlorophyta is generally well established, but the branching order of the Ulvophyceae, Trebouxiophyceae and Chlorophyceae (UTC) remains a matter of debate [4–6]. It has been proposed that a third lineage at the base of the Streptophyta and Chlorophyta is represented by Mesostigma viride [7–9], an alga traditionally classified within the prasinophytes. This green plant lineage, however, is debated, as some studies suggest that Mesostigma is an early offshoot of the phylum Streptophyta [10–12].
Investigations of chloroplast DNA (cpDNA) from green algae representing each of the five recognized classes have revealed that the genomes of the charophyte Chaetosphaeridium globosum  and the prasinophytes Mesostigma  and Nephroselmis olivacea  are highly similar to those of land plants. Like most land plants cpDNAs, these green algal genomes are partitioned into a quadripartite architecture by two copies of a large inverted repeat (IR) separating small (SSC) and large (LSC) single copy regions. Most notably, the great majority of the genes occupying a given single copy region in prasinophyte genomes map to the same single copy region in Chaetosphaeridium and land plant cpDNAs. The increased structural stability of the chloroplast genome conferred by the IR sequence has been hypothesized to limit gene exchanges between the SSC and LSC regions . The IR region readily expands or contracts and thus can easily gain or lose genes from the neighbouring single copy regions through a process known as the ebb and flow . Despite its variable gene content, the IR always features the ribosomal RNA (rRNA) operon (rrs-I(gau)-A(ugc)-rrl-rrf) and this operon is always transcribed toward the SSC region. In addition to their characteristic pattern of gene partitioning, prasinophyte and streptophyte chloroplast genomes share a number of features that were most probably inherited from the progenitor of all green plant cpDNAs. First, they have retained several gene clusters that date back to the cyanobacterial ancestor of all chloroplasts. Second, their genes are densely packed and their intergenic regions virtually lack short dispersed repeats (SDRs). Finally, with 128 to 137 genes, their gene repertoire is one of the largest among green plant cpDNAs.
In contrast, the chloroplast genome has been substantially reorganized in the UTC. The quadripartite architecture has been lost from the genome of the trebouxiophyte Chlorella vulgaris  following the disappearance of one copy of the IR sequence. Although the quadripartite architecture has been retained in the genome of the ulvophyte Pseudendoclonium akinetum , the IR sequence is atypical in featuring a rRNA operon transcribed towards the LSC region . In addition, the pattern of gene partitioning within the SSC/LSC regions of Pseudendoclonium cpDNA deviates significantly from those found in its prasinophyte and land plant counterparts; the small single copy region of this ulvophyte genome includes 14 genes that are usually located within the LSC region. In the chlorophycean alga Chlamydomonas reinhardtii , the two single copy regions are similar in size and the genes are so thoroughly scrambled that no distinction is possible between the SSC and LSC regions. The Chlorella, Pseudendoclonium and Chlamydomonas chloroplast genomes have lost many of the ancestral gene clusters that are shared between Mesostigma and Nephroselmis cpDNAs, feature a reduced gene content (from 94 genes in Chlamydomonas to 112 genes in Chlorella) compared to prasinophyte and streptophyte genomes, and contain SDRs in their intergenic regions. The low density of coding sequences in these genomes is explained not only by the smaller number of genes but also by the expansion of intergenic regions. Moreover, unlike Mesostigma and Nephroselmis cpDNAs, the chloroplast genomes of the three UTC algae have acquired group I introns (from three in Chlorella to 27 in Pseudendoclonium) and group II introns (two in Chlamydomonas).
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 Oltmannsiellopsis viridis. This marine unicellular green alga exhibits a counterclockwise arrangement of basal bodies [19, 20] and a single cup-shaped chloroplast . Previously classified in the Chlorophyceae [19, 21], Oltmannsiellopsis is currently considered to be the type species of the order Oltmannsiellopsidales (Ulvophyceae) . The Oltmannsiellopsidales have been shown to branch at the base of the Ulvophyceae  and have been used as outgroup for phylogenetic analyses of the Ulvophyceae [23–25]. Considering that Pseudendoclonium represents a distinct, early diverging lineage of the Ulvophyceae (Ulotrichales, see supplementary Figure S1 in ), identification of the set of features common to Oltmannsiellopsis and Pseudendoclonium cpDNAs should throw light into the chloroplast genome architecture of the earliest diverging ulvophytes and, accordingly, into the cpDNA changes that occurred in the separate lineages leading to Oltmannsiellopsis and Pseudendoclonium. We found that the IR-containing genome of Oltmannsiellopsis differs considerably from its Pseudendoclonium and other chlorophyte counterparts in intron content and gene order, but shares closer similarities with Pseudendoclonium cpDNA in terms of quadripartite architecture, gene content and gene density. In the context of the debate concerning the branching order of the UTC lineages, the predicted architecture of the chloroplast genome of the earliest members of the Ulvophyceae strengthens the notion that this lineage is sister to the Chlorophyceae [5, 6].