Data from: Distinctive architecture of the chloroplast genome in the chlorodendrophycean green algae Scherffelia dub and Tetraselmis sp. CCMP 881

The Chlorodendrophyceae is a small class of green algae belonging to the
core Chlorophyta, an assemblage that also comprises the Pedinophyceae,
Trebouxiophyceae, Ulvophyceae and Chlorophyceae. Here we describe for the
first time the chloroplast genomes of chlorodendrophycean algae
(Scherffelia dubia, 137,161 bp; Tetraselmis sp. CCMP 881, 100,264 bp).
Characterized by a very small single-copy (SSC) region devoid of any gene
and an unusually large inverted repeat (IR), the quadripartite structures
of the Scherffelia and Tetraselmis genomes are unique among all core
chlorophytes examined thus far. The lack of genes in the SSC region is
offset by the rich and atypical gene complement of the IR, which includes
genes from the SSC and large single-copy regions of prasinophyte and
streptophyte chloroplast genomes having retained an ancestral
quadripartite structure. Remarkably, seven of the atypical IR-encoded
genes have also been observed in the IRs of pedinophycean and
trebouxiophycean chloroplast genomes, suggesting that they were already
present in the IR of the common ancestor of all core chlorophytes.
Considering that the relationships among the main lineages of the core
Chlorophyta are still unresolved, we evaluated the impact of including the
Chlorodendrophyceae in chloroplast phylogenomic analyses. The trees we
inferred using data sets of 79 and 108 genes from 71 chlorophytes indicate
that the Chlorodendrophyceae is a deep-diverging lineage of the core
Chlorophyta, although the placement of this class relative to the
Pedinophyceae remains ambiguous. Interestingly, some of our phylogenomic
trees together with our comparative analysis of gene order data support
the monophyly of the Trebouxiophyceae, thus offering further evidence that
the previously observed affiliation between the Chlorellales and
Pedinophyceae is the result of systematic errors in phylogenetic
reconstruction.