Data from: Chloroplast phylogenomic analysis resolves deep-level relationships within the green algal class Trebouxiophyceae

Background: The green algae represent one of the most successful groups of
photosynthetic eukaryotes, but compared to their land plant relatives,
surprisingly little is known about their evolutionary history. This is in
great part due to the difficulty of recognizing species diversity behind
morphologically similar organisms. The Trebouxiophyceae is a species-rich
class of the Chlorophyta that includes symbionts (e.g. lichenized algae)
as well as free-living green algae. Members of this group display
remarkable ecological variation, occurring in aquatic, terrestrial and
aeroterrestrial environments. Because a reliable backbone phylogeny is
essential to understand the evolutionary history of the Trebouxiophyceae,
we sought to identify the relationships among the major trebouxiophycean
lineages that have been previously recognized in nuclear-encoded 18S rRNA
phylogenies. To this end, we used a chloroplast phylogenomic approach.
Results: We determined the sequences of 29 chlorophyte chloroplast genomes
and assembled amino acid and nucleotide data sets derived from 79
chloroplast genes of 61 chlorophytes, including 35 trebouxiophyceans. The
amino acid- and nucleotide-based phylogenies inferred using maximum
likelihood and Bayesian methods and various models of sequence evolution
revealed essentially the same relationships for the trebouxiophyceans. Two
major groups were identified: a strongly supported clade of 29 taxa (core
trebouxiophyceans) that is sister to the Chlorophyceae + Ulvophyceae and a
clade comprising the Chlorellales and Pedinophyceae that represents a
basal divergence relative to the former group. The core trebouxiophyceans
form a grade of strongly supported clades that include a novel lineage
represented by the desert crust alga Pleurastrosarcina brevispinosa. The
assemblage composed of the Oocystis and Geminella clades is the deepest
divergence of the core trebouxiophyceans. Like most of the chlorellaleans,
early-diverging core trebouxiophyceans are predominantly planktonic
species, whereas core trebouxiophyceans occupying more derived lineages
are mostly terrestrial or aeroterrestrial algae. Conclusions: Our
phylogenomic study provides a solid foundation for addressing fundamental
questions related to the biology and ecology of the Trebouxiophyceae. The
inferred trees reveal that this class is not monophyletic; they offer new
insights not only into the internal structure of the class but also into
the lifestyle of its founding members and subsequent adaptations to
changing environments.