Data from: Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae)

Background: The class Chlorophyceae (Chlorophyta) includes morphologically
and ecologically diverse green algae. Most of the documented species
belong to the clade formed by the Chlamydomonadales (also called
Volvocales) and Sphaeropleales. Although studies based on the nuclear 18S
rRNA gene or a few combined genes have shed light on the diversity and
phylogenetic structure of the Chlamydomonadales, the positions of many of
the monophyletic groups identified remain uncertain. Here, we used a
chloroplast phylogenomic approach to delineate the relationships among
these lineages. Results: To generate the analyzed amino acid and
nucleotide data sets, we sequenced the chloroplast DNAs (cpDNAs) of 24
chlorophycean taxa; these included representatives from 16 of the 21
primary clades previously recognized in the Chlamydomonadales, two taxa
from a coccoid lineage (Jenufa) that was suspected to be sister to the
Golenkiniaceae, and two sphaeroplealeans. Using Bayesian and/or maximum
likelihood inference methods, we analyzed an amino acid data set that was
assembled from 69 cpDNA-encoded proteins of 73 core chlorophyte (including
33 chlorophyceans), as well as two nucleotide data sets that were
generated from the 69 genes coding for these proteins and 29 RNA-coding
genes. The protein and gene phylogenies were congruent and robustly
resolved the branching order of most of the investigated lineages. Within
the Chlamydomonadales, 22 taxa formed an assemblage of five major
clades/lineages. The earliest-diverging clade displayed Hafniomonas laevis
and the Crucicarteria, and was followed by the Radicarteria and then by
the Chloromonadinia. The latter lineage was sister to two superclades, one
consisting of the Oogamochlamydinia and Reinhardtinia and the other of the
Caudivolvoxa and Xenovolvoxa. To our surprise, the Jenufa species and the
two spine-bearing green algae belonging to the Golenkinia and Treubaria
genera were recovered in a highly supported monophyletic group that also
included three taxa representing distinct families of the Sphaeropleales
(Bracteacoccaceae, Mychonastaceae, and Scenedesmaceae). Conclusions: Our
phylogenomic study advances our knowledge regarding the circumscription
and internal structure of the Chlamydomonadales, suggesting that a
previously unrecognized lineage is sister to the Sphaeropleales. In
addition, it offers new insights into the flagellar structures of the
founding members of both the Chlamydomonadales and Sphaeropleales.