DOI: 10.5061/dryad.nh149
title: Data from: Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae)

description: 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.
description: PCG-AA data
 setThe PCG-AA amino acid
 data set was used to infer the phylogenies presented in Figure 1. It
 contains 14,209 positions and was assembled from 69 proteins encoded in
 the chloroplast genomes of 73 green algae. The data set was prepared using
 Mesquite 3.04 and is in Nexus format.PCG-AA_dataset.nexPCG123RNA data setThe PCG123RNA nucleotide data set was used to generate the GC/AT-skew plots shown in Figure 2. It contains 48,172 positions and was assembled from 98 chloroplast genes of 73 green algae. The data set was prepared using Mesquite 3.04 and is in Nexus format. It comprises the sequences of 69 protein-coding genes (all three codon positions) as well as the sequences of 29 rRNA and tRNA genes.PCG123RNA_dataset.nexPCG123degenRNA data setThe PCG123degenRNA nucleotide data set was used to infer the phylogenies presented in Figure 3 and the additional file 1. It contains 48,172 positions and was assembled from 98 chloroplast genes of 73 green algae. The data set was prepared using Mesquite 3.04 and is in Nexus format. It comprises the sequences of 69 protein-coding genes (all three codon positions) that were degenerated using the Degen1.pl script of Regier et al. (Nature 2010 463:1079-1083) as well as the sequences of 29 rRNA and tRNA genes.PCG123degenRNA_dataset.nexPCG12RNA data setThe PCG12RNA nucleotide data set was used to infer the phylogenies presented in Figure 3 and the additional file 1. It contains 34,121 positions and was assembled from 98 chloroplast genes of 73 green algae. The data set was prepared using Mesquite 3.04 and is in Nexus format. It comprises the sequences of 69 protein-coding genes (first two codon positions) as well as the sequences of 29 rRNA and tRNA genes.PCG12RNA_dataset.nex