DOI: 10.5061/dryad.3n61r
title: Data from: Distinctive architecture of the chloroplast genome in the chlorodendrophycean green algae Scherffelia dub and Tetraselmis sp. CCMP 881

description: 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.
description: PCG-AA_datasetThe PCG-AA amino acid dataset was used to infer the phylogenies presented in Figs 5 and 6. It contains 15,350 positions and was assembled from 79 proteins encoded in the chloroplast genomes of 71 green algae. The data set was prepared using Mesquite 3.04 and is in Nexus format.PCG12_datasetThe PCG12 nucleotide dataset was used to infer the phylogeny presented in Fig 5. It contains 30,684 positions and was assembled from 79 chloroplast genes of 71 green algae. The data set was prepared using Mesquite 3.04 and is in Nexus format. It comprises the sequences of 79 protein-coding genes (first two codon positions).PCG123degen_datasetThe PCG123degen nucleotide dataset was used to infer the phylogeny presented in Fig 5. It contains 46,026 positions and was assembled from 79 chloroplast genes of 71 green algae. The data set was prepared using Mesquite 3.04 and is in Nexus format. It comprises the sequences of 79 protein-coding genes (all three codon positions) that were degenerated using the Degen1.pl script of Regier et al. (Nature 2010 463:1079-1083).PCG12RNA_datasetThe PCG12RNA nucleotide dataset was used to infer the phylogenies presented in Fig 7. It contains 36,658 positions and was assembled from 108 chloroplast genes of 71 green algae. The data set was prepared using Mesquite 3.04 and is in Nexus format. It comprises the sequences of 79 protein-coding genes (first two codon positions) as well as the sequences of 29 rRNA and tRNA genes.PCG123degenRNA_datasetThe PCG123degenRNA nucleotide dataset was used to infer the phylogenies presented in Fig 7. It contains 52,000 positions and was assembled from 108 chloroplast genes of 71 green algae. The data set was prepared using Mesquite 3.04 and is in Nexus format. It comprises the sequences of 79 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.