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

Lemieux C, Vincent AT, Labarre A, Otis C, Turmel M

Date Published: November 23, 2015

DOI: http://dx.doi.org/10.5061/dryad.nh149

 

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Title PCG-AA data set
Downloaded 27 times
Description The 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.
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Title PCG123RNA data set
Downloaded 18 times
Description The 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.
Download PCG123RNA_dataset.nex (3.528 Mb)
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Title PCG123degenRNA data set
Downloaded 21 times
Description The 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.
Download PCG123degenRNA_dataset.nex (3.530 Mb)
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Title PCG12RNA data set
Downloaded 9 times
Description The 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.
Download PCG12RNA_dataset.nex (2.503 Mb)
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When using this data, please cite the original publication:

Lemieux C, Vincent AT, Labarre A, Otis C, Turmel M (2015) Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae). BMC Evolutionary Biology 15: 264. http://dx.doi.org/10.1186/s12862-015-0544-5

Additionally, please cite the Dryad data package:

Lemieux C, Vincent AT, Labarre A, Otis C, Turmel M (2015) Data from: Chloroplast phylogenomic analysis of chlorophyte green algae identifies a novel lineage sister to the Sphaeropleales (Chlorophyceae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.nh149
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