Data from: Distinctive architecture of the chloroplast genome in the chlorodendrophycean green algae Scherffelia dub and Tetraselmis sp. CCMP 881

Turmel M, de Cambiaire J, Otis C, Lemieux C

Date Published: March 2, 2016

DOI: http://dx.doi.org/10.5061/dryad.3n61r

 

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Title PCG-AA_dataset
Downloaded 11 times
Description The 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.
Download PCG-AA_dataset.nex (1.103 Mb)
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Title PCG12_dataset
Downloaded 8 times
Description The 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).
Download PCG12_dataset.nex (2.365 Mb)
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Title PCG123degen_dataset
Downloaded 14 times
Description The 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).
Download PCG123degen_dataset.nex (3.282 Mb)
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Title PCG12RNA_dataset
Downloaded 14 times
Description The 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.
Download PCG12RNA_dataset.nex (2.615 Mb)
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Title PCG123degenRNA_dataset
Downloaded 7 times
Description The 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.
Download PCG123degenRNA_dataset.nex (3.705 Mb)
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When using this data, please cite the original publication:

Turmel M, de Cambiaire J, Otis C, Lemieux C (2016) Distinctive architecture of the chloroplast genome in the chlorodendrophycean green algae Scherffelia dub and Tetraselmis sp. CCMP 881. PLOS ONE 11(2): e0148934. http://dx.doi.org/10.1371/journal.pone.0148934

Additionally, please cite the Dryad data package:

Turmel M, de Cambiaire J, Otis C, Lemieux C (2016) Data from: Distinctive architecture of the chloroplast genome in the chlorodendrophycean green algae Scherffelia dub and Tetraselmis sp. CCMP 881. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.3n61r
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