Data from: Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae)

Huang DI, Hefer CA, Kolosova N, Douglas CJ, Cronk QCB

Date Published: May 18, 2015

DOI: http://dx.doi.org/10.5061/dryad.nj5h5

 

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Title Populus-aligned plastome sequence alignments
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Description WGS short reads were aligned to the Nisqually-1 chloroplast reference genome (GenBank: EF489041.1) using BWA version 0.6.2. For each position in the reference plastome, bases were called only if the coverage was greater than 1000 reads, as the average read depth for each base pair was 7000 or greater. To improve accuracy, bases were only called if the 1000+ calls agreed for either the reference or alternate base for at least 80% of the reads. Any position not meeting these criteria was called as missing data. Indels were excluded for all analyses.
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Title Manihot-aligned plastome sequence alignments
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Description Using the same protocol as the Populus-aligned dataset, but aligned to the Manihot esculenta reference plastome (NCBI Reference Sequence: NC_010433.1).
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Title pop_to_manihot_beauti.xml
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Description XML file generated by BEAUTi for use by BEAST for dating analyses.
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Title pop_to_manihot.log
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Description BEAST log file
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Title pop_to_manihot.trees
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Description NEXUS tree file containing trees generated by BEAST.
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Title ns_vs_s
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Description Divergence statistics for the four species that were de novo assembled (P. trichocarpa, P. balsamifera, P. fremontii, Salix interior). These were calculated using scripts "parse_fasta_to_genes.pl" and "diffs.pl" from https://github.com/daisieh/phylogenomics/releases/tag/v1.01-nph
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When using this data, please cite the original publication:

Huang DI, Hefer CA, Kolosova N, Douglas CJ, Cronk QCB (2014) Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae). New Phytologist 204(3): 693-703. http://dx.doi.org/10.1111/nph.12956

Additionally, please cite the Dryad data package:

Huang DI, Hefer CA, Kolosova N, Douglas CJ, Cronk QCB (2014) Data from: Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae). Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.nj5h5
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