Data from: Comparative analysis of Begonia plastid genomes and their utility for species-level phylogenetics

Kidner C, Harrison N, Harrison R

Date Published: April 12, 2016

DOI: http://dx.doi.org/10.5061/dryad.cp4mb

 

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Title Region21_Mulitiple_alignment
Downloaded 6 times
Description (ndhI-ndhG) Plastid sequences containing high sequence divergence that could be suitable for phylogenetic analyses at the species level in Begonia. Short (804 bp), Sanger-sequence-able region with average pairwise identity of 86.7%. Bayesian inference phylogenetic reconstruction analysed under a GTR+I+G model performed in MrBayes, with 13 taxa rooted on B.varipeltata.
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Title Region24_multiple_alignment
Downloaded 4 times
Description (rpoB–psbD) Plastid sequences containing high sequence divergence that could be suitable for phylogenetic analyses at the species level in Begonia. Medium length (1360 bp), with average pairwise identity of 93.9%. Bayesian inference phylogenetic reconstruction analysed under a GTR+I+G model performed in MrBayes, with 16 taxa rooted on B.bogneri.
Download Region24_multiple_alignment.nex (31.04 Kb)
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Title Whole_plastid_alignment
Downloaded 26 times
Description The draft sequence generated for B. peltata was used as a reference to map each set of assembled contigs for all sixteen Begonia species (including B. peltata). Plastid genome contigs were aligned to B. peltata using MAFFT v6.717 (Multiple Alignment using Fast Fourier Transform) (30) applying the iterative refinement method (FFT-NS-i) and using default parameter settings (gap opening penality: 1.53, offset-value: 0.0) and then visually inspected and manually adjusted in the software program Geneious Pro 5.6.3 (http://www.geneious.com/).
Download Whole_plastid_alignment.nex (2.903 Mb)
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When using this data, please cite the original publication:

Harrison N, Harrison RJ, Kidner C (2016) Comparative analysis of Begonia plastid genomes and their utility for species-level phylogenetics. PLOS ONE 11(4): e0153248. http://dx.doi.org/10.1371/journal.pone.0153248

Additionally, please cite the Dryad data package:

Kidner C, Harrison N, Harrison R (2016) Data from: Comparative analysis of Begonia plastid genomes and their utility for species-level phylogenetics. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.cp4mb
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