Recent, rapid radiations make species-level phylogenetics difficult to resolve. We used a multiplexed, high-throughput sequencing approach to identify informative genomic regions to resolve phylogenetic relationships at low taxonomic levels in Begonia from a survey of sixteen species. A long-range PCR method was used to generate draft plastid genomes to provide a strong phylogenetic backbone, identify fast evolving regions and provide informative molecular markers for species-level phylogenetic studies in Begonia.
Region21_Mulitiple_alignment
(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.
Region24_multiple_alignment
(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.
Whole_plastid_alignment
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/).
