Phylogeny of A. viridiflora complex chloroplast genomes
Taking the chloroplast genome of A. viridiflora (MN809220) as a reference genome, clean reads were aligned to the reference to obtain the variation of A. viridiflora complex in the chloroplast genome and called SNPs according to the above pipeline. SNPs in the chloroplast genome were also used to infer the phylogeny of the A. viridiflora complex by Splits Tree, and the chloroplast genomes ofParaquilegia microphylla and Semiaquilegia adoxoides were regarded as outgroups (Huson & Bryant, 2006). Haplotype network analysis was performed using Median Joining Network in PopART v 1.7 to analyze the A. viridiflora complex with default parameters (Leigh & Bryant, 2015).