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).