Rosaceae Mitochondrial Genome Comparative Analysis

Twenty-eight genes from 12 Rosaceae species’ mitochondrial genomes were series connected for polygenic nucleotide alignment to estimate the selective pressure at the species level. The 12 species were P. betulifolia, Pyrus pyrifolia, M. domestica, Malus hupehensis, Sorbus aucuparia, S. torminalis, C. speciosa, E. japonica, P. avium, Prunus salicina, F. orientalis, and R. chinensis. The Yn00 module in PAML (v4.9) [60 (link)] was used to estimate the separate non-synonymous substitutions (dNs), synonymous substitutions (dSs), and dN/dS rates. The parameters were as follows: verbose = 0, icode = 0, weighting = 0, common 3×4 = 0 (use one set of codon frequencies for all pairs), ndata = 1. The boxplot and heatmap were created using the R-package (v3.2.2) (ggplot2 and heatmaply) [61 ,62 (link)].