Fig. 2

Non-neutral evolution of CMT3 in the Brassicaceae is correlated with reduced levels of genic mCG and numbers of gbM loci. a Distribution of mCG upstream, downstream, and within gene bodies of Brassicaceae species and outgroup species Prunus persica. MCG levels within gene bodies of Brassicaceae species are within the bottom 38% of 34 angiosperms. Data used represent a subset of that previously published [19, 25]. TSS transcriptional start site, TTS transcriptional termination site. b Similarly, the number of gbM genes within the genome of Brassicaceae species are within the bottom 15% of 34 angiosperms. The size of the circle corresponds to the number of gbM genes within each genome. Data used represent a subset of that previously published [19, 25]. c Changes at the amino acid level of CMT3 is correlated to reduced genic levels of DNA methylation and number of gbM genes in the Brassicaceae. An overall higher rate of molecular evolution, measured as the number of non-synonymous substitutions per non-synonymous site (dN) divided by the number of synonymous substitutions per synonymous site (dS) (ω), was detected in the Brassicaceae. Also, a higher rate ratio of ω was detected in the Brassicaceae clade containing B. rapa and closely related species compared to the clade containing A. thaliana and closely related species. The higher rate ratio in the Brassicaceae, compared with the background branches, was not attributed to positive selection