Duplication, evolutionary and expression features important for Model 1 predictions of SM and GM genes. (A) Log10 of gene family size (number of paralogs) for the families GM (blue) and SM genes belong to. All P-values are from the Mann–Whitney U-tests between SM and GM genes. (B) Percent of GM and SM genes with at least one duplicates derived from tandem or syntenic mechanism. (C) Maximum dN/dS values from comparisons of tomato SM and GM genes to homologs in C. canephora. (D) Maximum dN/dS values of tomato SM and GM genes to their paralogs. (E) Phylogenetic tree of 26 species and a bar plot showing the percentage of tomato GM and SM genes that have at least one homologs in each species. (F–I) Distributions of maximum fold change (F–G) across all conditions in expression data sets including (F) the meristem development, (G) the circadian, and (H) between mutant and control in mutant data set and (I) treatment and control in hormone treatment data set.
