Tomato Model 4 and Arabidopsis Model 3 comparison. (A) Correlations between TomatoCyc GM genes SM scores based on Model 3 and Model 4. Colour: data point density ranges from high (yellow) to medium (purple), to low (fading purple). (B) Correlation of TomatoCyc SM genes SM scores based on Model 3 and Model 4. (C) Correlations in feature importance values based on Model 3 and Model 4. Arrows point to example consistent and inconsistent features. (D–F) Feature value distributions for annotated SM and GM genes that are predicted as SM or GM genes by Model 3 and Model 4. P-values are from Kruskal–Wallis tests and post hoc comparisons were made using the Dunn’s test. Different letters indicate statistically significant differences between groups (P < 0.05). (D) Log₂ of normalized gene family size. (E) Normalized expression breadth based on the meristem development data. (F) Normalized maximum dN/dS between tomato genes and their homologs in C. canephora.