Figure 5: Comparison of gene families between O. brachyantha and O. sativa.

(a) Size variation of gene families. All shared gene families between O. brachyantha and O. sativa, excluding one-to-one orthologues, were compared to show the variation in gene family sizes. Negative values indicate fewer family members in O. sativa, whereas positive values indicate more members in O. sativa. Os, O. sativa; Ob, O. brachyantha. (b) Copy number variation of conserved functional domains. The gene number belonging to each conserved functional domain was retrieved according to Pfam domain annotation (Methods). The χ²-test, or Fisher’s exact test when the expected frequency was smaller than five, was employed to select significantly different functional domains between O. brachyantha and O. sativa. Multiple comparisons were corrected by the Bonferroni method as implemented in R. Only significant functional domains with a total number of more than 100 members in two Oryza genomes are shown, ranked by P-value (P-value ≤2 × 10⁻⁴ and q-value ≤0.05).