Fig. 1

Identification of early mutations in O. sativa. a Manhattan plot of 756 Os mutations on 101 genes distributed across rice chromosomes (chr1–chr12). Details on sampled genes see Additional file 1: Table S1. b–h Gene genealogies of seven genes showing early mutations (in asterisks). Gene genealogies connecting indica (I) and japonica (J) of O. sativa to its wild relatives (O. rufipogon (Or) and O. nivara (On)) are shown in bar graph or tree. A graph of horizontal bars shows orthologs in bars and similarities in similar colors, with substitutions coded by colored sticks (A in green, T in red, C in blue, and G in black, and thick ones for nonsynonymous changes) and indels by arrows. A tree-like gene genealogy also uses colored sticks as above for substitutions but circles for indels. Aligned sticks refer to changes at the same nucleotide site. Number of repeated and adjacent changes is shown before x for simplicity. Allele of indica (I) is shown as the identical sequence among three indica genomes or for genome in the parentheses (Shuhui for Shuhui-498); allele of japonica (J) is from the japonica genome. Only the genic regions having early mutations are shown here