Fig. 3

Types of genes in O. sativa. a A flow chart showing the movement of parental genes into genomes of O. sativa and eight gene types in standing rice. The left panel classifies the parental orthologs into Or (O. rufipogon, in yellow) and On (O. nivara, in dark green) and their common ones (in dark red). The middle and right panels show the current types of rice genes observed in genomes of indica (i) and japonica (j), with the integrated types further broken down into four classes, along with new alleles, in the right panel. b A genealogy of Type 1 gene. The example by EPSPS of the shikimate pathway shows no changes. c A genealogy of Type 2 gene. A resemblance to On sequence is seen at PGMp of glycolysis. d A genealogy of Type 3 gene. A resemblance to Or sequence is shown by GS3, a regulator of grain size. e A genealogy of Type 4 gene. The well-mixed type is found in the coding regions of SSY3 in starch synthesis. f Type-5 gene genealogies with Or-j and On-i associations. It appears in both 5′ and coding regions of ACC7, a gene likely involved in ethylene synthesis. g Type-6 gene genealogies with Or-i and On-j associations. 5′ regions of two genes, B2 (a regulator on the anthocyanin pathway) and an unknown gene, show the associations. h Genealogies of a Type 7 gene. Different origins of 5′ and coding regions is at C1. i Genealogies of Type 8 genes. Mutations causing multiple amino-acid changes in Hd3a led to the Nipponbare allele of Hd3a. And an early stop codon led to a new allele of OsDFR in japonica lineage. Gene genealogies follow the format of Fig. 1