Fig. 5
From: Signatures of differential selection in chloroplast genome between japonica and indica
Nucleotide diversity and variant type of all accessions and subgroups. (a) Nucleotide diversity of whole collection, Asian rice, and wild rice. The 500 bp window size was used in this analysis. (b) Nucleotide diversity of subgroups. The sorted values were plotted in each group. Ind: indica; Niv: O. nivara; Ruf: O. rufipogon; Te_J; temperate japonica; Tr_J; tropical japonica. (c) Reduction of nucleotide diversity (πw/πc) between indica and japonica in the cp genome. The threshold of top 2.5 percentile is indicated as a red dotted circle for indica, blue circle for japonica. The regions within the 2.5 percentile are considered as candidate regions under selection. The number of genome position unit is kb. (d) Summary of variant types among the cp genome