Figure 6: Distribution of sequence rearrangements along the chromosomes of O. sativa.

Segmental duplications, tandem duplications, inversions and non-collinear sequence blocks were detected as described in Methods. (a), Donors and acceptors of segmental duplications on rice chromosomes are connected by red lines. (b), Chromosome ideograms in the inner circle are represented by different colours, with chromosome numbers indicated. The three internal heatmaps represent inversions (c), expansion of tandem gene duplications (d) and expansion of non-collinear sequence blocks (e), in which expansion in rice is indicated by red colour and expansion in O. brachyantha indicated by blue colour. Of the 214 inversions between O. brachyantha and rice genomes, only inversions with more than two collinear genes are shown. Of the 2,460 orthologous tandem gene clusters, 1,378 tandem clusters expanded in the rice genome are shown as red colour and 654 tandem clusters expanded in O. brachyantha are shown as blue colour. Of the non-collinear sequence blocks, only those regions that had expanded more than double in size in rice or O. brachyantha are shown in red or blue, respectively. (f), The densities of genes, RNA retrotransposons and DNA transposons are shown as green, red and orange histograms in the outer circle, respectively. Min–Max: gene (0–25%); RNA retrotransposon (0–80%); DNA transposon (0–80%). Centromeres are indicated by black bars in the outer circle.