a, Intragenomic and intergenomic dot plots show a clearly visible collinear region 1′ between Tu1 and Tu3 that is orthologous to the Os intragenomic collinear region 1. However, the collinearity of region 2′ between Tu1 and Tu3 is severely corrupted, but the corresponding Os intragenomic collinear region 2 was clearly visible. b–e, Similarly, Tu intragenomic collinear regions 10′, 3′, 4′ and 5′ were also clearly visible, which correspond to Os intragenomic collinear regions 10, 3, 4 and 5, respectively. However, the collinearity of Tu intragenomic regions corresponding to Os intragenomic collinear regions 11, 6, 7, 8 and 9 was disrupted. f, Data table showing the strong intragenomic collinear segments of Os and their corresponding regions of Tu (chromosomal positions are shown in Mb). *The corresponding seven pairs of ancient chromosomes based on the AGK structure24 that are ancestral to the Tu and Os chromosomes listed in the right columns. The five clearly visible regions in Tu are marked in bold. **Os regions without visible corresponding collinear regions in Tu dot plots. g, Data table showing the number of collinear genes between ancestrally duplicated chromosome segments in rice and their corresponding gene numbers in Tu.