Fig. 5

Megabase-level duplication and inversion on chromosome 4. a–c SyRI and CGRD results on chromosome 4. a The CGRD result using A188Ref1 as the reference genome. The Y-axis represents log2 values of ratios of read depths of B73 to A188, log2(B:A), signifying copy number variation (CNV). Regions with higher and lower sequence depths of B73 versus A188 were B73 plus (red) and B73 minus (blue), respectively. Green and orange represent conserved and ungrouped regions, respectively. b The SyRI result is displayed. Alignments of syntenic blocks larger than 10 kb and alignments of other rearrangements larger than 0.5 Mb are plotted. On each A188 and B73 chromosome, segments that were not aligned to the other genome or highly divergent with the other genome are highlighted. The red * labels a well-evidenced inversion. c The CGRD result using B73Ref4 as the reference genome. The similar color scheme to that in a is used. d Synteny of genes (rectangle blocks) in the well-evidenced inversion (ABinv4a) regions between A188 and B73. Blue and tan colors stand for plus and minus gene orientations. e A dot plot between the 1.8-Mb B73 region that was duplicated in A188 and its aligned regions in A188Ref1. f FISH of the PME probe on A188, B73, and F₁ (B73xA188). Cent4 probe (green) that is specifically from chromosome 4 centromere was used in F₁ FISH. Arrows and arrowheads point at PME signals of A188 and B73 chromosomes, respectively. Bar = 10 μm