Fig. 1.
Fig. 1.

The schematic diagram of hierarchical map of orthologous genomic regions (OGRs) between two genomes. The OGRs from different levels were detected through different types of markers. Since the average size of high-level OGRs would be much longer than low-level OGRs, each high-level OGR would contain one or more low-level OGRs, representing a parent–child structure. (A) A schematic diagram of high-level OGRs; (B) A schematic diagram of low-level OGRs, which position or orientation changes could represent the structural changes at the high-level OGR. The left one shows an intrachromosomal transposition and right one shows an inversion. The blue color indicates the regions are located at OGRs, and the yellow color indicates the regions are not located at OGRs.

 


Fig. 2.
Fig. 2.

The hierarchical map of orthologous genomic regions (OGRs) between two cucumbers. The hierarchical map with three levels was constructed including chrOGRs, proOGRs, and dnaOGRs. The chrOGRs were previously constructed based on simple-sequence repeats (Ren et al., 2009; Yang et al., 2012) and the proOGRs were detected by i-ADHoRe and the dnaOGRs by Mugsy (Angiuoli and Salzberg, 2011). Finally, in cucumber, seven chrOGRs (innermost circle), 540 proOGRs (inner circle), and 22,312 dnaOGRs (outmost circle) were detected.

 


Fig. 3.
Fig. 3.

An example of the large-scale genomic changes detected at the orthologous genomic regions (OGRs; chrOGR and proOGR levels) between two cucumbers. (A) There are four proOGRs present in the third chrOGR of the map (its identification is 3). Thus, according to their orders between the two chromosomes, there must have occurred an intrachromosomal transposition; (B) the third proOGR seems to be an inversion suggested by the orders of its 16 children dnaOGRs.