Figure 1

Collinearity of subgenomes in hexaploid bread wheat and allotetraploid oilseed rape. (a) Three homeologous regions from subgenomes A, B and D of bread wheat Triticum aestivum line Synthetic W7984 were aligned for direct sequence comparison [4]. Scaffold 946163 (position 27,539 to 55,967) of subgenome B, scaffold 1590518 (position 23,362 to 48,554) of subgenome D, and scaffold 235762 (position 75,800 to 97,583) of subgenome A were aligned. Collinear and inverted regions are represented by red and blue lines, respectively. For subgenomes A and D, but not B, a high degree of collinear genome duplication is observed in the central region. (b) Two homeologous regions from Brassica napus subgenome A (position 253,565 to 350,000) and subgenome C (position 409,878 to 514,393) were aligned for comparison. There were 4,331 SNPs (5.7%) within a 76 kb aligned region. A total of 32,411 bp (14.1%) InDels were detected and the length of the longest one is 4,808 bp. High collinearity between the two subgenomes was observed with minor inversion and duplication events.