Figure 3

Example of the A genome curing process for a section of unigene. Each panel shows an example alignment window for a section of a unigene between bases 110 and 150. Within each panel, the top line is the reference sequence, underneath are the aligned of 40 base B. rapa reads. Base differences from the reference are shown in blue. Cured bases in the reference and aligned reads are shown in orange. Panel A shows cycle 1 of the curing process. A small number of B. rapa reads are aligned against the naive reference sequences in sections of the unigene where there are no more than 3 mismatches. At the end of the curing process at position 116, the T will be changed to a G in the reference sequence, this will enable more reads to align in this section of the unigene on the next cycle. Panel B shows cycle 3. Changes have been made in the reference sequence for positions 116 (T → G), 125 (A → C), 141 (C → T), 149 (C → G), these are shown in orange. This has enabled more reads to align to the middle section of the unigene. Panel C shows cycle 6. A further two changes have been made in the reference sequence at positions 131 (G → A), 132 (C → G). At this stage, a large number of B. rapa reads are aligning against the reference sequence with no mismatches. The reference sequence now becomes the A genome ‘cured’ reference.