Figure 6

Alignment of O. officinalis contig to rice chromosome 1. A detailed view of the alignment of an O. officinalis BAC contig to the O. sativa chromosome 1 pseudomolecule using BAC end sequences (BES) and overgo markers. The hybridizations of overgos 4jp1069094 and 4jp1110186 in particular to O. officinalis BAC clones drove the merger of two initially separated contigs to form the O. officinalis contig shown here. The brown bar on the right side of the figure represents a portion of the O. sativa chromosome 1 pseudomolecule, and the coordinates along the pseudomolecule are listed in blue on the righthand side of the pseudomolecule. Blue vertical lines on the left half of the figure represent O. officinalis BAC clones. Circles on the ends of the clones represent BESs. Open circles are BESs that did not match sequences from O. sativa, while closed circles are BESs that matched O. sativa sequences. Purple lines stretching from a BES on the left to the pseudomolecule on the right show where the BES to which the line is attached aligns to the pseudomolecule. Red text on the left side of the figure shows the names of overgo markers with hits to clones in the O. officinalis BAC contig shown. In the case of overgo markers, a marker will often hit more than one BAC clone. Green lines stretch from the middle of all clones hit by that marker to a red "marker join dot." The green line stretching from the marker join dot to the pseudomolecule shows where the marker sequence is located on the pseudomolecule, thereby showing where the O. officinalis clones hit by the marker align to the O. sativa pseudomolecule.