PMC

Comparative physical map of O. nivara with rice chromosome 1. SyMap screenshots showing the completed physical map of O. nivara chromosome 1 aligned to the O. sativa chromosome 1 pseudomolecule. (A) Whole-chromosome view of the O. nivara pseudomolecule aligned to the O. sativa chromosome 1 pseudomolecule, showing overgo marker alignments only. (B) Whole-chromosome view of the O. nivara pseudomolecule aligned to the O. sativa chromosome 1 pseudomolecule, showing both overgo marker and BAC end sequence (BES) alignments. (C) Zoomed-in view of the overgo and BES alignments between O. nivara contig 1 and the O. sativa chromosome 1 pseudomolecule. (D) More detailed view of (C) showing the actual clones comprising O. nivara contig 1 and their BESs. In this view, the alignments of individual BES can be seen, as well as individual clones that were detected by overgo markers, and the alignments of those markers to the O. sativa chromosome 1 pseudomolecule. In (A-C), BAC contigs are represented by numbered blocks which are stacked vertically to form the O. nivara pseudomolecule shown on the left of each alignment, while the O. sativa pseudomolecule is shown in brown on the right of each alignment. The red 'X' on the O. sativa pseudomolecule represents the centromere. Overgo marker names are listed in red text to the left of each alignment, while coordinates along the O. sativa pseudomolecule are listed in blue text to the right of each alignment. Green lines stretching from the O. nivara pseudomolecule to the O. sativa pseudomolecule in each alignment show where clones from the O. nivara contig align to the O. sativa chromosome, while purple lines show where O. nivara clones' BESs align to the O. sativa pseudomolecule. In (D), blue vertical lines on the left half of the figure represent O. nivara 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. 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. nivara clones hit by the marker align to the O. sativa pseudomolecule.

Alignment of O. officinalis contig to region of rice chromosome 1 showing putative inversion. Alignment of an O. officinalis contig to rice chromosome 1. Overgos confirm the placement of clones in the contig such that a putative genomic inversion of the region stretching from approximately 21.94 MB to 23.40 MB on the rice pseudomolecule is apparent. 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 BAC end sequences (BES). 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.

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.

(A) Dot plot of the pilot BAC pseudochromosome (PI A11) as aligned to the corresponding NI A11 draft pseudomolecule. (B) Dot plot of the pilot BAC pseudochromosome (PI A11) as aligned to the corresponding BI A01 draft pseudomolecule. (C) Dot plot of the pilot BAC pseudochromosome (PI D11) as aligned to the corresponding NI D11 draft pseudomolecule. (D) Dot plot of the pilot BAC pseudochromosome (PI D11) as aligned to the corresponding BI D07 draft pseudomolecule.