Optical Map Description
Description
Optical Mapping is a single-molecule approach for the construction of ordered restriction maps developed by Dr. David Schwartz. It uses large (250-3,000 kb), randomly sheared genomic DNA molecules as the substrate for map construction. Optical mapping dispenses with electrophoretic approaches, and uses light microscopy to directly image individual DNA molecules that are bound to specially derivatized surfaces and then cleaved by restriction enzymes. Importantly, cleaved fragments retain their original order, and cut sites are flagged by small, visible gaps. By determining the existence of these sequence-specific cut sites and the distances between them, a landmark map of the DNA sequence can be created. Such restriction enzyme maps provide a useful backbone for the alignment and verification of sequence data.
Correlation to the physical map
The Phyrenophora Optical Maps have been constructed using the restriction enzyme AflII A. The resulting maps correspond to 98X physical coverage and consists of 11 linkage maps. In silico restriction maps of Phyrenophora assembly were generated. The correspondences of the restriction enzyme cutting sites and the predicted fragment lengths have been used to order and orient the scaffolds of the Phyrenophora assembly to the optical map. This procedure mapped more than 96% of the assembled scaffolds, which corresponds to more than 90% of the optical map. The table below contains detailed mapping information.
| Optical Linkage group | Estimated Size(Mb) | Mapped Scaffolds | Scaffold Size bases |
|---|---|---|---|
chr1 | 10.166 | 10, 33, 18,1,17 | 9504070 |
chr2 | 5.206 | 16,2,25,23 | 4322225 |
chr3 | 3.708 | 12,14,13, | 3360438 |
chr4 | 3.301 | 3 | 3079310 |
chr5 | 3.151 | 5 | 2676520 |
chr6 | 2.951 | 4 | 2786553 |
chr7 | 2.753 | 0,15,11 | 2612382 |
chr8 | 2.391 | 8,24,26 | 2114921 |
chr9 | 2.287 | 9,22,27 | 2025946 |
chr10 | 2.204 | 6 | 1984879 |
chr11 | 2.113 | 7 | 1887525 |
Total | 40.231 | 36354769 |
You can view the linkage group maps graphically using the links above, or you can download the complete set of all markers in the XML file pgmap.xml, which includes restriction enzyme cutting sites and their contig positions located in our assembly (see Download for data details).
A poster-sized version of the optical-physical maps is also available.
Discrepancies
The placement of the scaffold to the optical map is based on the statistical measure of the correspondence of the restriction enzyme sites between the assembly and the optical map. Discrepancies (indicated by - in the map) were created when some of the cutting sites are only presented in one of the two maps, even though the scaffold can be unambiguously placed.
For example, the resolution of the optical map will only allow the detection of fragments that are 5kb or larger. Therefore, some restriction enzyme cutting sites presented in the physical map are missed in the optical map.
In addition, some of the discrepancies may reflect the potential misassembly in the highly repetitive regions of the genome.
