S. sclerotiorum
Gene Search
Optical Map Description
Optical Map Description
- Description
- Correlation to Physical Map
- Discrepancies
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 Sclerotinia Optical Map was constructed by OpGen using the restriction enzyme BsiWI. The map consists of 16 linkage maps, which appear to correspond to chromosome units. The map labeled ChrR is linked to rDNA repeats, which are found in scaffold 35 (unmapped). An in silico restriction digest of Sclerotinia assembly was generated to compare the assembly to the optical map. Correspondence of the restriction enzyme cutting sites and the predicted fragment lengths were used to order and orient the scaffolds of the Sclerotinia assembly to the optical map. This procedure anchored more than 99% of the assembly to the optical map; the 34 anchored scaffolds cover 99% of the optical map. Note that scaffold 4 aligns to 2 optical contigs; inspection of the assembly supports that there is a mis-join in scaffold 4 between contigs 132 and 133. The table below contains detailed mapping information.
| Optical Linkage group | Estimated Size (bp) | Mapped Scaffolds | Scaffold Size (bp) |
|---|---|---|---|
| chr1 | 3,948,739 | 14,2 | 3,912,589 |
| chr2 | 3,640,719 | 23,5,22 | 3,641,033 |
| chr3 | 3,325,761 | 24,1 | 3,307,640 |
| chr4 | 2,840,231 | 3,31 | 2,845,027 |
| chr5 | 2,803,940 | 19,7 | 2,792,001 |
| chr6 | 2,460,180 | 21,9 | 2,447,375 |
| chr7 | 2,270,692 | 6,30 | 2,271,831 |
| chr8 | 2,086,271 | 4,16 | 2,087,807 |
| chr9 | 2,070,048 | 11,29,27 | 2,064,520 |
| chr10 | 2,037,788 | 28,34,10 | 2,013,218 |
| chr11 | 1,852,417 | 20,17 | 1,846,526 |
| chr12 | 1,846,714 | 8,33 | 1,840,847 |
| chr13 | 1,804,156 | 26,12 | 1,736,569 |
| chr14 | 1,741,303 | 13,25 | 1,724,183 |
| chr15 | 1,408,144 | 15,32 | 1,387,464 |
| chrR | 2,411,687 | 4,18 | 2,356,928 |
| Total | 38,548,792 | 38,275,558 |
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.