Genetic 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 Paracoccidioides brasiliensis Pb18 Optical Maps have been constructed using the restriction enzyme BsiWI(C^GTACG). The maps correspond to ~100X physical coverage and consists of 5 linkage maps. In silico restriction maps of the genome 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 to the optical map.

You can graphically view the correlation between the physical maps and the optical maps from the Optical Maps page.

Table

Optical Linkage group	Estimated Size (Mb)	Mapped Scaffolds	Scaffold Size (bases)
chr1	10.131	1,11,7,3	10078669
chr2	5.769	9,6,17,15,5	6040062
chr3	5.216	2,13	4482540
chr4	4.315	12,4,18	4249602
chr5	3.088	10,14,8	2664186
Total	28.519		27515059