Fusarium oxysporum mapping
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 F. oxysporum Optical Maps were constructed using the restriction enzyme BsiWI. The resulting map corresponds to ~55X physical coverage and consists of 15 linkage maps. In silico restriction maps of the F. oxysporum assembly were generated. The correspondences of the restriction enzyme cutting sites and the predicted fragment lengths were used to order and orient the scaffolds of the assembly to the optical map. This procedure mapped more than 96% of the assembled scaffolds, which corresponds to more than 91.4% of the optical map.
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 fusarium_oxysporum_2_assembly_map.xml, which includes restriction enzyme cutting sites and their contig positions located in our assembly (see Supplementary Download for data details). A poster-sized version of the optical-physical maps is also available.
Discrepancies
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 present in one of the two maps, even though the scaffold can be unambiguously placed. For example, resolution of the optical map will only allow the detection of fragments that are 5 kb or larger. Therefore, some restriction enzyme cutting sites present 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.