Optical Mapping
Optical mapping is a molecular technique that produces fingerprints of DNA sequences in order to construct genome-wide maps. The sequence markers can be ordered restriction fragments, or specific sequence motifs (nick sites).
The optical mapping procedure first stretches relatively intact (minimally-sheared) linear DNA fragments on a glass surface or in a nanochannel array, and then directly images the locations of the restriction sites or sequence motifs under light microscopes, with the aid of dye or fluorescent label.
Optical mapping has been widely used to improve de novo plant genome assemblies, including rice, maize, Medicago, Amborella, tomato and wheat, with more genomes in the pipeline.
We use Bionano Irys system to offer optical mapping service that provides long-range information of the genome and can more easily identify large structural variations.
The ability of optical mapping to assay long single DNA molecules nicely complements short-read sequencing which is more suitable for the identification of small and short-range variants.
Optical Map Guided Genome Assembly
There are several ways in the assembly process that optical mapping can assist in building high quality reference genomes. De novo constructed optical maps offer independent evidence to connect and bridge adjacent sequence contigs or scaffolds.
Genome assemblies guided by optical maps consist of three key computational steps. The initial step is the de novo assembly of optically mapped molecules to construct a ‘consensus’ optical map from single DNA molecules at high redundancy. The consensus map has to deal with errors specific to optical mapping including missing cuts, false cuts, inaccurate fragment sizes, and chimeric maps.
The next step is to align the in silico digested contig sequences to the consensus optical map.
The final step is the joining of neighbouring contig sequences to construct supercontigs on the basis of their locations on the optical map.
For small microbial genomes, the resulting assemblies could contain a single extent of sequence that spans the entire genome, while for large eukaryotic genomes the combined efforts of sequencing and optical mapping often result in substantially increased scaffold N50. In several cases, the mapping data allow the reconstruction of entire chromosomes.
Beyond ordering and orientating contigs, optical maps provide an additional layer of validation to the sequence assemblies. Optical maps could potentially identify and resolve misassemblies – false joins, inversions or translocations that are artifacts, which occurred during the sequence assembly.