Abstract
Optical mapping is a technology that gathers long-range information on genome sequences similar to ordered restriction digest maps. Because it is not subject to cloning, amplification, hybridisation or sequencing bias, it is ideally suited to the improvement of fragmented genome assemblies that can no longer be improved by classical methods. In addition, its low cost and rapid turnaround make it equally useful during the scaffolding process of de novo assembly from high throughput sequencing reads. We describe how optical mapping has been used in practice to produce high quality vertebrate genome assemblies. In particular, we detail the efforts undertaken by the Genome Reference Consortium (GRC), which maintains the reference genomes for human, mouse, zebrafish and chicken, and uses different optical mapping platforms for genome curation.
Highlights
Optical Mapping ‘Optical mapping’ is a term originally coined for a method to produce ordered restriction maps by optical inspection and sizing of restriction fragments created from single linearised DNA molecules
Whilst the initial approaches focussed on quality checking of selected genome regions, gap sizing, placement of previously unlocalised contigs and variation detection, the applications extend into de novo sequence assembly creation and the investigation of methylation profiles [2,3]
Optical mapping was successfully used to confirm eight large insertions identified by fosmid one-end-anchoring to the human reference assembly NCBI35 [8]. This analysis was performed on an automated platform and involved assembling individual single-molecule restriction map (Rmap) into consensus maps, which could subsequently be aligned to an in silico digest of the reference genome, covering 95% of the reference sequence
Summary
Optical Mapping ‘Optical mapping’ is a term originally coined for a method to produce ordered restriction maps by optical inspection and sizing of restriction fragments created from single linearised DNA molecules. This analysis was performed on an automated platform and involved assembling individual Rmaps into consensus maps, which could subsequently be aligned to an in silico digest of the reference genome, covering 95% of the reference sequence. In an approach combining curation of existing assemblies and the contiguation of de novo assemblies, the rat reference genome sequence was improved through largeinsert mate pair library-assisted re-scaffolding of the RGSC3.4 reference, and optical consensus maps were used to confirm observed discordances [18].
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