Optical Mapping and Nanocoding Systems Potentiate Genome Assembly and Discover Structural Variants

Current DNA sequencing technologies are producing copious amounts of sequence data that are enabling extensive analysis of genomes. However, such data are not of sufficient quality and read length for driving the assembly, or finishing of many plant and animal genomes. This failure is a major problem facing the genomics community because comparative analysis requires reference-quality, whole-genome sequence for the comprehensive discovery and understanding of all forms of polymorphism, incluing structural variation. In this regard, sequence-compatible physical maps, constructed using Optical Mapping, or Nanocoding (both systems developed by our group), offer clone-free, independent scaffolds to guide many stages of genome assembly and validation. We meet this challenge using the Optical Mapping and Nanocoding Systems, which are single-molecule platforms designed to create genome-wide ordered restriction maps from the assembly of massive datasets comprising genomic DNA molecules (~500 kb). Our analysis of such genome-wide restriction maps critically addresses several key applications where Optical Mapping, or Nanocoding:

1) provide an independent scaffold for genome sequence assembly, finishing, and validation;

2) reveal structural variation, in a comprehensive way, through identification of altered loci not discoverable, or characterizable using sequencing, CNV chips, or cytogenetic approaches.

Here, we will present the workings of our genome analysis systems and their applications to the analysis and assembly of several plant and animal genomes (rice, maize, medicago, cow, rat, and human).