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 that includes 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).