Structural Variation Detection and de novo Assembly in Complex Genomes using Extremely Long Single-Molecule Imaging

De novo genome assemblies using only short read data are generally incomplete and highly fragmented due to the intractable complexity found in most genomes.  This complexity, consisting mainly of large duplications and repetitive regions, hinders sequence assembly and subsequent comparative analyses.  We present a single molecule genome analysis system (Irys) based on NanoChannel Array technology that linearizes extremely long DNA molecules for observation.  This high-throughput platform automates the imaging of single molecules of genomic DNA hundreds of kilobases in size to measure sufficient sequence uniqueness for unambiguous assembly of complex genomes. High-resolution genome maps assembled de novo from the extremely long single molecules retain the original context and architecture of the genome, making them extremely useful for structural variation and assembly applications. 

Genome map-based scaffolding in shotgun sequencing experiments performed in parallel with second or third generation sequence production offers an integrated pipeline for whole genome de novo assembly solving many of the ambiguities inherent when using sequencing alone. Additionally, genome maps serve as a much-needed orthogonal validation method to NGS assemblies. As a result, genome maps improve contiguity and accuracy of whole genome assemblies, permitting a more comprehensive analysis of functional genome biology and structural variation.

In addition to providing an introduction to this newly available technology, we will demonstrate a number of examples of its utility in a variety of organisms, including an arthropod and crop plant.