Genome-Wide, Highly Accurate and Sensitive Structural Variation Detection in Plants and Animals by Next-Generation Mapping

Establishing reference genomes for large, and complex genomes such as maize, rice, barley, wheat and other grass plants is now made possible by the combination of single molecule methodologies of BioNano Genomics next-generation mapping (NGM) and Pacific Biosciences sequencing as well as other long-range enabling technologies.. However, to fully reveal the level of structural diversity one needs to be able to compare multiple cultivars and organism at the whole genome level. This is being accomplished by NGM where genome wide structural variation in the form of insertions and deletion >1 kbp and inversion and large scale rearrangements can be identified in a highly efficient manner.

We report on the structural relationship between different maize and barley cultivars, where we identify thousands of insertions and deletions and hundreds of large rearrangements. We show that these rearrangements affect genic regions and predict rearrangements that effect the expression of genes and alter protein coding regions. Taken together, NGM is not only a highly efficient method to compare the structure of plant and animal genomes (SV analysis) but it is the most comprehensive as a result of exploitation of the longest read lengths by available technologies that allow access into the “dark matter” of the genome.