Comparative Genomics in Cotton Using High-Throughput, Whole Genome Mapping

Massively parallel sequencing (MPS) has enabled great strides forward in comparative genomics.  However, certain large genomic differences known as structural variants (SVs) are difficult to detect with the short DNA inserts typically used for MPS.  Characterization of much longer, contiguous DNA molecules gives more genomic context and so it may facilitate the discovery of SVs that exist between closely related species. One method for such characterization is to use a modified restriction enzyme to detect specific sequence motifs, revealing a pattern of intervening distances. Long DNA molecules characterized in this way can be assembled into maps that represent the whole genome.  Here we apply this method of high-throughput, whole genome mapping for SV detection between three different species of Cotton.