Accurate Construction of the Genomic Architecture of Plants and Animals Using the Whole Genome Mapping Technology

High accuracy genomic architecture characterization is a critical element of reference genome assembly as it enables detection of potentially important structural variations, such as indels, inversions and translocations. Rapid advances in Next Gen Sequencing (NGS) technology have facilitated detailed analysis of small variation detection, including SNPs and local rearrangements. However, global genomic rearrangements remain elusive due to short read lengths of NGS data.  OpGen’s Whole Genome Mapping (WGM) generates long single molecule maps (>250 kb to 2.5Mb in length) using an automated and rapid approach. Combining sequence assembly and WGM data, OpGen’s Genome-Builder™ bioinformatics software applies a hybrid approach for long range pair-wise scaffolding to span large gaps. This provides an effective method for quickly bringing the reference genome assembly to a complete, chromosome level view. Data from initial Genome-Builder studies demonstrate a dramatic reduction in  scaffold number and increased in N90/N50 values.   With de novo genome assembly projects for plants and animals, OpGen demonstrated that WGM can eliminate the need for BAC-end sequencing, a costly and time-consuming assembly approach.   Furthermore, we  recently developed a WGM assembly pipeline that generates consensus restriction maps of targeted regions of selected chromosomes.  These initial studies  demonstrate the capability for  correction of assembly errors and  detection of large balanced and unbalanced structural variations.  This WGM application for plant and animal sequence assembly may refine the accuracy of  reference genomes for a comprehensive genomic characterization.