Accurate Characterization of the Drosophila Genome Using Whole Genome Mapping Technology

Obtaining an accurate and complete genomic reference sequence for a model animal such as Drosophila melanogaster provides a valuable genetic research tool.  While advances in sequencing technologies have allowed for copious amounts of information to be generated, assembling data with short read lengths into the sequence of a complex, repeat-rich genome of a multicellular eukaryote remains a significant and important challenge. OpGen’s Whole Genome Mapping (WGM) technology offers the advantage of long single molecule restriction maps that are typically hundreds of kilbases to megabases in length in an automated and rapid fashion. These very long “reads” enable a broader genome view to generate consensus restriction maps spanning each chromosome.  Using a recently developed de novo WGM assembly pipeline, this strategy was applied to assist in validation and refinement of the D. melanogaster Release 6 reference genome, which has been finished using a traditional BAC mapping and long-read sequencing approach.  Comparisons discovered potential discrepant or evolving regions in the sequence assembly by revealing apparent insertions and deletions.    This approach was used as an effective way to determine the genomic distance across several persistent gaps in the assembly that are not represented in BAC libraries.  Therefore, WGM can be utilized as a cloning- and sequencing-independent technology to assist in resolving challenging areas of genomic architecture and also assess existing assembly quality.  Producing a high quality reference genome using a strategy that leverages Whole Genome Mapping may aid in constructing efficient, accurate and more complete genomic analyses.