De Novo Assembly of High Density Electronic Maps Reveal Structural Diversity in Bordetella pertussis

Long-range information is able to reveal structural differences between Bordetella pertussis strains. Long read sequence information has recently shown utility in identifying structural heterogeneity in strains isolated from a... [ view full abstract ]

Long-range information is able to reveal structural differences between Bordetella pertussis strains. Long read sequence information has recently shown utility in identifying structural heterogeneity in strains isolated from a single outbreak. We demonstrate that high density physical maps assembled from single-molecule data also enable the differentiation of closely related strains and are able to delineate genomic rearrangements.

To provide the necessary long-range information while maintaining sufficient resolution to complement next generation sequencing technologies, Nabsys has developed its HD-Mapping^TM platform to construct electronic whole genome maps. The major advantages of electronic sensing over optical methods are higher sensitivity, accuracy, scalability, and speed of detection. Single-molecule events translocate through the detector at velocities above 1 megabase pair per second. By analyzing reads that are hundreds of kilobases in length, electronic detection preserves long-range information while simultaneously achieving unparalleled resolution and accuracy. Single-molecule reads have high resolution and low false-negative and false-positive error rates resulting in high information content per read.

Electronic detection results in the resolution of small intervals. The high information density resulting from electronic detection enables standard DNA isolation methods to be used. Maps of Bordetella pertussis strains having much tighter probe spacing than optical methods have been assembled from data obtained on genomic DNA isolated by solution based procedures. Examples of high density assembled maps using several recognition sequences will be shown.