de novo Assembly of Complex Genomes Using Extremely Long Single-Molecule Imaging Technology

De novo genome assemblies using only short read data are generally incomplete and highly fragmented due to the intractable complexity found in most genomes. The complexity present in most genomes consists mainly of large duplications and repetitive regions such as rDNA, centromeres, and telomeres. These features hinder sequence assembly and, in turn, narrow the scope of biological questions that can be addressed.

The BioNano Genomics Irys System linearizes extremely long DNA molecules and provides single-molecule reads containing this essential long-range information. These reads, which are hundreds of kilobases to megabases in length, retain and capture far more structural information than is possible with sequencing platforms. Assembled genome maps are useful for scaffolding sequence contigs and validating sequence assemblies. Free from reference or amplification bias, de novogenome maps also identify novel structural variations and repeats which are challenging to find with existing methods. Additionally, genome maps serve as a much-needed orthogonal validation method to NGS assemblies.

In addition to providing an introduction to this technology, we will demonstrate a number of examples of its utility in a variety of organisms, including honey bee (Apis cerena) and Zi Zhi (Gandoerma Sinesis).  Genome maps are used to resolve repetitive functional elements, validate or scaffold de novo sequence assemblies, and discover differences in haplotypes.