Practical Aspects of BioNano Mapping of the Wheat Genome

Genome mapping in nanochannel arrays (IRYS platform), known as BioNano mapping, generates physical maps of a short sequence motif (recognition site of a nicking enzyme) along DNA stretches of hundreds to thousands kb in length. These can serve as a guide to validate and improve physical map and sequence assemblies.

Following the chromosome-based strategy of IWGSC, we proposed to couple BioNano mapping with chromosome flow sorting and construct BioNano maps for individual chromosomes/arms. A pilot experiment conducted on 7DS arm resulted in a high-resolution map, which, combined with BAC-by-BAC sequences of the 7DS arm, enabled validation, correction and anchoring of the BAC contig assembly, scaffolding sequences and sizing gaps and identification of large regions of tandem repeats. We have demonstrated that the BioNano map had a sufficient resolution to position and orient contigs consisting of as little as three BAC clones, a feature that can contribute to higher completeness of reference chromosome sequences. As such, the BioNano mapping provides a missing tool needed to complement the extant genomics tools to deliver high quality reference genome sequences and analyse structural genome variation. Subsequent projects on other group 7 chromosome arms confirmed that producing de novo BioNano maps for the whole wheat genome in chromosome-by-chromosome manner is feasible. Practical aspects, such as requirements on input sequence quality and current technology limitations will be discussed during the talk.