BioNano Genome Map of Bread Wheat 7DS Arm Supports Sequence Assembly and Analysis

Optical mapping and its modification - genome mapping in nanochannel arrays (BioNano mapping) - provides a complementary tool to next-generation sequencing technologies. It generates maps of a short sequence motif along DNA stretches of hundreds to thousands kb in length. The BioNano technology excels in accurate length measurement and high throughput, which makes mapping gigabase-sized genomes feasible. Still, the 17-Gb hexaploid genome of bread wheat appears too complex to be tackled as a whole. Moreover, as the wheat reference genome sequence is being produced by sequencing physical maps of individual chromosomes/arms, it seems practical to follow the chromosome-based strategy of IWGSC and produce BioNano maps from individual chromosomes. Here we chose the short arm of chromosome 7D (7DS) as a model to demonstrate that it is possible to couple chromosome flow sorting with BioNano mapping to create a de novo genome map.

We have constructed a high-resolution map of  chromosome 7DS composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules obtained from flow-sorted chromosomes facilitated chromosome-scale analysis of repetitive sequences and revealed a ~800-kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone-by-clone sequencing to the 7DS BioNano map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly. Moreover, a BioNano map was also constructed from 7DS arm flow-sorted from wheat line CI2401, which enabled characterizing structural variation between two wheat accessions at chromosome-arm level.