BioNano Genome Map of a Wheat Chromosome Arm: A Tool to Support Sequence Assembly in a Complex Genome

Specific features of the bread wheat genome, such as its size (17 Gbp), polyploid nature and prevalence of repetitive sequences make whole-genome-sequencing a challenge. BAC-by-BAC sequencing based on chromosomal physical maps, which has been adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems due to the complexity and polyploidy. However, high content of repeats still hampers sequence assembly. Availability of a high-resolution genomic map having a potential to reveal discrepancies in sequence assemblies and provide a clue for sequence scaffolding would be highly beneficial for obtaining an accurate and complete genome sequence in wheat.

Aiming to produce a quality reference genome sequence of the short arm of chromosome 7D (7DS), we constructed de novo genome map of the 7DS arm using BioNano IRYS platform. The mapping was based on direct visualization of sequence motifs (7-bp recognition sites of Nt.BspQI nickase) on single DNA molecules hundreds to thousands of kilobases in length prepared from flow-sorted 7DS arm. The obtained high-resolution map consists of 371 fragments with N50 of 1.3 Mb. Anchoring sequence assemblies of 7DS BAC clones to the BioNano map helped revealing discrepancies in the sequence assemblies and provided clues for assembly improvement. Moreover, it aided verification of the 7DS physical map, anchoring contigs and sizing gaps in the physical map. The obtained results suggest that BioNano maps derived from individual wheat chromosomes/arms will become an affordable tool to support sequence assembly and lead to the production of improved pseudomolecules.