Construction of Whole-Genome BioNano Maps for Aegilops tauschii, the D Genome Progenitor of Wheat

Aegilops tauschii, the diploid progenitor of the D genome of hexaploid wheat (Triticum aestivum), has a genome size larger than 4 Gb with repetitive DNA estimated at 90%. Due to genome complexity and the limitations of current sequencing technologies, it is challenging to build high quality super-scaffolds or pseudomolecules of a genome of this size and complexity, even if the ordered-clone sequencing approach is used. A sequence-independent technology that can aid sequence assembly is needed. To address this problem, we have employed a novel technology, BioNano genome map, which is an optical restriction map of megabase size DNA contigs built by analyzing genomic DNA fragments with the BioNano Genomics’s Irys™platform. We have generated whole-genome consensus BioNano maps. These maps are being used to assist the assembly of the BAC clone minimum tilling path (MTP) sequences, rectify the order and orientations of BAC sequence scaffolds, size sequence gaps, and ultimately build pseudomolecules for the seven chromosomes of the Ae. tauschii genome. This work is a part of the NSF-funded Project IOS-1238231 to generate a reference sequence for the genome of Ae. tauschii (http://aegilops.wheat.ucdavis.edu/ATGSP/).