A 4.3 Gb Genome Map of the Barley Genome As a Tool for Assembly

Barley is the one of the world’s oldest and most extensively cultivated crops and is important worldwide for food, feed, and malt. Facing future global challenges of climate change, decreased inputs, and increased biotic and abiotic stresses will require exploitation of the genetic resources available from the landraces of barley and from its wild relative Hordeum spontaneum. As a basis for better tools to accelerate barley breeding, the worldwide community represented by the International Barley Sequencing Consortium (IBSC) is engaged in producing a reference genome of barley. Given the highly repetitive nature of its large (5.1 Gb) genome, de novo assembly of genome sequences is not trivial and is best accomplished by integrating data from several approaches. Optical mapping retains the physical order of restriction sites along DNA molecules, and can serve as a valuable tool in sequence assembly.  We have applied this approach to generate a genome map from DNA molecules isolated from flow-sorted barley chromosomes. The molecules were fluorescently labelled at sites recognized by a nicking enzyme, separated on nanochannel arrays, and maps generated and assembled using the technologies of BioNano Genomics, Inc. A total of 4.3 Gb, representing 84.1% of the genome was thereby assembled from all chromosomes together. Using a single flow-sorted chromosome only marginally improved the assembly. Given the long arrays of repetitive units such as retrotransposon nests and rDNA arrays, this assembly illustrates the power of the technology. This genome map is now serving in the whole-genome MTP assembly of barley.