title: BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes.
abstract: The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC-by-BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high-resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high-resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach 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 genome map provided a valuable tool to improve the BAC-contig physical map and validate sequence assembly on a chromosome-arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome-by-chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.
authors.affiliation: Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
authors.forename: Helena
authors.initials: H
authors.lastname: Staňková
authors.affiliation: BioNano Genomics, San Diego, CA, USA.
authors.forename: Alex R
authors.initials: AR
authors.lastname: Hastie
authors.affiliation: BioNano Genomics, San Diego, CA, USA.
authors.forename: Saki
authors.initials: S
authors.lastname: Chan
authors.affiliation: Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
authors.forename: Jan
authors.initials: J
authors.lastname: Vrána
authors.affiliation: Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
authors.forename: Zuzana
authors.initials: Z
authors.lastname: Tulpová
authors.affiliation: Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
authors.forename: Marie
authors.initials: M
authors.lastname: Kubaláková
authors.affiliation: Australian Centre for Plant Functional Genomics, University of Queensland, Brisbane, QLD, Australia.
authors.forename: Paul
authors.initials: P
authors.lastname: Visendi
authors.affiliation: School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia.
authors.forename: Satomi
authors.initials: S
authors.lastname: Hayashi
authors.affiliation: Department of Plant Sciences, University of California, Davis, CA, USA.
authors.forename: Mingcheng
authors.initials: M
authors.lastname: Luo
authors.affiliation: School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia.|School of Plant Biology, University of Western Australia, Crawley, WA, Australia.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Batley
authors.affiliation: School of Plant Biology, University of Western Australia, Crawley, WA, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Edwards
authors.affiliation: Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
authors.forename: Jaroslav
authors.initials: J
authors.lastname: Doležel
authors.affiliation: Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
authors.forename: Hana
authors.initials: H
authors.lastname: Šimková
mesh_terms: D001709:Biotechnology / Q000379:methods; D002874:Chromosome Mapping / Q000379:methods*; D022202:Chromosomes, Artificial, Bacterial; D032461:Chromosomes, Plant / Q000235:genetics*; D018745:Genome, Plant; D017422:Sequence Analysis, DNA / Q000379:methods; D020080:Tandem Repeat Sequences; D014908:Triticum / Q000235:genetics*
keywords: chromosomes; flow sorting; optical mapping; physical map; sequencing; wheat