BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

Stankova, Helena, Hastie, Alex R., Chan, Saki, Vrana, Jan, Tulpova, Zuzana, Kubalakova, Marie, Visendi, Paul, Hayashi, Satomi, Luo, Mingcheng, Batley, Jacqueline, Edwards, David, Dolezel, Jaroslav and Simkova, Hana (2016) BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes. Plant Biotechnology Journal, 14 7: 1523-1531. doi:10.1111/pbi.12513


Author Stankova, Helena
Hastie, Alex R.
Chan, Saki
Vrana, Jan
Tulpova, Zuzana
Kubalakova, Marie
Visendi, Paul
Hayashi, Satomi
Luo, Mingcheng
Batley, Jacqueline
Edwards, David
Dolezel, Jaroslav
Simkova, Hana
Title BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes
Journal name Plant Biotechnology Journal   Check publisher's open access policy
ISSN 1467-7652
1467-7644
Publication date 2016-07-01
Year available 2016
Sub-type Article (original research)
DOI 10.1111/pbi.12513
Open Access Status DOI
Volume 14
Issue 7
Start page 1523
End page 1531
Total pages 9
Place of publication Chichester, West Sussex, United Kingdom
Publisher Wiley-Blackwell Publishing
Collection year 2017
Language eng
Formatted 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.
Keyword Chromosomes
Flow sorting
Optical mapping
Physical map
Sequencing
Wheat
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
School of Agriculture and Food Sciences
 
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