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

SYSNO ASEP	0461946
Document Type	J - Journal Article
R&D Document Type	Journal Article
Subsidiary J	Článek ve WOS
Title	BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes
Author(s)	Staňková, Helena (UEB-Q)_RID Hastie, A. (US) Chan, S. (US) Vrána, Jan (UEB-Q)_{RID, ORCID} Tulpová, Zuzana (UEB-Q)_ORCID Kubaláková, Marie (UEB-Q)_RID Visendi, P. (AU) Hayashi, S. (AU) Luo, M. (US) Batley, J. (AU) Edwards, D. (AU) Doležel, Jaroslav (UEB-Q)_{RID, ORCID} Šimková, Hana (UEB-Q)_{RID, ORCID}
Source Title	Plant Biotechnology Journal. - : Wiley - ISSN 1467-7644 Roč. 14, č. 7 (2016), s. 1523-1531
Number of pages	9 s.
Language	eng - English
Country	US - United States
Keywords	optical mapping ; wheat ; sequencing
Subject RIV	EB - Genetics ; Molecular Biology
R&D Projects	GAP501/12/2554 GA ČR - Czech Science Foundation (CSF)
	LO1204 GA MŠMT - Ministry of Education, Youth and Sports (MEYS)
Institutional support	UEB-Q - RVO:61389030
UT WOS	000378741200004
DOI	10.1111/pbi.12513
Annotation	The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17Gbp, 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 1.3Mb. 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.
Workplace	Institute of Experimental Botany
Contact	David Klier, knihovna@ueb.cas.cz, Tel.: 220 390 469
Year of Publishing	2017

Number of the records: 1