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

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61389030%3A_____%2F16%3A00461946" target="_blank" >RIV/61389030:_____/16:00461946 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.1111/pbi.12513" target="_blank" >http://dx.doi.org/10.1111/pbi.12513</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1111/pbi.12513" target="_blank" >10.1111/pbi.12513</a>

Result language

angličtina

Original language name

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

Original language description

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.

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

EB - Genetics and molecular biology

OECD FORD branch

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Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2016

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Plant Biotechnology Journal

ISSN

1467-7644

e-ISSN

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Volume of the periodical

14

Issue of the periodical within the volume

7

Country of publishing house

US - UNITED STATES

Number of pages

9

Pages from-to

1523-1531

UT code for WoS article

000378741200004

EID of the result in the Scopus database

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