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primary topic: Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome

Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome
type: AcademicArticle
type: Article
abstract: Abstract: Background Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results: Using chromosome 7A of wheat as a model, sequence-finished megabase-scale sections of this chromosome were established by combining a new independent assembly using a bacterial artificial chromosome (BAC)-based physical map, BAC pool paired-end sequencing, chromosome-arm-specific mate-pair sequencing and Bionano optical mapping with the International Wheat Genome Sequencing Consortium RefSeq v1.0 sequence and its underlying raw data. The combined assembly results in 18 super-scaffolds across the chromosome. The value of finished genome regions is demonstrated for two approximately 2.5 Mb regions associated with yield and the grain quality phenotype of fructan carbohydrate grain levels. In addition, the 50 Mb centromere region analysis incorporates cytological data highlighting the importance of non-sequence data in the assembly of this complex genome region. Conclusions Sufficient genome sequence information is shown to now be available for the wheat community to produce sequence-finished releases of each chromosome of the reference genome. The high-level completion identified that an array of seven fructosyl transferase genes underpins grain quality and that yield attributes are affected by five F-box-only-protein-ubiquitin ligase domain and four root-specific lipid transfer domain genes. The completed sequence also includes the centromere.
date: 2018
volume: 19
issue: 112
is part of: Genome Biology
author list: authors
type: EPrint
type: ArticleEPrint
is part of: repository
has document: Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (PDF)
has document: Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (Other)
subject: 570 Biowissenschaften, Biologie

Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (PDF)
type: Document
has file: 13059_2018_Article_1475.pdf
has part: 13059_2018_Article_1475.pdf

BioMed Central
type: Organization

Genome Biology
type: Collection
issn: 1474760X

Benoît Darrier
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Matthew Hayden
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Raj Pasam
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Philippe Rigault
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Delphine Fleury
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Aurélien Bernard
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David Konkin
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Gabriel Keeble-Gagnère
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family name: Keeble-Gagnère

Francisco Câmara
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Nathan Watson-Haigh
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Zeev Frenkel
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given name: Zeev
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Helena Toegelová
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given name: Helena
family name: Toegelová

Jen Taylor
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Ming-Cheng Luo
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given name: Ming-Cheng
family name: Luo

Rudi Appels
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Jan Šafář
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given name: Jan
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Marc-Alexandre Nolin
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given name: Marc-Alexandre
family name: Nolin

Abraham Korol
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Pierre Sourdille
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Paul Eckermann
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Hana Šimková
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Sébastien Boisvert
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Adam Dimech
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Johan Nyström-Persson
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Michael Abrouk
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Colin Cavanagh
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Don Isdale
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Andrew Sharpe
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Zhengang Ru
type: Person
given name: Zhengang
family name: Ru

Frédéric Choulet
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given name: Frédéric
family name: Choulet

Matthew Tinning
type: Person
given name: Matthew
family name: Tinning

Jaroslav Doležel
type: Person
given name: Jaroslav
family name: Doležel

B. Emma Huang
type: Person
given name: B. Emma
family name: Huang

Dangqun Cui
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given name: Dangqun
family name: Cui

Josquin Tibbits
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given name: Josquin
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Dal-Hoe Koo
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given name: Dal-Hoe
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Ute Baumann
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Matthias Pfeifer
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Kerrie Forrest
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given name: Kerrie
family name: Forrest

International Wheat Genome Sequencing Consortium (IWGSC)
type: Organization

Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (Other)
type: Document
is version of: Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (PDF)
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Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (Other)
type: Document
is version of: Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (PDF)
is volatile version of: Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (PDF)
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Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (Other)
type: Document
is version of: Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (PDF)
is volatile version of: Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (PDF)
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Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (Other)
type: Document
is version of: Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (PDF)
is volatile version of: Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (PDF)
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Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (Other)
type: Document
is version of: Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (PDF)
is volatile version of: Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome (PDF)
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primary topic: Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome

570 Biowissenschaften, Biologie
type: Concept
preferred label: 570 Life sciences @en