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

Keeble-Gagnère, Gabriel ; Rigault, Philippe ; Tibbits, Josquin ; Pasam, Raj ; Hayden, Matthew ; Forrest, Kerrie ; Frenkel, Zeev ; Korol, Abraham ; Huang, B. Emma ; Cavanagh, Colin ; Taylor, Jen ; Abrouk, Michael ; Sharpe, Andrew ; Konkin, David ; Sourdille, Pierre ; Darrier, Benoît ; Choulet, Frédéric ; Bernard, Aurélien ; Rochfort, Simone ; Dimech, Adam ; Watson-Haigh, Nathan ; Baumann, Ute ; Eckermann, Paul ; Fleury, Delphine ; Juhasz, Angela ; Boisvert, Sébastien ; Nolin, Marc-Alexandre ; Doležel, Jaroslav ; Šimková, Hana ; Toegelová, Helena ; Šafář, Jan ; Luo, Ming-Cheng ; Câmara, Francisco ; Pfeifer, Matthias ; Isdale, Don ; Nyström-Persson, Johan ; Koo, Dal-Hoe ; Tinning, Matthew ; Cui, Dangqun ; Ru, Zhengang ; Appels, Rudi

In: Genome Biology, 19 (2018), Nr. 112. pp. 1-18. ISSN 1474-760X

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Download (3MB) | Lizenz: Creative Commons LizenzvertragOptical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome by Keeble-Gagnère, Gabriel ; Rigault, Philippe ; Tibbits, Josquin ; Pasam, Raj ; Hayden, Matthew ; Forrest, Kerrie ; Frenkel, Zeev ; Korol, Abraham ; Huang, B. Emma ; Cavanagh, Colin ; Taylor, Jen ; Abrouk, Michael ; Sharpe, Andrew ; Konkin, David ; Sourdille, Pierre ; Darrier, Benoît ; Choulet, Frédéric ; Bernard, Aurélien ; Rochfort, Simone ; Dimech, Adam ; Watson-Haigh, Nathan ; Baumann, Ute ; Eckermann, Paul ; Fleury, Delphine ; Juhasz, Angela ; Boisvert, Sébastien ; Nolin, Marc-Alexandre ; Doležel, Jaroslav ; Šimková, Hana ; Toegelová, Helena ; Šafář, Jan ; Luo, Ming-Cheng ; Câmara, Francisco ; Pfeifer, Matthias ; Isdale, Don ; Nyström-Persson, Johan ; Koo, Dal-Hoe ; Tinning, Matthew ; Cui, Dangqun ; Ru, Zhengang ; Appels, Rudi underlies the terms of Creative Commons Attribution 4.0

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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.

Item Type: Article
Journal or Publication Title: Genome Biology
Volume: 19
Number: 112
Publisher: BioMed Central
Place of Publication: London
Date Deposited: 07 Nov 2018 17:35
Date: 2018
ISSN: 1474-760X
Page Range: pp. 1-18
Faculties / Institutes: Service facilities > Centre for Organismal Studies Heidelberg (COS)
Subjects: 570 Life sciences
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