title: Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome
creator: Keeble-Gagnère, Gabriel
creator: Rigault, Philippe
creator: Tibbits, Josquin
creator: Pasam, Raj
creator: Hayden, Matthew
creator: Forrest, Kerrie
creator: Frenkel, Zeev
creator: Korol, Abraham
creator: Huang, B. Emma
creator: Cavanagh, Colin
creator: Taylor, Jen
creator: Abrouk, Michael
creator: Sharpe, Andrew
creator: Konkin, David
creator: Sourdille, Pierre
creator: Darrier, Benoît
creator: Choulet, Frédéric
creator: Bernard, Aurélien
creator: Rochfort, Simone
creator: Dimech, Adam
creator: Watson-Haigh, Nathan
creator: Baumann, Ute
creator: Eckermann, Paul
creator: Fleury, Delphine
creator: Juhasz, Angela
creator: Boisvert, Sébastien
creator: Nolin, Marc-Alexandre
creator: Doležel, Jaroslav
creator: Šimková, Hana
creator: Toegelová, Helena
creator: Šafář, Jan
creator: Luo, Ming-Cheng
creator: Câmara, Francisco
creator: Pfeifer, Matthias
creator: Isdale, Don
creator: Nyström-Persson, Johan
creator: Koo, Dal-Hoe
creator: Tinning, Matthew
creator: Cui, Dangqun
creator: Ru, Zhengang
creator: Appels, Rudi
subject: ddc-570
subject: 570 Life sciences
description: 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.
publisher: BioMed Central
date: 2018
type: Article
type: info:eu-repo/semantics/article
type: NonPeerReviewed
format: application/pdf
identifier: https://archiv.ub.uni-heidelberg.de/volltextserverhttps://archiv.ub.uni-heidelberg.de/volltextserver/25447/1/13059_2018_Article_1475.pdf
identifier: DOI:
identifier: urn:nbn:de:bsz:16-heidok-254475
identifier:   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  (2018) Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome.  Genome Biology, 19 (112).  pp. 1-18.  ISSN 1474-760X     
relation: https://archiv.ub.uni-heidelberg.de/volltextserver/25447/
rights: info:eu-repo/semantics/openAccess
rights: Please see front page of the work (Sorry, Dublin Core plugin does not recognise license id)
language: eng