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

Gabriel Keeble-Gagnère 1 Philippe Rigault 2, 3 Josquin Tibbits 1 Raj Pasam 1 Matthew Hayden 1 Kerrie Forrest 1 Zeev Frenkel 4 Abraham Korol 4 B. Emma Huang 5 Colin Cavanagh 5 Jen Taylor 5 Michael Abrouk 6, 7 Andrew Sharpe 8 David Konkin 8 Pierre Sourdille 9 Benoît Darrier 9 Frédéric Choulet 9 Aurélien Bernard 9 Simone Rochfort 1 Adam Dimech 1 Nathan Watson-Haigh 10 Ute Baumann 10 Paul Eckermann 10 Delphine Fleury 10 Angela Juhasz 11 Sébastien Boisvert 2 Marc-Alexandre Nolin 2 Jaroslav Doležel 7 Hana Šimková 7 Helena Toegelová 7 Jan Šafář 7 Ming-Cheng Luo 12 Francisco Câmara 13, 14, 15 Matthias Pfeifer 13, 14 Don Isdale 1 Johan Nyström-Persson 16 Dal-Hoe Koo 17 Matthew Tinning 18 Dangqun Cui 19 Zhengang Ru 20 Rudi Appels 1, 11
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.
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Genome Biology, BioMed Central, 2018, 19, 18 p. 〈10.1186/s13059-018-1475-4〉
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Gabriel Keeble-Gagnère, Philippe Rigault, Josquin Tibbits, Raj Pasam, Matthew Hayden, et al.. Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome. Genome Biology, BioMed Central, 2018, 19, 18 p. 〈10.1186/s13059-018-1475-4〉. 〈hal-01869898〉

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