PT  - JOURNAL ARTICLE
AU  - G. Keeble-Gagnère
AU  - P. Rigault
AU  - J. Tibbits
AU  - R. Pasam
AU  - M. Hayden
AU  - K. Forrest
AU  - Z. Frenkel
AU  - A. Korol
AU  - E. Huang
AU  - C. Cavanagh
AU  - J. Taylor
AU  - M. Abrouk
AU  - A. Sharpe
AU  - D. Konkin
AU  - P. Sourdille
AU  - B. Darrier
AU  - F. Choulet
AU  - A. Bernard
AU  - S. Rochfort
AU  - AM. Dimech
AU  - N. Watson-Haigh
AU  - U. Baumann
AU  - P. Eckermann
AU  - D. Fleury
AU  - A. Juhasz
AU  - S. Boisvert
AU  - M-A. Nolin
AU  - J. Doležel
AU  - H. Šimková
AU  - H. Toegelová
AU  - Jan Šafář
AU  - M-C. Luo
AU  - F. Camara
AU  - M. Pfeifer
AU  - D. Isdale
AU  - J. Nystrom-Persson
AU  - IWGSC
AU  - D-H Koo
AU  - M. Tinning
AU  - D. Cui
AU  - Z. Ru
AU  - R. Appels
TI  - Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome
AID  - 10.1101/363465
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 363465
4099  - http://biorxiv.org/content/early/2018/07/09/363465.short
4100  - http://biorxiv.org/content/early/2018/07/09/363465.full
AB  - 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 based on a BAC-based physical map, BAC pool paired end sequencing, chromosome arm specific mate-pair sequencing and Bionano optical mapping with the IWGSC 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 be now 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 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.Contigconsensus region of DNA sequence represented by overlapping sequence reads. Can have unresolved bases (N), but no gaps.Scaffoldconsensus region of DNA sequence represented by ordered (but not necessarily oriented) contigs, separated by gaps of known (estimated) length.Islandgenomic region represented by overlapping sets of DNA sequences (scaffolds), physical entities (optical map or molecule, physical clone), or both.Super-scaffolda portion of the genome sequence where scaffolds have been ordered and oriented relative to each other