RT Journal Article
SR Electronic
T1 Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 363465
DO 10.1101/363465
A1 G. Keeble-Gagnère
A1 P. Rigault
A1 J. Tibbits
A1 R. Pasam
A1 M. Hayden
A1 K. Forrest
A1 Z. Frenkel
A1 A. Korol
A1 E. Huang
A1 C. Cavanagh
A1 J. Taylor
A1 M. Abrouk
A1 A. Sharpe
A1 D. Konkin
A1 P. Sourdille
A1 B. Darrier
A1 F. Choulet
A1 A. Bernard
A1 S. Rochfort
A1 AM. Dimech
A1 N. Watson-Haigh
A1 U. Baumann
A1 P. Eckermann
A1 D. Fleury
A1 A. Juhasz
A1 S. Boisvert
A1 M-A. Nolin
A1 J. Doležel
A1 H. Šimková
A1 H. Toegelová
A1 Jan Šafář
A1 M-C. Luo
A1 F. Camara
A1 M. Pfeifer
A1 D. Isdale
A1 J. Nystrom-Persson
A1 IWGSC
A1 D-H Koo
A1 M. Tinning
A1 D. Cui
A1 Z. Ru
A1 R. Appels
YR 2018
UL http://biorxiv.org/content/early/2018/07/09/363465.abstract
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