RT Journal Article
SR Electronic
T1 An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 080796
DO 10.1101/080796
A1 Bernardo J. Clavijo
A1 Luca Venturini
A1 Christian Schudoma
A1 Gonzalo Garcia Accinelli
A1 Gemy Kaithakottil
A1 Jonathan Wright
A1 Philippa Borrill
A1 George Kettleborough
A1 Darren Heavens
A1 Helen Chapman
A1 James Lipscombe
A1 Tom Barker
A1 Fu-Hao Lu
A1 Neil McKenzie
A1 Dina Raats
A1 Ricardo H. Ramirez-Gonzalez
A1 Aurore Coince
A1 Ned Peel
A1 Lawrence Percival-Alwyn
A1 Owen Duncan
A1 Josua Trösch
A1 Guotai Yu
A1 Dan Bolser
A1 Guy Namaati
A1 Arnaud Kerhornou
A1 Manuel Spannagl
A1 Heidrun Gundlach
A1 Georg Haberer
A1 Robert P. Davey
A1 Christine Fosker
A1 Federica Di Palma
A1 Andrew Phillips
A1 A. Harvey Millar
A1 Paul J. Kersey
A1 Cristobal Uauy
A1 Ksenia V. Krasileva
A1 David Swarbreck
A1 Michael W. Bevan
A1 Matthew D. Clark
YR 2016
UL http://biorxiv.org/content/early/2016/10/13/080796.abstract
AB Advances in genome sequencing and assembly technologies are generating many high quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimised data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents more than 78% of the genome with a scaffold N50 of 88.8kbp that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNAseq and PacBio full-length cDNAs to identify 104,091 high confidence protein-coding genes and 10,156 non-coding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop. [Supplemental material is available for this article.]