PT - JOURNAL ARTICLE AU - Bernardo J. Clavijo AU - Luca Venturini AU - Christian Schudoma AU - Gonzalo Garcia Accinelli AU - Gemy Kaithakottil AU - Jonathan Wright AU - Philippa Borrill AU - George Kettleborough AU - Darren Heavens AU - Helen Chapman AU - James Lipscombe AU - Tom Barker AU - Fu-Hao Lu AU - Neil McKenzie AU - Dina Raats AU - Ricardo H. Ramirez-Gonzalez AU - Aurore Coince AU - Ned Peel AU - Lawrence Percival-Alwyn AU - Owen Duncan AU - Josua Trösch AU - Guotai Yu AU - Dan Bolser AU - Guy Namaati AU - Arnaud Kerhornou AU - Manuel Spannagl AU - Heidrun Gundlach AU - Georg Haberer AU - Robert P. Davey AU - Christine Fosker AU - Federica Di Palma AU - Andrew Phillips AU - A. Harvey Millar AU - Paul J. Kersey AU - Cristobal Uauy AU - Ksenia V. Krasileva AU - David Swarbreck AU - Michael W. Bevan AU - Matthew D. Clark TI - An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations AID - 10.1101/080796 DP - 2016 Jan 01 TA - bioRxiv PG - 080796 4099 - http://biorxiv.org/content/early/2016/10/13/080796.short 4100 - http://biorxiv.org/content/early/2016/10/13/080796.full 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.]