An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations.

Authors: Clavijo, Bernardo J and Venturini, Luca and Schudoma, Christian and Accinelli, Gonzalo Garcia and Kaithakottil, Gemy and Wright, Jonathan and Borrill, Philippa and Kettleborough, George and Heavens, Darren and Chapman, Helen and Lipscombe, James and Barker, Tom and Lu, Fu-Hao and McKenzie, Neil and Raats, Dina and Ramirez-Gonzalez, Ricardo H and Coince, Aurore and Peel, Ned and Percival-Alwyn, Lawrence and Duncan, Owen and Trösch, Josua and Yu, Guotai and Bolser, Dan M and Namaati, Guy and Kerhornou, Arnaud and Spannagl, Manuel and Gundlach, Heidrun and Haberer, Georg and Davey, Robert P and Fosker, Christine and Palma, Federica Di and Phillips, Andrew and Millar, A Harvey and Kersey, Paul J and Uauy, Cristobal and Krasileva, Ksenia V and Swarbreck, David and Bevan, Michael W and Clark, Matthew D

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 optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding 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. © 2017 Clavijo et al.; Published by Cold Spring Harbor Laboratory Press.

Journal: Genome research
DOI: 10.1101/gr.217117.116
Year: 2017

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