Genome Research volume 27, issue 5, P885-896 2017 DOI: 10.1101/gr.217117.116

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

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