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

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Clavijo, Bernardo J., Venturini, Luca, Schudoma, Christian, Accinelli, Gonzalo Garcia, Kaithakottil, Gemy, Wright, Jonathan, Borrill, Philippa, Kettleborough, George, Heavens, Darren, Chapman, Helen, Lipscombe, James, Barker, Tom, Lu, Fu-Hao, McKenzie, Neil, Raats, Dina, Ramirez-Gonzalez, Ricardo H., Coince, Aurore, Peel, Ned, Percival-Alwyn, Lawrence, Duncan, Owen, Trösch, Josua, Yu, Guotai, Bolser, Dan M., Namaati, Guy, Kerhornou, Arnaud, Spannagl, Manuel, Gundlach, Heidrun, Haberer, Georg, Davey, Robert P., Fosker, Christine, Palma, Federica Di, Phillips, Andrew L., Millar, A. Harvey, Kersey, Paul J., Uauy, Cristobal, Krasileva, Ksenia V., Swarbreck, David, Bevan, Michael W. and Clark, Matthew D. (2017) An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations. Genome Research, 27 (5). pp. 885-896. ISSN 1088-9051

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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.

Item Type:	Article
Faculty \ School:	Faculty of Science > The Sainsbury Laboratory Faculty of Science > School of Biological Sciences Faculty of Science Faculty of Medicine and Health Sciences > Norwich Medical School Faculty of Science > School of Environmental Sciences
Related URLs:	http://genome.cshlp.org/content/27/5/885
Depositing User:	Pure Connector
Date Deposited:	05 May 2017 05:11
Last Modified:	02 Aug 2023 19:30
URI:	https://ueaeprints.uea.ac.uk/id/eprint/63395
DOI:	10.1101/gr.217117.116

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