@article{Clavijo2017, 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.}, author = {Clavijo, Bernardo J. and Yu, Guotai and Bj, Clavijo and Accinelli, Gonzalo Garcia and Venturini, Luca and Schudoma, Christian and Garcia Accinelli, Gonzalo and Barker, Tom and Lu, Fu-Hao and Kaithakottil, Gemy and McKenzie, Neil and Raats, Dina and Wright, Jonathan and Ramirez-Gonzalez, Ricardo H. and Coince, Aurore and Borrill, Philippa and Peel, Ned and Percival-Alwyn, Lawrence and Kettleborough, George and Duncan, Owen and Trösch, Josua and Lipscombe, James and Bolser, Dan M. and Heavens, Darren and Naamati, Guy and Namaati, Guy and Kerhornou, Arnaud and Chapman, Helen and Spannagl, Manuel and Gundlach, Heidrun and Haberer, Georg and Davey, Robert P. and Fosker, Christine and Di Palma, Federica and Palma, Federica Di and Phillips, Andrew L. and Harvey Millar, A. 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. and Md, Clark}, doi = {10.1101/gr.217117.116}, journal = {Genome Research}, month = {apr}, pages = {885-896}, title = {An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations}, url = {https://doi.org/10.1101/gr.217117.116}, volume = {27}, year = {2017} }