TY - JOUR
T1 - An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
AU - Clavijo, Bernardo J.
AU - Venturini, Luca
AU - Schudoma, Christian
AU - Accinelli, Gonzalo Garcia
AU - Kaithakottil, Gemy
AU - Wright, Jonathan
AU - Borrill, Philippa
AU - Kettleborough, George
AU - Heavens, Darren
AU - Chapman, Helen
AU - Lipscombe, James
AU - Barker, Tom
AU - Lu, Fu-Hao
AU - McKenzie, Neil
AU - Raats, Dina
AU - Ramirez-Gonzalez, Ricardo H.
AU - Coince, Aurore
AU - Peel, Ned
AU - Percival-Alwyn, Lawrence
AU - Duncan, Owen
AU - Trösch, Josua
AU - Yu, Guotai
AU - Bolser, Dan M.
AU - Namaati, Guy
AU - Kerhornou, Arnaud
AU - Spannagl, Manuel
AU - Gundlach, Heidrun
AU - Haberer, Georg
AU - Davey, Robert P.
AU - Fosker, Christine
AU - Palma, Federica Di
AU - Phillips, Andrew L.
AU - Millar, A. Harvey
AU - Kersey, Paul J.
AU - Uauy, Cristobal
AU - Krasileva, Ksenia V.
AU - Swarbreck, David
AU - Bevan, Michael W.
AU - Clark, Matthew D.
PY - 2017/5
Y1 - 2017/5
N2 - 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.
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 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.
U2 - 10.1101/gr.217117.116
DO - 10.1101/gr.217117.116
M3 - Article
VL - 27
SP - 885
EP - 896
JO - Genome Research
JF - Genome Research
SN - 1088-9051
IS - 5
ER -
