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

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 88.8kb 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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Author Clavijo, Bernardo J.
Last Updated November 20, 2019, 16:51 (UTC)
Created August 1, 2019, 10:30 (UTC)
Article Host Type publisher
Article Is Open Access true
Article License Type cc-by
Article Version Type publishedVersion
Citation Report https://scite.ai/reports/10.1101/gr.217117.116
DOI 10.1101/gr.217117.116
Date Last Updated 2019-05-27T11:10:31.164381
Evidence open (via page says license)
Funder code(s) Biotechnology and Biological Sciences Research Council (BB/J00328X/1, BB/J003743/1, BB/J003913/1, BB/J003557/1); Australian Research Council (LP120200102, CE140100008); Agilent Technologies (); BBSRC Anniversary Future Leader Fellowship (BB/M014045/1); BBSRC Institute Strategic Programme Grants GRO (BB/J004669/1, BB/J004588/1, BBS/E/C/00005202); The German Ministry of Education and Research (BMBF) (031A536); BBSRC National Capability in Genomics (BB/J010375/1)
Journal Is Open Access false
Open Access Status hybrid
PDF URL http://genome.cshlp.org/content/27/5/885.full.pdf
Publisher URL https://doi.org/10.1101/gr.217117.116