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Cold Spring Harbor Laboratory Press, Genome Research, 5(27), p. 885-896, 2017
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An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
,
Guotai Yu,
Clavijo Bj,
Gonzalo Garcia Accinelli,
Luca Venturini ,
Christian Schudoma ,
Gonzalo Garcia Accinelli,
Tom Barker,
Fu-Hao Lu ,
Gemy Kaithakottil ,
Neil McKenzie,
Dina Raats ,
Jonathan Wright,
Ricardo H. Ramirez-Gonzalez ,
Aurore Coince
and other authors.
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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.