Gigascience. 2017 Nov 1;6(11):1-7. doi: 10.1093/gigascience/gix097.

The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum.

Zimin AV^1,², Puiu D¹, Hall R³, Kingan S³, Clavijo BJ⁴, Salzberg SL^1,⁵.

Author information

1: Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
2: Institute for Physical Sciences and Technology, University of Maryland, College Park, MD 20742, USA.
3: Pacific Biosciences, 1305 O'Brien Dr, Menlo Park, CA 94025, USA.
4: Earlham Institute, Norwich Research Park Innovation Centre, Colney Ln, Norwich NR4 7UZ, UK.
5: Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA.

Abstract

Common bread wheat, Triticum aestivum, has one of the most complex genomes known to science, with 6 copies of each chromosome, enormous numbers of near-identical sequences scattered throughout, and an overall haploid size of more than 15 billion bases. Multiple past attempts to assemble the genome have produced assemblies that were well short of the estimated genome size. Here we report the first near-complete assembly of T. aestivum, using deep sequencing coverage from a combination of short Illumina reads and very long Pacific Biosciences reads. The final assembly contains 15 344 693 583 bases and has a weighted average (N50) contig size of 232 659 bases. This represents by far the most complete and contiguous assembly of the wheat genome to date, providing a strong foundation for future genetic studies of this important food crop. We also report how we used the recently published genome of Aegilops tauschii, the diploid ancestor of the wheat D genome, to identify 4 179 762 575 bp of T. aestivum that correspond to its D genome components.