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. 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

Aleksey V Zimin  1   2 , Daniela Puiu  1 , Richard Hall  3 , Sarah Kingan  3 , Bernardo J Clavijo  4 , Steven L Salzberg  1   5
Affiliations

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

Aleksey V Zimin et al. Gigascience. .

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.

Keywords: PacBio sequencing; genome assembly; hybrid assembly; plant genomes; wheat genome.

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Figures

Figure 1:
Figure 1:
Illustration of the merging process for the Triticum 2.0 and FALCON Trit 1.0 assemblies. If 2 contigs A and B from the FALCON assembly overlapped a Triticum 2.0 contig by at least 5000 bp, then A and B were merged together using the Triticum 2.0 contig to fill the gap.
Figure 2:
Figure 2:
K-mer uniqueness ratios for the wheat genome (Triticum aestivum) compared to the cow, fruit fly, rice, loblolly pine, and Ae. tauschii genomes. The plot shows the percentage of each genome that is covered (y-axis) by unique sequences of length k for various values of k (x-axis).
Figure 3:
Figure 3:
Missing 31-mers in the different assemblies of Triticum aestivum. Using the Illumina read data from a previously published assembly of the same genome, we counted all 31-mers in the reads and then plotted how many of these 31-mers are missing from each assembly. The x-axis shows how often the k-mers occur in the reads. The y-axis shows how many distinct k-mers are missing from each assembly. The FALCON Trit 1.0 assembly had the most missing k-mers, while the MaSuRCA-driven Triticum 2.0 assembly had the fewest.
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