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. 2023 Oct 25;10(1):739.
doi: 10.1038/s41597-023-02658-2.

Chromosome-scale assembly of the wild wheat relative Aegilops umbellulata

Michael Abrouk  1   2 , Yajun Wang  3   4 , Emile Cavalet-Giorsa  3   4 , Maxim Troukhan  5 , Maksym Kravchuk  5 , Simon G Krattinger  6   7
Affiliations

Chromosome-scale assembly of the wild wheat relative Aegilops umbellulata

Michael Abrouk et al. Sci Data. .

Abstract

Wild wheat relatives have been explored in plant breeding to increase the genetic diversity of bread wheat, one of the most important food crops. Aegilops umbellulata is a diploid U genome-containing grass species that serves as a genetic reservoir for wheat improvement. In this study, we report the construction of a chromosome-scale reference assembly of Ae. umbellulata accession TA1851 based on corrected PacBio HiFi reads and chromosome conformation capture. The total assembly size was 4.25 Gb with a contig N50 of 17.7 Mb. In total, 36,268 gene models were predicted. We benchmarked the performance of hifiasm and LJA, two of the most widely used assemblers using standard and corrected HiFi reads, revealing a positive effect of corrected input reads. Comparative genome analysis confirmed substantial chromosome rearrangements in Ae. umbellulata compared to bread wheat. In summary, the Ae. umbellulata assembly provides a resource for comparative genomics in Triticeae and for the discovery of agriculturally important genes.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Construction of an Aegilops umbellulata chromosome-scale assembly. (a) An Ae. umbellulata plant (left) is shown next to a bread wheat plant (right) (b) Circos plot of Ae. umbellulata genome with (1) collinearity blocks against Ae. tauschii, (2) gene density and (3) repeat density along each pseudomolecule.
Fig. 2
Fig. 2
Genome visualization with Persephone. (a) Persephone genome browser visualization. The upper panel represents the position along chromosome 3U. The middle panel shows an example of three gene models with their predicted isoforms. In the lower panel, the CpG methylation profile is represented in blue and red for the unmethylated and methylated bases, respectively. (b) Synteny matrix between the seven Ae. umbellulata chromosomes (x-axis) and the 21 chromosomes of the bread wheat line Chinese spring v2.1 (y-axis) (c) Synteny comparison of the highly rearranged Ae. umbellulata chromosome 6U (in central position) in comparison to bread wheat chromosomes 1D, 2D, 4D, 6D and 7D. The links between chromosomes represented orthologous gene relationships.
Fig. 3
Fig. 3
Contact map after the integration of the Omni-C data and manual correction. Green and blue boxes represent contigs and pseudomolecules, respectively.
See this image and copyright information in PMC

References

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