Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding

Gigascience. 2022 Apr 28;11:giac034. doi: 10.1093/gigascience/giac034.


Background: The sequencing of the wheat (Triticum aestivum) genome has been a methodological challenge for many years owing to its large size (15.5 Gb), repeat content, and hexaploidy. Many initiatives aiming at obtaining a reference genome of cultivar Chinese Spring have been launched in the past years and it was achieved in 2018 as the result of a huge effort to combine short-read sequencing with many other resources. Reference-quality genome assemblies were then produced for other accessions, but the rapid evolution of sequencing technologies offers opportunities to reach high-quality standards at lower cost.

Results: Here, we report on an optimized procedure based on long reads produced on the Oxford Nanopore Technology PromethION device to assemble the genome of the French bread wheat cultivar Renan.

Conclusions: We provide the most contiguous chromosome-scale assembly of a bread wheat genome to date. Coupled with an annotation based on RNA-sequencing data, this resource will be valuable for the crop community and will facilitate the rapid selection of agronomically important traits. We also provide a framework to generate high-quality assemblies of complex genomes using ONT.

Keywords: genome assembly; haplotype characterization; hexaploid genome; introgressions; long-reads; nanopore sequencing; wheat.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Breeding
  • Chromosomes
  • Genome*
  • Sequence Analysis, DNA / methods
  • Triticum* / genetics