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

Authors
  • Aury, Jean-Marc1
  • Engelen, Stefan1
  • Istace, Benjamin1
  • Monat, Cécile2
  • Lasserre-Zuber, Pauline2
  • Belser, Caroline1
  • Cruaud, Corinne3
  • Rimbert, Hélène2
  • Leroy, Philippe2
  • Arribat, Sandrine4
  • Dufau, Isabelle4
  • Bellec, Arnaud4
  • Grimbichler, David5
  • Papon, Nathan2
  • Paux, Etienne2
  • Ranoux, Marion2
  • Alberti, Adriana1
  • Wincker, Patrick1
  • Choulet, Frédéric2
  • 1 Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, France , (France)
  • 2 GDEC, Université Clermont Auvergne, INRAE, UMR1095, France , (France)
  • 3 Commissariat à l'Energie Atomique (CEA), Institut François Jacob, Genoscope, France , (France)
  • 4 INRAE, CNRGV French Plant Genomic Resource Center, France , (France)
  • 5 Mésocentre Clermont Auvergne, DOSI / Bâtiment Turing, France , (France)
Type
Published Article
Journal
GigaScience
Publisher
Oxford University Press
Publication Date
Apr 28, 2022
Volume
11
Identifiers
DOI: 10.1093/gigascience/giac034
PMID: 35482491
PMCID: PMC9049114
Source
PubMed Central
Keywords
Disciplines
  • AcademicSubjects/SCI00960
  • AcademicSubjects/SCI02254
License
Unknown

Abstract

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.

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