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

View ORCID ProfileJean-Marc Aury, Stefan Engelen, Benjamin Istace, Cécile Monat, Pauline Lasserre-Zuber, Caroline Belser, Corinne Cruaud, Hélène Rimbert, Philippe Leroy, Sandrine Arribat, Isabelle Dufau, Arnaud Bellec, David Grimbichler, Nathan Papon, Etienne Paux, Marion Ranoux, Adriana Alberti, Patrick Wincker, View ORCID ProfileFrédéric Choulet
doi: https://doi.org/10.1101/2021.08.24.457458
Jean-Marc Aury
1Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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  • ORCID record for Jean-Marc Aury
  • For correspondence: jmaury@genoscope.cns.fr
Stefan Engelen
1Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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Benjamin Istace
1Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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Cécile Monat
2GDEC, Université Clermont Auvergne, INRAE, UMR1095, 63000 Clermont-Ferrand, France
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Pauline Lasserre-Zuber
2GDEC, Université Clermont Auvergne, INRAE, UMR1095, 63000 Clermont-Ferrand, France
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Caroline Belser
1Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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Corinne Cruaud
3Commissariat à l’Energie Atomique (CEA), Institut François Jacob, Genoscope, F-91057 Evry, France
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Hélène Rimbert
2GDEC, Université Clermont Auvergne, INRAE, UMR1095, 63000 Clermont-Ferrand, France
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Philippe Leroy
2GDEC, Université Clermont Auvergne, INRAE, UMR1095, 63000 Clermont-Ferrand, France
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Sandrine Arribat
4INRAE, CNRGV French Plant Genomic Resource Center, F-31320, Castanet Tolosan, France
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Isabelle Dufau
4INRAE, CNRGV French Plant Genomic Resource Center, F-31320, Castanet Tolosan, France
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Arnaud Bellec
4INRAE, CNRGV French Plant Genomic Resource Center, F-31320, Castanet Tolosan, France
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David Grimbichler
5Mésocentre Clermont Auvergne, DOSI / Bâtiment Turing, 7 avenue Blaise Pascal, 63178 Aubière CEDEX
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Nathan Papon
2GDEC, Université Clermont Auvergne, INRAE, UMR1095, 63000 Clermont-Ferrand, France
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Etienne Paux
2GDEC, Université Clermont Auvergne, INRAE, UMR1095, 63000 Clermont-Ferrand, France
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Marion Ranoux
2GDEC, Université Clermont Auvergne, INRAE, UMR1095, 63000 Clermont-Ferrand, France
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Adriana Alberti
1Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
6Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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Patrick Wincker
1Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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Frédéric Choulet
2GDEC, Université Clermont Auvergne, INRAE, UMR1095, 63000 Clermont-Ferrand, France
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  • ORCID record for Frédéric Choulet
  • For correspondence: jmaury@genoscope.cns.fr
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Abstract

The sequencing of the wheat (Triticum aestivum) genome has been a methodological challenge for many years due 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. Here, we report on an optimized procedure based on long-reads produced on the ONT (Oxford Nanopore Technology) PromethION device to assemble the genome of the French bread wheat cultivar Renan. We provide the most contiguous and complete chromosome-scale assembly of a bread wheat genome to date. Coupled with an annotation based on RNA-Seq 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.

Competing Interest Statement

The authors declare that they have no competing interests. Jean-Marc Aury received travel and accommodation expenses to speak at Oxford Nanopore Technologies conferences. Jean-Marc Aury and Caroline Belser received accommodation expenses to speak at Bionano Genomics user meetings.

Footnotes

  • http://www.genoscope.cns.fr/plants/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding
Jean-Marc Aury, Stefan Engelen, Benjamin Istace, Cécile Monat, Pauline Lasserre-Zuber, Caroline Belser, Corinne Cruaud, Hélène Rimbert, Philippe Leroy, Sandrine Arribat, Isabelle Dufau, Arnaud Bellec, David Grimbichler, Nathan Papon, Etienne Paux, Marion Ranoux, Adriana Alberti, Patrick Wincker, Frédéric Choulet
bioRxiv 2021.08.24.457458; doi: https://doi.org/10.1101/2021.08.24.457458
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Long-read and chromosome-scale assembly of the hexaploid wheat genome achieves high resolution for research and breeding
Jean-Marc Aury, Stefan Engelen, Benjamin Istace, Cécile Monat, Pauline Lasserre-Zuber, Caroline Belser, Corinne Cruaud, Hélène Rimbert, Philippe Leroy, Sandrine Arribat, Isabelle Dufau, Arnaud Bellec, David Grimbichler, Nathan Papon, Etienne Paux, Marion Ranoux, Adriana Alberti, Patrick Wincker, Frédéric Choulet
bioRxiv 2021.08.24.457458; doi: https://doi.org/10.1101/2021.08.24.457458

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