Long-read assembly of the Brassica napus reference genome Darmor-bzh

  1. Mathieu Rousseau-Gueutin
  2. Caroline Belser
  3. Corinne Da Silva
  4. Gautier Richard
  5. Benjamin Istace
  6. Corinne Cruaud
  7. Cyril Falentin
  8. Franz Boideau
  9. Julien Boutte
  10. Regine Delourme
  11. Gwenaëlle Deniot
  12. Stefan Engelen
  13. Julie Ferreira de Carvalho
  14. Arnaud Lemainque
  15. Loeiz Maillet
  16. Jérôme Morice
  17. Patrick Wincker
  18. France Denoeud
  19. Anne-Marie Chèvre
  20. Jean-Marc Aury

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Abstract

Background

The combination of long reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a given species but also reveals the architecture and organization of chromosomes, including complex regions such as telomeres and centromeres. The Brassica genus is not exempt, and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, was produced using short reads and its contiguity was extremely low compared with current assemblies of the Brassica genus.

Findings

Herein, we report the new long-read assembly of Darmor-bzh genome (Brassica napus) generated by combining long-read sequencing data and optical and genetic maps. Using the PromethION device and 6 flowcells, we generated ∼16 million long reads representing 93× coverage and, more importantly, 6× with reads longer than 100 kb. This ultralong-read dataset allows us to generate one of the most contiguous and complete assemblies of a Brassica genome to date (contig N50 > 10 Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes.

Conclusion

Using these cutting-edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable to the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.

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  1. GigaScience

    Now published in GigaScience doi: 10.1093/gigascience/giaa137

    Mathieu Rousseau-Gueutin 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Mathieu Rousseau-GueutinFor correspondence: jmaury@genoscope.cns.frCaroline Belser 2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Caroline BelserCorinne Da Silva 2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Corinne Da SilvaGautier Richard 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Gautier RichardBenjamin Istace 2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Benjamin IstaceCorinne Cruaud 3Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteCyril Falentin 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Cyril FalentinFranz Boideau 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteJulien Boutte 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteRegine Delourme 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Regine DelourmeGwenaëlle Deniot 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteStefan Engelen 2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Stefan EngelenJulie Ferreira de Carvalho 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Julie Ferreira de CarvalhoArnaud Lemainque 3Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteLoeiz Maillet 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Loeiz MailletJérôme Morice 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this sitePatrick Wincker 2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Patrick WinckerFrance Denoeud 2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for France DenoeudAnne-Marie Chèvre 1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Anne-Marie ChèvreJean-Marc Aury 2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, FranceFind this author on Google ScholarFind this author on PubMedSearch for this author on this siteORCID record for Jean-Marc AuryFor correspondence: jmaury@genoscope.cns.fr

    A version of this preprint has been published in the Open Access journal GigaScience (see paper https://doi.org/10.1093/gigascience/giaa137 ), where the paper and peer reviews are published openly under a CC-BY 4.0 license.

    These peer reviews were as follows:

    Reviewer 1: http://dx.doi.org/10.5524/REVIEW.102545 Reviewer 2: http://dx.doi.org/10.5524/REVIEW.102546 Reviewer 3: http://dx.doi.org/10.5524/REVIEW.102548

  2. Version published to 10.1093/gigascience/giaa137
  3. Version published to 10.1101/2020.07.22.215749v1 on bioRxiv