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Long-reads assembly of the Brassica napus reference genome, Darmor-bzh

View ORCID ProfileMathieu Rousseau-Gueutin, View ORCID ProfileCaroline Belser, View ORCID ProfileCorinne Da Silva, View ORCID ProfileGautier Richard, View ORCID ProfileBenjamin Istace, Corinne Cruaud, View ORCID ProfileCyril Falentin, Franz Boideau, Julien Boutte, View ORCID ProfileRegine Delourme, Gwenaëlle Deniot, View ORCID ProfileStefan Engelen, View ORCID ProfileJulie Ferreira de Carvalho, Arnaud Lemainque, View ORCID ProfileLoeiz Maillet, Jérôme Morice, View ORCID ProfilePatrick Wincker, View ORCID ProfileFrance Denoeud, View ORCID ProfileAnne-Marie Chèvre, View ORCID ProfileJean-Marc Aury
doi: https://doi.org/10.1101/2020.07.22.215749
Mathieu Rousseau-Gueutin
1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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  • ORCID record for Mathieu Rousseau-Gueutin
  • For correspondence: jmaury@genoscope.cns.fr
Caroline Belser
2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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Corinne Da Silva
2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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  • ORCID record for Corinne Da Silva
Gautier Richard
1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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  • ORCID record for Gautier Richard
Benjamin Istace
2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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Corinne Cruaud
3Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
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Cyril Falentin
1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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Franz Boideau
1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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Julien Boutte
1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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Regine Delourme
1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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Gwenaëlle Deniot
1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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Stefan Engelen
2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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  • ORCID record for Stefan Engelen
Julie Ferreira de Carvalho
1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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Arnaud Lemainque
3Genoscope, Institut François Jacob, Commissariat à l’Energie Atomique (CEA), Université Paris-Saclay, Evry, France
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Loeiz Maillet
1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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Jérôme Morice
1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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Patrick Wincker
2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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France Denoeud
2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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Anne-Marie Chèvre
1IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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  • ORCID record for Anne-Marie Chèvre
Jean-Marc Aury
2Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
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  • For correspondence: jmaury@genoscope.cns.fr
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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 allow to access the gene catalogue of a given species but also reveals the architecture and organisation of chromosomes, including complex regions like 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, has been produced using short-reads and its contiguity was extremely low if compared to current assemblies of the Brassica genus.

Findings Here, we report the new long-reads assembly of Darmor-bzh genome (Brassica napus) generated by combining long-reads sequencing data, optical and genetic maps. Using the PromethION device and six flowcells, we generated about 16M long-reads representing 93X coverage and more importantly 6X with reads longer than 100Kb. This ultralong-reads dataset allows us to generate one of the most contiguous and complete assembly of a Brassica genome to date (contigs N50 > 10Mb). 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 for the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.

Competing Interest Statement

The authors declare that they have no competing interests. JMA received travel and accommodation expenses to speak at Oxford Nanopore Technologies conferences. JMA and CB received accommodation expenses to speak at Bionano Genomics user meeting.

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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Posted July 22, 2020.
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Long-reads assembly of the Brassica napus reference genome, Darmor-bzh
Mathieu Rousseau-Gueutin, Caroline Belser, Corinne Da Silva, Gautier Richard, Benjamin Istace, Corinne Cruaud, Cyril Falentin, Franz Boideau, Julien Boutte, Regine Delourme, Gwenaëlle Deniot, Stefan Engelen, Julie Ferreira de Carvalho, Arnaud Lemainque, Loeiz Maillet, Jérôme Morice, Patrick Wincker, France Denoeud, Anne-Marie Chèvre, Jean-Marc Aury
bioRxiv 2020.07.22.215749; doi: https://doi.org/10.1101/2020.07.22.215749
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Long-reads assembly of the Brassica napus reference genome, Darmor-bzh
Mathieu Rousseau-Gueutin, Caroline Belser, Corinne Da Silva, Gautier Richard, Benjamin Istace, Corinne Cruaud, Cyril Falentin, Franz Boideau, Julien Boutte, Regine Delourme, Gwenaëlle Deniot, Stefan Engelen, Julie Ferreira de Carvalho, Arnaud Lemainque, Loeiz Maillet, Jérôme Morice, Patrick Wincker, France Denoeud, Anne-Marie Chèvre, Jean-Marc Aury
bioRxiv 2020.07.22.215749; doi: https://doi.org/10.1101/2020.07.22.215749

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