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09 07, 2021;4 (1): 1047.

Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing.

Caroline Belser, Franc-Christophe Baurens, Benjamin Noel, Guillaume Martin, Corinne Cruaud, Benjamin Istace, Nabila Yahiaoui, Karine Labadie, Eva Hřibová, Jaroslav Doležel, Arnaud Lemainque, Patrick Wincker, Angélique D'Hont, Jean-Marc Aury
Author Information
  1. Caroline Belser: Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France. ORCID
  2. Franc-Christophe Baurens: CIRAD, UMR AGAP Institut, Montpellier, France.
  3. Benjamin Noel: Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France. ORCID
  4. Guillaume Martin: CIRAD, UMR AGAP Institut, Montpellier, France. ORCID
  5. Corinne Cruaud: Commissariat à l'Energie Atomique (CEA), Institut François Jacob, Genoscope, Evry, France.
  6. Benjamin Istace: Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France. ORCID
  7. Nabila Yahiaoui: CIRAD, UMR AGAP Institut, Montpellier, France.
  8. Karine Labadie: Commissariat à l'Energie Atomique (CEA), Institut François Jacob, Genoscope, Evry, France. ORCID
  9. Eva Hřibová: Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic.
  10. Jaroslav Doležel: Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic. ORCID
  11. Arnaud Lemainque: Commissariat à l'Energie Atomique (CEA), Institut François Jacob, Genoscope, Evry, France.
  12. Patrick Wincker: Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France. ORCID
  13. Angélique D'Hont: CIRAD, UMR AGAP Institut, Montpellier, France.
  14. Jean-Marc Aury: Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France. jmaury@genoscope.cns.fr. ORCID
PMID: 34493830 DOI: 10.1038/s42003-021-02559-3

Abstract

Long-read technologies hold the promise to obtain more complete genome assemblies and to make them easier. Coupled with long-range technologies, they can reveal the architecture of complex regions, like centromeres or rDNA clusters. These technologies also make it possible to know the complete organization of chromosomes, which remained complicated before even when using genetic maps. However, generating a gapless and telomere-to-telomere assembly is still not trivial, and requires a combination of several technologies and the choice of suitable software. Here, we report a chromosome-scale assembly of a banana genome (Musa acuminata) generated using Oxford Nanopore long-reads. We generated a genome coverage of 177X from a single PromethION flowcell with near 17X with reads longer than 75 kbp. From the 11 chromosomes, 5 were entirely reconstructed in a single contig from telomere to telomere, revealing for the first time the content of complex regions like centromeres or clusters of paralogous genes.

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Grants

  1. ANR-10-LABX-0001-01/Agence Nationale de la Recherche (French National Research Agency)
  2. ANR-10-INBS-09-08/Agence Nationale de la Recherche (French National Research Agency)

MeSH Term

Chromosomes, Plant
Genome, Plant
Musa
Nanopore Sequencing
Nanopores
Telomere
Journal Article Research Support, Non-U.S. Gov't

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