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High-quality genome (re)assembly using chromosomal contact data

Author

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  • Hervé Marie-Nelly

    (Institut Pasteur, Groupe Régulation Spatiale des Génomes
    CNRS, UMR 3525
    Institut Pasteur, Unité Imagerie et Modélisation
    CNRS, URA 2582)

  • Martial Marbouty

    (Institut Pasteur, Groupe Régulation Spatiale des Génomes
    CNRS, UMR 3525)

  • Axel Cournac

    (Institut Pasteur, Groupe Régulation Spatiale des Génomes
    CNRS, UMR 3525)

  • Jean-François Flot

    (Max Planck Institute for Dynamics and Self-Organization, Group Biological Physics and Evolutionary Dynamics)

  • Gianni Liti

    (Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284—INSERM U108, Université de Nice Sophia Antipolis)

  • Dante Poggi Parodi

    (Sorbonne Universités, UPMC Univ Paris06, IFD
    IFP Energies Nouvelles)

  • Sylvie Syan

    (Institut Pasteur, Unité Cell Biology of Parasitism)

  • Nancy Guillén

    (Institut Pasteur, Unité Cell Biology of Parasitism)

  • Antoine Margeot

    (IFP Energies Nouvelles)

  • Christophe Zimmer

    (Institut Pasteur, Unité Imagerie et Modélisation
    CNRS, URA 2582)

  • Romain Koszul

    (Institut Pasteur, Groupe Régulation Spatiale des Génomes
    CNRS, UMR 3525)

Abstract

Closing gaps in draft genome assemblies can be costly and time-consuming, and published genomes are therefore often left ‘unfinished.’ Here we show that genome-wide chromosome conformation capture (3C) data can be used to overcome these limitations, and present a computational approach rooted in polymer physics that determines the most likely genome structure using chromosomal contact data. This algorithm—named GRAAL—generates high-quality assemblies of genomes in which repeated and duplicated regions are accurately represented and offers a direct probabilistic interpretation of the computed structures. We first validated GRAAL on the reference genome of Saccharomyces cerevisiae, as well as other yeast isolates, where GRAAL recovered both known and unknown complex chromosomal structural variations. We then applied GRAAL to the finishing of the assembly of Trichoderma reesei and obtained a number of contigs congruent with the know karyotype of this species. Finally, we showed that GRAAL can accurately reconstruct human chromosomes from either fragments generated in silico or contigs obtained from de novo assembly. In all these applications, GRAAL compared favourably to recently published programmes implementing related approaches.

Suggested Citation

  • Hervé Marie-Nelly & Martial Marbouty & Axel Cournac & Jean-François Flot & Gianni Liti & Dante Poggi Parodi & Sylvie Syan & Nancy Guillén & Antoine Margeot & Christophe Zimmer & Romain Koszul, 2014. "High-quality genome (re)assembly using chromosomal contact data," Nature Communications, Nature, vol. 5(1), pages 1-10, December.
  • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms6695
    DOI: 10.1038/ncomms6695
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    Cited by:

    1. Robert Schöpflin & Uirá Souto Melo & Hossein Moeinzadeh & David Heller & Verena Laupert & Jakob Hertzberg & Manuel Holtgrewe & Nico Alavi & Marius-Konstantin Klever & Julius Jungnitsch & Emel Comak & , 2022. "Integration of Hi-C with short and long-read genome sequencing reveals the structure of germline rearranged genomes," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    2. Jacques Serizay & Cyril Matthey-Doret & Amaury Bignaud & Lyam Baudry & Romain Koszul, 2024. "Orchestrating chromosome conformation capture analysis with Bioconductor," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    3. Simone Mozzachiodi & Lorenzo Tattini & Agnes Llored & Agurtzane Irizar & Neža Škofljanc & Melania D’Angiolo & Matteo De Chiara & Benjamin P. Barré & Jia-Xing Yue & Angela Lutazi & Sophie Loeillet & Ra, 2021. "Aborting meiosis allows recombination in sterile diploid yeast hybrids," Nature Communications, Nature, vol. 12(1), pages 1-13, December.

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