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

Hervé Marie-Nelly (), Martial Marbouty, Axel Cournac, Jean-François Flot, Gianni Liti, Dante Poggi Parodi, Sylvie Syan, Nancy Guillén, Antoine Margeot, Christophe Zimmer () and Romain Koszul ()
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Hervé Marie-Nelly: Institut Pasteur, Groupe Régulation Spatiale des Génomes
Martial Marbouty: Institut Pasteur, Groupe Régulation Spatiale des Génomes
Axel Cournac: Institut Pasteur, Groupe Régulation Spatiale des Génomes
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
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
Romain Koszul: Institut Pasteur, Groupe Régulation Spatiale des Génomes

Nature Communications, 2014, vol. 5, issue 1, 1-10

Abstract: 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.

Date: 2014
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DOI: 10.1038/ncomms6695

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