High-quality genome (re)assembly using chromosomal contact data
In: ISSN: 2041-1723, 2014
Online
academicJournal
Zugriff:
International audience ; 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.
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High-quality genome (re)assembly using chromosomal contact data
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Autor/in / Beteiligte Person: | Marie-Nelly, Hervé ; Marbouty, Martial ; Cournac, Axel ; Flot, Jean-François ; Liti, Gianni ; Poggi-Parodi, Dante ; Syan, Sylvie ; Guillén, Nancy ; Margeot, Antoine ; Zimmer, Christophe ; Koszul, Romain ; Imagerie et Modélisation ; Institut Pasteur Paris (IP)-Centre National de la Recherche Scientifique (CNRS) ; Université Pierre et Marie Curie - Paris 6 (UPMC) ; Régulation spatiale des Génomes - Spatial Regulation of Genomes ; Génétique des génomes - Genetics of Genomes (UMR 3525) ; Group Biological Physics and Evolutionary Dynamics ; Max Planck Institute for Dynamics and Self-Organization (MPIDS) ; Max-Planck-Gesellschaft-Max-Planck-Gesellschaft ; Institut de Recherche sur le Cancer et le Vieillissement (IRCAN) ; Université Nice Sophia Antipolis (1965 - 2019) (UNS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UniCA) ; IFP Energies nouvelles (IFPEN) ; Biologie Cellulaire du Parasitisme ; Institut Pasteur Paris (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM) ; This research was supported by funding to R.K. from the European Research Council under the 7th Framework Program (FP7/2007-2013)/ERC grant agreement 260822 and by the Agence Nationale de la Recherche to C.Z. (ANR-09-PIRI-0024 and ANR-11-MONU-020-02) and R.K. (ANR-09-PIRI-0024 ) H.M.-N. was also supported by a fellowship from the Fondation pour la Recherche Médicale (FRM). M.M. is the recipient of a fellowship from the Association pour la Recherche sur le Cancer (20100600373). J.-F.F. is supported by the European Research Council (ERC-2012-AdG 322790). ; We thank Julien Mozziconacci, Emmanuelle Fabre and members of the RSG and IM laboratories for fruitful discussions. We thank Jean-Yves Coppée and Caroline Proux from the PF2 at the IP Genopole for technical help regarding sequencing. |
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Zeitschrift: | ISSN: 2041-1723, 2014 |
Veröffentlichung: | HAL CCSD ; Nature Publishing Group, 2014 |
Medientyp: | academicJournal |
DOI: | 10.1038/ncomms6695 |
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