metaVaR: Introducing metavariant species models for reference-free metagenomic-based population genomics.

Autor: Laso-Jadart R; Institut François Jacob, CEA, CNRS, Génomique Métabolique - UMR 8030, Univ Evry, Université Paris-Saclay, Evry, France., Ambroise C; IBGBI-LaMME, Univ Evry, Université Paris-Saclay, Evry, France., Peterlongo P; Inria, CNRS, IRISA, Univ Rennes, Rennes, France., Madoui MA; Institut François Jacob, CEA, CNRS, Génomique Métabolique - UMR 8030, Univ Evry, Université Paris-Saclay, Evry, France.
Jazyk: angličtina
Zdroj: PloS one [PLoS One] 2020 Dec 30; Vol. 15 (12), pp. e0244637. Date of Electronic Publication: 2020 Dec 30 (Print Publication: 2020).
DOI: 10.1371/journal.pone.0244637
Abstrakt: The availability of large metagenomic data offers great opportunities for the population genomic analysis of uncultured organisms, which represent a large part of the unexplored biosphere and play a key ecological role. However, the majority of these organisms lack a reference genome or transcriptome, which constitutes a technical obstacle for classical population genomic analyses. We introduce the metavariant species (MVS) model, in which a species is represented only by intra-species nucleotide polymorphism. We designed a method combining reference-free variant calling, multiple density-based clustering and maximum-weighted independent set algorithms to cluster intra-species variants into MVSs directly from multisample metagenomic raw reads without a reference genome or read assembly. The frequencies of the MVS variants are then used to compute population genomic statistics such as FST, in order to estimate genomic differentiation between populations and to identify loci under natural selection. The MVS construction was tested on simulated and real metagenomic data. MVSs showed the required quality for robust population genomics and allowed an accurate estimation of genomic differentiation (ΔFST < 0.0001 and <0.03 on simulated and real data respectively). Loci predicted under natural selection on real data were all detected by MVSs. MVSs represent a new paradigm that may simplify and enhance holistic approaches for population genomics and the evolution of microorganisms.
Competing Interests: The authors have declared that no competing interests exist.
Databáze: MEDLINE
Externí odkaz:
Nepřihlášeným uživatelům se plný text nezobrazuje