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Estimating virus effective population size and selection without neutral markers

hal.structure.identifierUnité de Pathologie Végétale [PV]
hal.structure.identifierBiological control of artificial ecosystems [BIOCORE]
hal.structure.identifierInstitut Sophia Agrobiotech [ISA]
dc.contributor.authorROUSSEAU, Elsa
hal.structure.identifierUnité de Pathologie Végétale [PV]
dc.contributor.authorMOURY, Benoît
hal.structure.identifierInstitut Sophia Agrobiotech [ISA]
hal.structure.identifierBiological control of artificial ecosystems [BIOCORE]
dc.contributor.authorMAILLERET, Ludovic
hal.structure.identifierBiostatistique et Processus Spatiaux [BioSP]
dc.contributor.authorSENOUSSI, Rachid
hal.structure.identifierGénétique et Amélioration des Fruits et Légumes [GAFL]
dc.contributor.authorPALLOIX, Alain
hal.structure.identifierBiologie du fruit et pathologie [BFP]
hal.structure.identifierUnité de Pathologie Végétale [PV]
dc.contributor.authorSIMON, Vincent
hal.structure.identifierGénome et Transcriptome - Plateforme Génomique [GeT-PlaGe]
hal.structure.identifierUnité Animalerie Rongeurs [UAR]
dc.contributor.authorVALIÈRE, Sophie
hal.structure.identifierBiological control of artificial ecosystems [BIOCORE]
dc.contributor.authorGROGNARD, Frédéric
hal.structure.identifierUnité Mixte de Recherche en Santé Végétale (INRA/ENITA) [UMRSV]
dc.contributor.authorFABRE, Frédéric
dc.date.issued2017-11-20
dc.identifier.issn1553-7366
dc.description.abstractEnBy combining high-throughput sequencing (HTS) with experimental evolution, we can observe the within-host dynamics of pathogen variants of biomedical or ecological interest. We studied the evolutionary dynamics of five variants of Potato virus Y (PVY) in 15 doubled-haploid lines of pepper. All plants were inoculated with the same mixture of virus variants and, variant frequencies were determined by HTS in eight plants of each pepper line, at each of six sampling dates. We developed a method for estimating the intensities of selection and genetic drift in a multi-allelic Wright-Fisher model, applicable whether these forces are strong or weak, and in the absence of neutral markers. This method requires variant frequency determination at several time points, in independent hosts. The parameters are the selection coefficients for each PVY variant and four effective population sizes N e at different time-points of the experiment. Numerical simulations of asexual haploid Wright-Fisher populations subjected to contrasting genetic drift (N e 2 [10, 2000]) and selection (|s| 2 [0, 0.15]) regimes were used to validate the method proposed. The experiment in closely related pepper host genotypes revealed that viruses experienced a considerable diversity of selection and genetic drift regimes. The resulting variant dynamics were accurately described by Wright-Fisher models. The fitness ranks of the variants were almost identical between host genotypes. By contrast, the dynamics of N e were highly variable, although a bottleneck was often identified during the systemic movement of the virus. We demonstrated that, for a fixed initial PVY population, virus effective population size is a heritable trait in plants. These findings pave the way for the breeding of plant varieties exposing viruses to stronger genetic drift, thereby slowing virus adaptation. PLOS Pathogens | https://doi.org/10.1371/journal.ppat.
dc.language.isoen
dc.publisherPublic Library of Science
dc.rights.urihttp://creativecommons.org/licenses/by/
dc.title.enEstimating virus effective population size and selection without neutral markers
dc.typeArticle de revue
dc.identifier.doi10.1371/journal.ppat.1006702
dc.subject.halInformatique [cs]/Automatique
dc.subject.halMathématiques [math]
dc.subject.halSciences de l'ingénieur [physics]
dc.subject.halSciences du Vivant [q-bio]
bordeaux.journalPLoS Pathogens
bordeaux.pagee1006702
bordeaux.volume13
bordeaux.issue11
bordeaux.peerReviewedoui
hal.identifierhal-01658535
hal.version1
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-01658535v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.jtitle=PLoS%20Pathogens&rft.date=2017-11-20&rft.volume=13&rft.issue=11&rft.spage=e1006702&rft.epage=e1006702&rft.eissn=1553-7366&rft.issn=1553-7366&rft.au=ROUSSEAU,%20Elsa&MOURY,%20Beno%C3%AEt&MAILLERET,%20Ludovic&SENOUSSI,%20Rachid&PALLOIX,%20Alain&rft.genre=article


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