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About the Authors:
Elsa Rousseau
Contributed equally to this work with: Elsa Rousseau, Frédéric Fabre
Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Visualization, Writing - original draft, Writing - review & editing
* E-mail: [email protected] (ER); [email protected] (FF)
Affiliations Université Côte d’Azur, Inria, INRA, CNRS, UPMC Univ Paris 06, Biocore team, Sophia Antipolis, France, Université Côte d’Azur, INRA, CNRS, ISA, Sophia Antipolis, France, Pathologie Végétale, INRA, 84140 Montfavet, France
ORCID http://orcid.org/0000-0001-7013-6024
Benoît Moury
Roles Conceptualization, Data curation, Formal analysis, Funding acquisition, Investigation, Methodology, Supervision, Writing - original draft, Writing - review & editing
Affiliation: Pathologie Végétale, INRA, 84140 Montfavet, France
ORCID http://orcid.org/0000-0003-3081-1034
Ludovic Mailleret
Roles Conceptualization, Formal analysis, Funding acquisition, Methodology, Supervision, Writing - original draft
Affiliations Université Côte d’Azur, Inria, INRA, CNRS, UPMC Univ Paris 06, Biocore team, Sophia Antipolis, France, Université Côte d’Azur, INRA, CNRS, ISA, Sophia Antipolis, France
Rachid Senoussi
Roles Conceptualization, Methodology, Writing - original draft
Affiliation: UR BioSp, INRA, Avignon, France
Alain Palloix
† Deceased.
Roles Conceptualization, Funding acquisition, Investigation, Methodology
Affiliation: UR GAFL, INRA, Montfavet, France
Vincent Simon
Roles Data curation, Investigation
Affiliations Pathologie Végétale, INRA, 84140 Montfavet, France, UMR BFP, INRA, Villenave d’Ornon, France
Sophie Valière
Roles Data curation, Investigation
Affiliations GeT-PlaGe, INRA, Genotoul, Castanet-tolosan, France, UAR DEPT GA, INRA, Castanet-Tolosan, France
Frédéric Grognard
Roles Conceptualization, Formal analysis, Funding acquisition, Methodology, Supervision, Writing - original draft
Affiliation: Université Côte d’Azur, Inria, INRA, CNRS, UPMC Univ Paris 06, Biocore team, Sophia Antipolis, France
ORCID http://orcid.org/0000-0003-0805-775X
Frédéric Fabre
Contributed equally to this work with: Elsa Rousseau, Frédéric Fabre
Roles Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Supervision, Visualization, Writing - original draft, Writing - review & editing
* E-mail: [email protected] (ER); [email protected] (FF)
Affiliation: UMR SAVE, INRA, Villenave d’Ornon, France
ORCID http://orcid.org/0000-0001-8271-7678Abstract
By 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...