1. Genomic Signatures of a Major Adaptive Event in the Pathogenic Fungus Melampsora larici-populina
- Author
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Antoine Persoons, Agathe Maupetit, Clémentine Louet, Axelle Andrieux, Anna Lipzen, Kerrie W Barry, Hyunsoo Na, Catherine Adam, Igor V Grigoriev, Vincent Segura, Sébastien Duplessis, Pascal Frey, Fabien Halkett, Stéphane De Mita, Alba, Mar, Interactions Arbres-Microorganismes (IAM), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), University of California [Berkeley] (UC Berkeley), University of California (UC), Biologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt (BioForA), Office national des forêts (ONF)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Plant Health Institute of Montpellier (UMR PHIM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, The work within the framework of the poplar rust genome project (CSP 1416) conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No.DE-AC02-05CH11231., A.P. was supported by a PhD fellowship from the Region Lorraine and INRAE and a partial post doc fellowship from the Region Grand-Est., A.M. was supported by a PhD fellowship from the Region Lorraine and INRAE., C.L. was supported by a PhD fellowship from the Region Lorraine, ANR-12-ADAP-0009,GANDALF,Génomique et adaptation des traits de vie des champignons impliqués dans les interactions plante-pathogène(2012), ANR-11-LABX-0002,ARBRE,Recherches Avancées sur l'Arbre et les Ecosytèmes Forestiers(2011), and ANR-18-CE32-0001,Clonix2D,Les conséquences génétiques de reproduction partiellement clonale dans les populations colonisant de nouveaux territoires(2018)
- Subjects
AcademicSubjects/SCI01140 ,0106 biological sciences ,population genomics ,[SDV]Life Sciences [q-bio] ,genome scan ,01 natural sciences ,03 medical and health sciences ,Genetics ,plant–pathogen interactions ,Ecology, Evolution, Behavior and Systematics ,Plant Diseases ,030304 developmental biology ,Evolutionary Biology ,0303 health sciences ,Basidiomycota ,plant-pathogen interactions ,Human Genome ,AcademicSubjects/SCI01130 ,Genomics ,Populus ,coevolution ,genome-wide association studies ,Biochemistry and Cell Biology ,Research Article ,Biotechnology ,Developmental Biology ,010606 plant biology & botany - Abstract
The recent availability of genome-wide sequencing techniques has allowed systematic screening for molecular signatures of adaptation, including in nonmodel organisms. Host–pathogen interactions constitute good models due to the strong selective pressures that they entail. We focused on an adaptive event which affected the poplar rust fungus Melampsora larici-populina when it overcame a resistance gene borne by its host, cultivated poplar. Based on 76 virulent and avirulent isolates framing narrowly the estimated date of the adaptive event, we examined the molecular signatures of selection. Using an array of genome scan methods based on different features of nucleotide diversity, we detected a single locus exhibiting a consistent pattern suggestive of a selective sweep in virulent individuals (excess of differentiation between virulent and avirulent samples, linkage disequilibrium, genotype–phenotype statistical association, and long-range haplotypes). Our study pinpoints a single gene and further a single amino acid replacement which may have allowed the adaptive event. Although our samples are nearly contemporary to the selective sweep, it does not seem to have affected genome diversity further than the immediate vicinity of the causal locus, which can be explained by a soft selective sweep (where selection acts on standing variation) and by the impact of recombination in mitigating the impact of selection. Therefore, it seems that properties of the life cycle of M. larici-populina, which entails both high genetic diversity and outbreeding, has facilitated its adaptation.
- Published
- 2021
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