A. Andrieux’s research while affiliated with University of Lorraine and other places

The rust fungus Uromyces plumbarius Peck was reported in Europe for the first time on Oenothera lindheimeri (Engelm. & A. Gray) W.L. Wagner & Hoch (Lindheimer's beeblossom), a highly popular ornamental plant widely cultivated since the 2000s. The fungus was found in 11 locations across France and two locations in the Netherlands. The identification was based on an analysis of morphological characteristics and ITS rDNA sequences. The pathogenicity was confirmed through reinoculation using fresh urediniospores. This represents the first record of U. plumbarius outside its native range in North America. Its widespread distribution in France appears to result from rapid dissemination, likely facilitated by the plant trade between nursery gardeners. The discovery of U. plumbarius was accompanied by the detection of the hyperparasitic fungus Sphaerellopsis sp. (teleomorph Eudarluca sp.), which may play a role in limiting the impact of rust infections.

Sexual to asexual transition is described as a process whereby asexual lineages emerge within sexual species. This phenomenon gives rise to many questions about the maintenance of sexual reproduction and the evolution of asexuality in these organisms. The poplar rust fungus Melampsora larici-populina has a complex life cycle, which is typical of rust fungi (Pucciniales). It alternates between a sexual reproduction phase on larch trees (Larix spp.) and rounds of asexual multiplication on poplar trees (Populus spp.). This study challenges the classic understanding of the M. larici-populina life cycle. We conducted a comprehensive population genetic analysis, utilizing 21 microsatellite markers and data from 2,122 individuals gathered over an extended time from various locations in France. Our results demonstrate the existence of many distinct lineages that reproduce asexually through the years, skipping the sexual phase. A clustering analysis identified a group of multilocus lineages that displayed all hallmarks of the genetic consequences of asexual reproduction, including highly negative and large variance among loci of the inbreeding coefficient (FIS). This indirect evidence for asexual reproduction was confirmed by the direct observation of these asexual lineages being repeatedly sampled over the years. While sexual lineages are predominant throughout France, asexual lineages are more prevalent in the south of the country, due to possible environmental or ecological factors that allow the overwintering of asexual forms. The discovery of variations in the life cycle in this species offers insights into the evolution from sexual to asexual reproduction encountered in many pathogen species. It could serve as a model organism for studying the transition from sexual to asexual reproductive mode.

Adaptation can occur at remarkably short timescales in natural populations, leading to drastic changes in phenotypes and genotype frequencies over a few generations only. The inference of demographic parameters can allow understanding how evolutionary forces interact and shape the genetic trajectories of populations during rapid adaptation. Here we propose a new Approximate Bayesian Computation (ABC) framework that couples a forward and individual-based model with temporal genetic data to disentangle genetic changes and demographic variations in a case of rapid adaptation. We test the accuracy of our inferential framework and evaluate the benefit of considering a dense versus sparse sampling. Theoretical investigations demonstrate high accuracy in both model and parameter estimations, even if a strong thinning is applied to time series data. Then, we apply our ABC inferential framework to empirical data describing the population genetic changes of the poplar rust pathogen following a major event of resistance overcoming. We successfully estimate key demographic and genetic parameters, including the proportion of resistant hosts deployed in the landscape and the level of standing genetic variation from which selection occurred. Inferred values are in accordance with our empirical knowledge of this biological system. This new inferential framework, which contrasts with coalescent-based ABC analyses, is promising for a better understanding of evolutionary trajectories of populations subjected to rapid adaptation.

Adaptation can occur at remarkably short timescales in natural populations, leading to drastic changes in phenotypes and genotype frequencies over a few generations only. The inference of demographic parameters can allow understanding how evolutionary forces interact and shape the genetic trajectories of populations during rapid adaptation. Here we propose a new Approximate Bayesian Computation (ABC) framework that couples a forward and individual-based model with temporal genetic data to disentangle genetic changes and demographic variations in a case of rapid adaptation. We test the accuracy of our inferential framework and evaluate the benefit of considering the full trajectory compared to few time samples. Theoretical investigations demonstrate high accuracy in both model and parameter estimations, even if a strong thinning is applied to time series data. Then, we apply our ABC inferential framework to empirical data describing the population genetics changes of the poplar rust pathogen following a major event of resistance overcoming. We successfully estimate key demographic and genetic parameters, including the proportion of resistant hosts deployed in the landscape and the level of standing genetic variation from which selection occurred. Inferred values are in accordance with our empirical knowledge of this biological system. This new inferential framework, which contrasts with coalescent-based ABC analyses, is promising for a better understanding of evolutionary trajectories of populations subjected to rapid adaptation.

The recent availability of genome-wide sequencing techniques has allowed systematic screening for molecular signatures of adaptation, including in non-model 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.

The deployment of plant varieties carrying resistance genes (R) exerts strong selection pressure on pathogen populations. Rapidly evolving avirulence genes (Avr) allow pathogens to escape R‐mediated plant immunity through a variety of mechanisms, leading to virulence. The poplar rust fungus Melampsora larici‐populina is a damaging pathogen of poplars in Europe. It underwent a major adaptive event in 1994, with the breakdown of the poplar RMlp7 resistance gene. Population genomics studies identified a locus in the genome of M. larici‐populina that likely corresponds to the candidate avirulence gene AvrMlp7. Here, to further characterize this effector, we used a population genetics approach on a comprehensive set of 281 individuals recovered throughout a 28‐year period encompassing the resistance breakdown event. Using two dedicated molecular tools, genotyping at the candidate locus highlighted two different alterations of a predominant allele found mainly before the resistance breakdown: a non‐synonymous mutation and a complete deletion of this locus. This results in six diploid genotypes: three genotypes related to the avirulent phenotype and three related to the virulent phenotype. The temporal survey of the candidate locus revealed that both alterations were found in association during the resistance breakdown event. They pre‐existed before the breakdown in a heterozygous state with the predominant allele cited above. Altogether, these results suggest that the association of both alterations at the candidate locus AvrMlp7 drove the poplar rust adaptation to RMlp7‐mediated immunity. This study demonstrates for the first time a case of adaptation from standing genetic variation in rust fungi during a qualitative resistance breakdown.

Background The recent availability of genome-wide sequencing techniques has allowed systematic screening for molecular signatures of adaptation, including in non-model 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. Results Using an array of genome scan methods, 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 the selective sweep occurred only four years earlier, it does not seem to have affected genome diversity further than the immediate vicinity of the causal locus. Conclusions Our results suggest that M. larici-populina under-went a soft selective sweep and possibly a prominent effect of outbreeding and recombination, which we speculate have increased the efficiency of selection.

Crop varieties carrying qualitative resistance to targeted pathogens lead to strong selection pressure on parasites, often resulting in resistance breakdown. It is well known that qualitative resistance breakdowns modify pathogen population structure but few studies have analyzed the consequences on their quantitative aggressiveness related traits. The aim of this study was to characterize the evolution of these traits following a resistance breakdown in the poplar rust fungus, Melampsora larici-populina. We based our experiment on three temporal populations sampled just before the breakdown event, immediately after and four years later. First, we quantified phenotypic differences among populations for a set of aggressiveness traits on a universally susceptible cultivar (infection efficiency, latent period, lesion size, my-celium quantity, and sporulation rate) and one morphological trait (mean spore volume). Then, we estimated heritability to establish which traits could be subjected to adaptive evolution and tested for evidence of selection. Our results revealed significant changes in the morphological trait but no variation in aggressiveness traits. By contrast, recent works have demonstrated that quantitative resistance (initially assumed more durable) could be eroded and lead to increased aggressiveness. Hence, this study is one example suggesting that the use of qualitative resistance may be revealed to be less detrimental to long-term sustainable crop production. K E Y W O R D S disease-associated traits, heritability, mixed model, plant pathogen, Q ST-F ST comparisons, temporal sampling

Melampsora larici-populina is a basidiomycete fungus (diploid) responsible for poplar rust. This partially asexual organism has its sexual stage on larch (Larix sp.) and its asexual stage on poplar (Populus sp.), a life cycle that amounts to cyclical parthenogenesis in insects. A poplar cultivar ‘Beaupré’ (R7) was selected to be completely resistant to M. larici-populina and planted widely in northern France between 1982 and 1996. A major resistance breakdown event occurred in 1994 when virulent rust genotypes (avr7) emerged (Xhaard et al., 2011). Beaupré revealed to be highly susceptible to avr7 pathogen genotypes, and this rapid breakdown led to a replacement of the pathogen population by a new genetic group (Persoons et al., 2017).A candidate locus for the avr7 gene was identified in M. larici-populina (Persoons et al., in prep., Maupetit et al., in prep.). The virulent allele is recessive and there are two independent causal mutations at the same locus: a single nucleotide polymorphism (from T to C) and the deletion of this locus. Research goal: To study the dynamics of virulence allele fixation both theoretically and empirically, by (1) Modeling virulence fixation in different evolutionary scenarios. (2) Tracing back the polymorphism evolution at the candidate locus before, during and after the resistance breakdown.