Biology subjects

Frey, P.

Publications and source records attributed to Frey, P..

9 recordsLinked to original sources

bioRxiv2026

Haplotype-phased assemblies of the two poplar rust fungi species: Melampsora larici-populina and Melampsora allii-populina

Dikaryotic rust fungi maintain two distinct haploid nuclei for most of their life cycle, making their large, repeat-rich genomes difficult to assemble and phase. Here we present haplotype-phased, near chromosome-scale genome assemblies for the poplar rust pathogens Melampsora larici-populina 98AG31 and Melampsora allii-populina 12AY07, generated using PacBio HiFi sequencing and Hi-C-guided scaffolding. For each species, we resolved 18 chromosomes per haplotype, providing the first near chromosome-level representations of poplar rust fungal species. M. larici-populina diploid assembly spans ~203 Mb, while M. allii-populina reaches ~416 Mb, with high completeness and strong collinearity between haplotypes. Compared with previous fragmented or collapsed references, these assemblies greatly improve contiguity, recover centromeric and telomeric features, and support the transposable element-driven genome size expansion in M. allii-populina. The haplotype-aware annotations of genes and predicted effectors derived from these resources will enable detailed analyses of genome architecture, repeat dynamics, and key loci such as avirulence genes. Together, these assemblies provide a robust genomic resource for investigating host adaptation, virulence evolution, and population diversity in poplar rust fungi.

genomics↗

bioRxiv2025

Behind the shadow play: Shedding light on the population genetics of partially clonal organisms through clone age distributions

Partial clonality is widespread in natural populations; however, the distributions of clone ages under different rates of clonality and their effects on genetic diversity remain unexplored. To fill this gap, we simulated partially clonal populations over 10,000 generations across a range of clonality and mutation rates. Using a forward-in-time individual-based model, we evaluated genetic and genotypic indices alongside measures of clone age distribution to examine how different clonality rates influence clone age distributions, and how these distributions impact population structure and genetic diversity over time. Our results reveal two distinct trajectories: (i) at low to moderate rates of clonality evolution is driven by sharp and predictable patterns of rapid clone turnovers, resulting in predominantly young clones which relative abundances well align with genotypic indices ; (ii) at extreme rates of clonality, demographic stochasticity generates very variable clone age distributions which mirror the high variance of mean and variance of FIS that summarize gene reshuffling between individuals. Interestingly, a portion of the variability of these indices can be explained by differences in clone age distribution that occur by chance. Our results, therefore, complement previous theoretical studies on the population genetics of partial clonality by providing biological insights into how clonal turnover dynamics shape the temporal evolution and variability of highly clonal populations. These results have practical implications for inferring evolutionary trajectories and managing partially clonal species.

evolutionary biology↗

bioRxiv2025

Uromyces plumbarius first reported on Oenothera lindheimeri in Europe with widespread distribution and association with the rust hyperparasite Sphaerellopsis sp.

The rust fungus Uromyces plumbarius Peck was reported in Europe for the first time on Oenothera lindheimeri (Engelm. & A. Gray) W.L. Wagner & Hoch (Lindheimers 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 28S 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. and fungivorous larvae of Mycodiplosis sp.--two native, non-specific natural enemies which may play a role in limiting the impact of rust infections.

microbiology↗

bioRxiv2025

Long-lasting coexistence of multiple asexual lineages alongside their sexual counterparts in a fungal plant pathogen

Sexual-to-asexual transitions within species are crucial for understanding reproductive evolution, yet the coexistence of both modes of fungal species in the same environment is poorly documented. Here, we report this transition in a plant pathogen species that coexists within the same geographical environment. Our biological model is the poplar rust fungus Melampsora larici-populina, which displays a complex life cycle typical of rust fungi (Pucciniales). It alternates between two unrelated hosts to complete an obligate sexual life cycle once a year. We conducted a comprehensive population genetic analysis, using 21 microsatellite markers and data from 2,122 individuals gathered over 30 years from various locations in France. Our results demonstrate the existence of many distinct lineages that reproduce asexually through the years, skipping the sexual phase. 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 across multiple years. This result demonstrates the coexistence of these lineages with their sexual counterparts in the same ecological niche, challenging conventional assumptions about geographical sorting of reproductive modes. These considerations are of paramount importance for understanding the contemporary evolution of major pathogen species. This switch from sexual to asexual reproduction has contributed to devastating epidemics worldwide.

evolutionary biology↗

bioRxiv2023

Inferring invasion determinants with mechanistic models and multitype samples

Dispersal, and in particular the frequency of long-distance dispersal (LDD) events, has strong implications for population dynamics with possibly the acceleration of the colonisation front, and for evolution with possibly the conservation of genetic diversity along the colonised domain. However, accurately inferring LDD is challenging as it requires both large-scale data and a methodology that encompasses the redistribution of individuals in time and space. Here, we propose a mechanistic-statistical framework to estimate dispersal from one-dimensional invasions. The mechanistic model takes into account population growth and grasps the diversity in dispersal processes by using either diffusion, leading to a reaction-diffusion (R.D.) formalism, or kernels, leading to an integro-differential (I.D.) formalism. The latter considers different dispersal kernels (e.g. Gaussian, Exponential, and Exponential-power) differing in their frequency of LDD events. The statistical model relies on dedicated observation laws that describe two types of samples, clumped or not. As such, we take into account the variability in both habitat suitability and occupancy perception. We first check the identifiability of the parameters and the confidence in the selection of the dispersal process. We observed good identifiability for all parameters (correlation coefficient > 0.9 between true and fitted values). The dispersal process that is the most confidently identified is Exponential-Power (i.e. fat-tailed) kernel. We then applied our framework to data describing an annual invasion of the poplar rust disease along the Durance River valley over nearly 200 km. This spatio-temporal survey consisted of 12 study sites examined at seven time points. We confidently estimated that the dispersal of poplar rust is best described by an Exponential-power kernel with a mean dispersal distance of 1.94 km and an exponent parameter of 0.24 characterising a fat-tailed kernel with frequent LDD events. By considering the whole range of possible dispersal processes our method forms a robust inference framework. It can be employed for a variety of organisms, provided they are monitored in time and space along a one-dimension invasion.

evolutionary biology↗

bioRxiv2022

A remarkable expansion of oligopeptide transporter genes in rust fungi (Pucciniales) suggests a specialization in nutrients acquisition for obligate biotrophy

Nutrients acquisition by rust fungi during their biotrophic growth has been assigned to a few transporters expressed in haustorial infection structures. We performed a comparative genomic analysis of all transporter genes (hereafter termed transportome) classified according to the Transporter Classification Database (TCDB) focusing specifically on rust fungi (order Pucciniales) versus other species in the Dikarya. We also surveyed expression of transporter genes in the poplar rust fungus for which transcriptomics data are available across the whole life cycle. Despite a significant increase in gene number, rust fungi presented a reduced transportome compared to a vast majority of fungi in the Dikarya. However, a few transporter families in the subclass Porters showed significant expansions. Noteworthy, three metal transport-related families involved in the import, export and sequestration of metals were expanded in Pucciniales and expressed at various stages of the rust life cycle suggesting a tight regulation of metal homeostasis. The most remarkable gene expansion in the Pucciniales was observed for the oligopeptide transporter (OPT) family with 25 genes in average compared to seven to 14 genes in the other surveyed taxonomical ranks. A phylogenetic analysis showed several specific expansion events at the root of the order Pucciniales with subsequent expansions in rust taxonomical families. The OPT genes showed dynamic expression patterns along the rust life cycle and more particularly during infection of the poplar host tree, suggesting a specialization for the acquisition of nitrogen and sulfur through the transport of oligopeptides from the host during biotrophic growth.

microbiology↗

bioRxiv2021

Expert annotation and life-cycle transcriptomics of transcription factors in rust fungi (Pucciniales) highlight the role of cold shock proteins in dormancy exit

Fungi of the order Pucciniales are obligate plant biotrophs causing rust diseases. They exhibit a complex life cycle with the production of up to five spore types, infection of two unrelated hosts and an overwintering stage. Transcription factors (TFs) are key regulators of gene expression in eukaryote cells. In order to better understand genetic programs expressed during major transitions of the rust life cycle, we surveyed the complement of TFs in fungal genomes with an emphasis on Pucciniales. We found that despite their large gene numbers, rust genomes have a reduced repertoire of TFs compared to other fungi. The proportions of C2H2 and Zinc cluster - two of the most represented TF families in fungi-indicate differences in their evolutionary relationships in Pucciniales and other fungal taxa. The cold shock protein (CSP) family showed a striking expansion in Pucciniomycotina with specific duplications in the order Pucciniales. The survey of expression profiles collected by transcriptomics along the life cycle of the poplar rust fungus revealed TF genes related to major biological transitions, e.g. response to environmental cues and host infection. Particularly, poplar rust CSPs were strongly expressed in basidia produced after the overwintering stage suggesting a possible role in dormancy exit. Expression during transition from dormant telia to basidia confirmed the specific expression of the three poplar rust CSP genes. Their heterologous expression in yeast improved cell growth after cold stress exposure, strengthening their implication in dormancy exit. This study addresses for the first time TF involved in developmental transition in the rust life cycle opening perspectives to further explore molecular regulation in the biology of the Pucciniales.

microbiology↗

bioRxiv2021

Genomic signatures of a major adaptive event in the pathogenic fungus Melampsora larici-populina

BackgroundThe 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. ResultsUsing 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. ConclusionsOur 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.

evolutionary biology↗

bioRxiv2017

The rust fungus Melampsora larici-populina expresses a conserved genetic program and distinct sets of secreted protein genes during infection of its two host plants, larch and poplar

Mechanims required for broad spectrum or specific host colonization of plant parasites are poorly understood. As a perfect illustration, heteroecious rust fungi require two alternate host plants to complete their life cycle. Melampsora larici-populina infects two taxonomically unrelated plants, larch on which sexual reproduction is achieved and poplar on which clonal multiplication occurs leading to severe epidemics in plantations. High-depth RNA sequencing was applied to three key developmental stages of M. larici-populina infection on larch: basidia, pycnia and aecia. Comparative transcriptomics of infection on poplar and larch hosts was performed using available expression data. Secreted protein was the only significantly over-represented category among differentially expressed M. larici-populina genes in basidia, pycnia and aecia compared together, highlighting their probable involvement in the infection process. Comparison of fungal transcriptomes in larch and poplar revealed a majority of rust genes commonly expressed on the two hosts and a fraction exhibiting a host-specific expression. More particularly, gene families encoding small secreted proteins presented striking expression profiles that highlight probable candidate effectors specialized on each host. Our results bring valuable new information about the biological cycle of rust fungi and identify genes that may contribute to host specificity.

microbiology↗