Biology subjects

Mathieu-Begne, E.

Publications and source records attributed to Mathieu-Begne, E..

5 recordsLinked to original sources

bioRxiv2025

Ancient MAX Effector Variants of a Fungal Pathogen Evade Apoplastic Immunity in Apple

Venturia inaequalis is an Ascomycota fungus responsible for apple scab, the main disease in apple orchards. During infection, the pathogen colonizes the subcuticular space and secretes effectors to promote virulence. To mitigate disease impact, resistance genes such as Rvi6, which encodes a membrane-localized receptor-like protein, have been introduced into apple cultivars. However, over the past three decades, Rvi6-mediated resistance has been circumvented in orchards, with the emergence of virulent V. inaequalis strains. Through comparative genomics analyses and functional validation by complementation, we identified AvrRvi6 as the fungal determinant that activates Rvi6-mediated immunity. Screening 122 V. inaequalis strains worldwide, we identified 20 distinct AvrRvi6 alleles, of which only five are not recognized by Rvi6. Evolution analysis demonstrated that the emergence of these virulent alleles predates the domestication of apple, thus revealing that wild Malus species constitute a reservoir of virulence. Using AlphaFold structural modeling, we showed that AvrRvi6 belongs to an expanded family that adopts a MAX effector fold, originally described for cytoplasmic effectors of the blast fungus Pyricularia oryzae. Transient expression in Nicotiana benthamiana demonstrated that AvrRvi6 triggers allele-specific apoplastic immunity and validated three different molecular mechanisms (mutation, partial deletion and transposon insertion in the promoter) that V. inaequalis employs to circumvent Rvi6 recognition. This study delivers the first characterization of a V. inaequalis avirulence factor, uncovers an unexpected apoplastic role for a MAX effector, and demonstrates how ancestral virulence diversity maintained in wild populations compromises resistance durability in apple.

microbiology↗

bioRxiv2024

Transcriptomic plasticity in hybrid schistosomes can contribute to their zoonotic potential

Hybrids between Schistosoma haematobium and S. bovis are linked to both human and animal infections, highlighting the complex interspecies interactions that contribute to the spread of schistosomiasis. Additionally, S. bovis can infect multiple ruminant hosts, facilitating cross- species transmission and increasing the risk of zoonotic outbreaks. In this study, we investigated transcriptomic plasticity as a potential mechanism enabling hybrid schistosomes to adapt to alternative definitive hosts. We focused on two contexts: 1) introgressed S. haematobium x S. bovis hybrids, which demonstrated higher virulence in sheep compared to parental S. bovis, and 2) S. bovis infecting different host species. Our analysis uncovered 366 differentially expressed genes (DEGs), representing 4% of the total protein-coding genes, between introgressed hybrids and parental S. bovis in sheep. We also identified transcriptomic changes in S. bovis across different mammalian hosts (hamster and sheep), with around 30% of the total genes differentially expressed, demonstrating that S. bovis parasites display a high transcriptomic plasticity, allowing them to infect different definitive hosts. Shared enriched biological processes during introgression and host change include nuclear-transcribed mRNA catabolic processes, inner mitochondrial membrane organization, microtubule-based movement, response to endoplasmic reticulum stress, and sensory perception. These findings suggest that transcriptomic plasticity in S. bovis and hybrid worms enhance their ability to adapt and infect diverse host species, potentially increasing their zoonotic potential. This raises concerns for schistosomiasis epidemiology, as this plasticity could expand the parasites transmission capacity and complicate control efforts.

evolutionary biology↗

bioRxiv2024

Genetic basis of resistance in hosts facing alternative infection strategies by a virulent bacterial pathogen

Having alternative infection routes is thought to help parasites circumvent host resistance, provided that these routes are associated with different host resistance loci. This study examines whether alternate infection routes of the parasite Pasteuria ramosa are linked to distinct resistance loci in its crustacean host, Daphnia magna. We focus on the P. ramosa isolate P15, which can attach and penetrate the host through either the hindgut or the foregut. Using a global panel of 174 D. magna genotypes supplemented with breeding experiments, we analyzed resistance patterns for each of these infection routes. Our findings confirm our hypothesis: in D. magna, hindgut attachment is determined by the D locus, while foregut attachment is controlled by a newly identified G locus. We established a gene model for the G locus that indicated Mendelian segregation and epistatic interaction with at least one other resistance locus for P. ramosa, the C locus. Using genomic Pool-sequencing data, we localized the G locus within a known Pasteuria Resistance Complex on chromosome 4 of D. magna, whereas the D locus is on chromosome 7. Two candidate genes for the G locus, belonging to the Glycosyltransferase gene family, were identified. Our study sheds new light on host-parasite coevolution and enhances our understanding of how parasites evolve infection strategies. Author summaryParasites continuously evolve strategies to overcome host resistance, including the use of alternative infection routes. However, this strategy is advantageous only if host resistance loci are specific to each entry point; otherwise, a single host gene could provide resistance to all infection routes. In this study, we tested this hypothesis using the freshwater crustacean Daphnia magna and a strain of the parasite Pasteuria ramosa that can infect its host via the esophagus (foregut) or the hindgut. By conducting a phenotypic assay of P. ramosa attachment on a global panel of D. magna genotypes, we demonstrate that foregut and hindgut infections are associated with independent genetic host resistance loci. Through a breeding experiment on a subset of D. magna genotypes, we were able to propose a gene model for the newly discovered G locus linked to foregut attachment, while the previously identified D locus is linked to hindgut attachment. We also discovered that the foregut infection route is influenced by an epistatic interaction between the G locus and another P. ramosa resistance locus, the C locus. Using genomic data, we confirmed that the G and D loci are not overlapping, with the G locus being part of the Pasteuria Resistance Complex on chromosome 4, whereas the D locus is on chromosome 7. Two potential genes involved in glycosylation processes were identified as candidates for the G locus. Overall, our study confirms a key postulate in the understanding of host-parasite co-evolution, highlighting the importance of infection strategies in host resistance.

evolutionary biology↗

bioRxiv2023

Schistosoma haematobium and Schistosoma bovis first generation hybrids undergo large gene expressions remodeling consistent with species compatibility

When two species hybridize, the two parental genomes are brought together and some alleles might interact for the first time. To the date, the extent of the transcriptomic changes in first hybrid generations, along with their functional outcome constitute an important knowledge gap especially in non-model organisms. Here we explored the molecular and functional outcomes of hybridization in first-generation hybrid between the blood fluke parasites S. haematobium and S. bovis. To this aim we fist assembled a hybrid reference transcriptome allowing us to measure gene expression in both parental species and hybrids to further described and quantified the profiles of gene expression encountered in hybrids. We identified large-scale gene expression remodeling since up to 55% of genes were differentially expressed in hybrids compared to at least one of the parental species. We further showed that intermediate level of expression in hybrids compared to parental species was the most prevalent expression profile (38% of genes) in agreement with S. haematobium x S. bovis high genomic compatibility and limited divergence. Also, among the differentially expressed genes of each of the identified profiles (intermediate, under-, over-expressed, or matching the expression of one of the parental species), only a few biological processes were found enriched without patterns being consistent through crosses and sexes. Our findings suggest that hybrid heterosis could be due to change in expression of a large portion of random genes which affect various biological processes. Author SummaryWhen two species manage to produce a viable offspring, due to different parental genetic material, new allelic interactions might arise. We do not know much about how genes are expressed in such hybrids compared to their parental species and especially for non-model species. Here we gene expressions in first generation hybrids of two blood flukes parasites Schistosoma haematobium and S. bovis. We quantified and categorized gene differentially expressed in first generation hybrids. We showed that more than half the genes of the hybrids were differentially expressed compared to at least one of their parental species, hence showing major gene expression remodeling occurring during hybridization. However, the most common hybrid expression pattern was intermediate level of expression compared to parental species and various but no specific biological processes were associated with hybrids differentially expressed genes. We hypothesized that because S. haematobium and S. bovis remain very compatible, when hybridizing many non-specific genes can have their expression level remodeled hence impacting the overall molecular machinery of the offspring while still sustaining highly operational hybrids.

evolutionary biology↗

bioRxiv2018

Intraspecific genetic and phenotypic diversity: parallel processes and correlated patterns?

Intraspecific diversity plays a key role for evolutionary and ecological dynamics. It is the raw material on which acts selection, it improves species and communities resilience to disturbance and it affects the way species modulate their biotic and abiotic environment. Understanding patterns and underlying determinants of genetic and phenotypic intraspecific diversity is therefore of critical importance for ecological, evolutionary and conservation sciences. Here, focusing on two freshwater fish species (Gobio occitaniae and Phoxinus phoxinus) sampled across a large river basin (the Garonne-Dordogne river basin, France), we used causal analyses to test for genetic-phenotypic intraspecific diversity correlations (GPIDCs) and unravel the processes underlying intraspecific diversity patterns. Genetic diversity was assessed using microsatellite markers and phenotypic diversity was assessed through geometric morphometrics. We found disparities in the distribution of genetic and phenotypic diversity in the two species, suggesting higher level of local adaptation in G. occitaniae, and our results revealed common and contrasted processes shaping diversity at the - and {beta}-level. At the -level, we found no GPIDC in both species despite common relations between isolation and genetic and phenotypic -diversity in G. occitaniae. At the {beta}-level, we found no GPIDC in P. phoxinus but we found a positive GPIDC in G. occitaniae. This correlation appeared to be caused by a direct impact of one facet of intraspecific diversity on the other, and we speculated that it could originate from positive assortative mating. Studying neutral genetic diversity and phenotypic diversity within an integrative framework appears as a valuable way of deciphering the complex and diverse impacts of neutral and adaptive processes on intraspecific diversity patterns.

evolutionary biology↗