Biology subjects

Ravel, S.

Publications and source records attributed to Ravel, S..

18 recordsLinked to original sources

bioRxiv2026

Population genetic structure and connectivity of Glossina palpalis gambiensis and G. morsitans submorsitans in Southwestern Senegal

In sub-Saharan Africa, human and animal health is threatened by African trypanosomoses. These diseases are caused by trypanosomes that are transmitted primarily by tsetse flies. Vector control remains one of the most effective strategies for reducing disease transmission, but requires a minimum level of knowledge of the population biology, ecology and dispersal patterns of the targeted vectors. In this respect, population genetic approaches using appropriate polymorphic genetic markers can provide valuable tools to inform and optimize control strategies. Senegal is currently engaged in a national tsetse control programme and has been identified as a study country within a European Union-funded research initiative, COMBAT (controlling and progressively minimizing the burden of animal trypanosomosis). Baseline entomological studies are currently underway in the Sine Saloum (Southern Senegal). This preliminary study aimed to characterize the population genetic structure and connectivity of tsetse fly species present in Southern Senegal, Glossina palpalis gambiensis and G. morsitans submorsitans, in order to assess their population sizes (geographically and demographically), population densities and dispersal capacities. The two species exhibited markedly contrasting population structures. The first, G. p. gambiensis, displayed an isolation by distance with rather dense subpopulations exchanging immigrants at short distances (1.6 km/generation) and continuously from Sine-Saloum to Casamance, in line with the apparent continuity of the mangrove network found along this coast. In contrast, G. m. submorsitans presented a relatively dense population over a 75 km wide area, fragmented into sparsely distributed, very dense and interconnected pockets. These findings indicate that G. p. gambiensis likely constitutes a large metapopulation comprising 3266 effective individuals on average (and up to 7765), whereas G. m. submorsitans appeared as a single and large population, scattered in small pockets that could be readily replenished by immigrants from distant areas in case of control. These results suggest that elimination is not a realistic option for any of these two populations. Alternatively, localized integrated pest management is likely to be the most effective approach for controlling the negative effects of these biting flies on domestic animals, by reducing trypanosome transmission. However, further entomological investigations and the use of more informative genetic markers are needed to obtain a more precise understanding of the epidemiological processes involved.

ecology↗

bioRxiv2026

MIRA: an open source and user-friendly software to automate counting and sizing of fungal spores

BackgroundThe quantification of fungal spores constitutes a fundamental metric in phytopathology, serving as the primary variable for inoculum standardization and being used as a proxy for disease severity. Historically, spore quantification has relied on manual hemocytometry, which remains the most precise counting process to date, where chambers such as the Malassez slide are used to count a subsample of the inoculum. However, this method applied manually is highly labor-intensive, time-consuming, and can be prone to operator-dependent variability. To overcome these limitations, we introduce MIRA (Microscopy Image Recognition & Analysis), a novel open-source software integrating You Only Look Once (YOLO) deep learning algorithms. Featuring a user-friendly graphical interface, MIRA is adaptable to multiple camera systems and supports advanced object detection models, including YOLOv11 and YOLOv26. ResultsWe demonstrate that MIRA can be used to accurately detect and count spores from several phytopathogenic fungi, automatically measure spore surface area, and to differentiate spores across different genera. In an exhaustive comparative analysis using Pyricularia oryzae spores as an example, MIRA was benchmarked against manual gold-standard counting slides (Malassez and Kova) and indirect spectrophotometric methods (SPARK). The P. oryzae model loaded via MIRA achieved a strong correlation (R = 0.96) with manual gold standards while reducing processing time by over 90% for high-concentration samples (10 spores/mL). Beyond this benchmark, we also successfully tested specific YOLO models designed to recognize macro- and microconidia of Fusarium oxysporum f. sp. cubense, a model for Pseudocercospora fijiensis, and a single multiclass model capable of identifying six different rice pathogenic fungi. We provide comprehensive tutorials for operating the software and training custom detection models for free using Roboflow and Google Colab. MIRA is available both as open-source Python code and as standalone executables for Windows and Linux. ConclusionsMIRA provides a rapid, accurate, and highly reproducible alternative to manual spore counting, effectively removing a major bottleneck in phytopathology workflows. By combining advanced YOLO-based deep learning with an accessible interface and comprehensive training resources, MIRA makes accessible automated image analysis for researchers without programming expertise. Moreover, MIRA drastically improves the efficiency of high-throughput disease phenotyping and can be adapted for a wide range of microscopic quantification tasks across various biological disciplines.

plant biology↗

bioRxiv2026

Population structure, genetic diversity and global migration of the banana Fusarium wilt pathogen, Fusarium oxysporum f. sp. cubense tropical race 4

O_LIThe current epidemic of banana Fusarium wilt is caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4). Foc TR4 originates in Asia and was first reported in the early 1990s, whereafter it was restricted to five Asian countries and the Northern Territory of Australia for two decades. Since 2013, the fungus was detected in the Middle East, the Indian subcontinent, Africa and Latin America. Its recent spread may be caused by the expansion of Cavendish banana production and the movement of contaminated planting materials. C_LIO_LIWhole genome sequences of 119 Foc TR4 isolates were compared based on single nucleotide polymorphisms (SNPs) to assess the population structure, genetic diversity and relation among isolates from 20 countries to reveal the evolutionary origin and likely migration. C_LIO_LIFoc TR4 is a monophyletic lineage divided into four clusters. Two of the clusters included isolates mostly from eastern Indonesia and seem to be ancestral with many rare alleles and high genetic diversity supporting this region as centre of origin. The remaining clusters were less diverse and associated with pandemic expansion. C_LIO_LIKnowledge on Foc TR4 emergence and dispersal can be used to inform more effective biosecurity and management practice. C_LI

evolutionary biology↗

bioRxiv2026

Population structure of the rice blast fungus Pyricularia oryzae in the context of elevated host heterogeneity

In a context where pathogen emergence threatens global food security, crop resistance to pathogens is crucial for preventing and controlling epidemics. Agrosystems with high intraspecific cultivated diversity are expected to better mitigate infectious diseases compared with homogeneous ones. However, the long-term impact of cultivated genotypic heterogeneity on pathogen populations is still under debate. The 1,300-year-old traditional agrosystem of the Yuanyang Terraces (YYT) in China exhibits an outstanding level of rice diversity. The rice blast fungus Pyricularia oryzae has been recorded in the area, making this area ideal for studying the impact of long term heterogeneous cultivation on plant-pathogen coevolution. In this study, we analysed 94 P. oryzae genomes from the YYT and compared them to 198 genomes representative of the worldwide diversity. We report elevated levels of genomic diversity of P. oryzae in the YYT. Whereas the worldwide diversity of this species is organized in four lineages, we detected seven lineages within the YYT, four of which are restricted to this area. The sampling dates of the YYT isolates (2009 to 2017) provided sufficient temporal signal to date nodes of the phylogenetic tree of isolates. Endemic lineages appeared to have arisen several centuries ago but later than the origin of the YYT themselves. We also detected recent introductions of worldwide lineages. Linkage disequilibrium analyses and in vitro cross experiments suggest that P. oryzae reproduces asexually in the YYT. These results suggest that long-term intraspecific crop diversity in the YYT has promoted the emergence and maintenance of a highly diverse, locally adapted pathogen population.

evolutionary biology↗

bioRxiv2025

Development of microsatellite markers with the SSR-seq method on Glossina palpalis gambiensis, and G. p. palpalis, and analysis of corresponding field samples from three sleeping sickness foci: Boffa, Dubreka (Guinea), and Bonon (Cote d'Ivoire).

Tsetse flies are strictly found is sub-Saharan Africa where they are responsible for the transmission and maintenance of African trypanosomiases in humans (HAT) and animals (AAT). Vector control has been recognized as an essential tool to fight against these diseases. Nevertheless, it requires the best possible knowledge of the biology of the targeted population. Population genetics tools can prove very useful to obtain such information but require the use of polymorphic and reliable genetic markers. In this paper we present the development of microsatellite markers using a new high-throughput sequencing based technology (SSRseq). We applied it on two species of tsetse flies from three HAT foci and obtained more accurate results as compared to microsatellite loci developed with classic methods. We could indeed use 9 to 14 SSRseq loci without the several problems generally met with classic microsatellites, as all were located in autosomes, without short allele dominance or stuttering and very few null alleles. SSRseq loci appeared much more polymorphic in tsetse flies as compared to other species (fungi, trees, bees, or fishes), which suggested much higher effective population sizes, much higher mutation rates of the genome or both, suggesting high capacities for evolutionary adaptation. With the 9-14 loci kept, we confirmed the propensity of these flies to move almost freely in the whole zones investigated, and also highlighted the possible evolutionary response of one of the unkept loci regarding vector control devices used in these HAT foci, which will require further studies. We suggest for further population structure studies to use only loci with less than 1% missing data, which proved being a good and fast selection strategy to get the most reliable results.

genomics↗

bioRxiv2025

GraTools, an user-friendly tool for exploring and manipulating pangenome variation graphs

BackgroundPangenome variation graphs (PVGs), which represent genomic diversity through multiple genomes alignment, are powerful tools for studying genomic variations in populations. However, current tools often lack integration, efficiency, or require format conversions, to use them, hindering their usability. ResultsHere, we introduce GraTools, a member of the GraSuite [1], and a fast and user-friendly command-line tool for manipulating PVGs using the original GFA file. After a one-time graph import, GraTools enables rapid subgraph extraction, FASTA sequence retrieval, and comprehensive analyses, including core/dispensable genome ratio calculation or group-specific segment identification. The import step results in conversion in standard data formats (BAM/BED), enabling the reuse of well-optimized existing tools, allowing an efficient storage and the querying of the PVGs large complex data structures. Scalability is ensured by a modular architecture supporting parallel processing and asynchronous I/O operations. GraTools supports coordinates defined on both the primary reference as well as from alternative genomes within the graph without re-import, and its outputs can be easily visualized or manipulated using external tools. Using an Asian rice pangenome graph (13 accessions), we demonstrate its ability to easily extract subgraphs, compute depth statistics, and identify subspecies-specific segments. An intuitive command-line interface, a real-time execution feedback and a detailed logging system make this tool suitable for a wide range of applications, from population genetics to breeding and genomic medicine, for both biologists and bioinformaticians. ConclusionsThrough its unified graph manipulation interface, GraTools offers an interesting alternative to the few existing tools for manipulating PVGs, facilitating rapid, efficient and flexible downstream analyses. It is available as an open-source tool (GNU GPLv3), with its documentation available at https://gratools.readthedocs.io.

bioinformatics↗

bioRxiv2025

Unravelling genetic differentiation between Glossina brevipalpis populations from two distant National Parks in Mozambique

African trypanosomosis (AT), caused by protozoan parasites of the genus Trypanosoma, has plagued the African continent for centuries, affecting both humans and animals. Vector control represents an efficient way to reduce the burden of AT. In Mozambique, control campaigns reshaped tsetse fly distribution to what it is today, with Glossina brevipalpis and G. austeni as the dominant species in the South. Additionally, G. brevipalpis can be found in two National parks, Gorongosa National Park in the Centre and Maputo National Park in the South, with an 840 km wide tsetse-free zone between them. In order to improve our knowledge of the genetic diversity and gene flow of these populations and their probable isolation, we undertook a population genetics study with 11 microsatellite loci. We found that these two zones behave as isolated subpopulations, only exchanging a few individuals per year. To explain this finding, we suggest the existence of undocumented pocket populations between the two parks, or, in the absence of these, the accidental translocation of tsetse flies during human-driven animal transportation. We concluded that such undocumented means of dispersal should be explored further in studies investigating Glossina populations, to allow for the design of more efficient control strategies.

evolutionary biology↗

bioRxiv2023

Trypanosoma brucei gambiense group 2 experimental in vivo life cycle: from procyclic to bloodstream form.

Trypanosoma brucei gambiense (Tbg) group 2 is a subgroup of trypanosomes able to infect humans in West and Central Africa. Unlike other agents causing sleeping sickness such as Tbg group 1 and Trypanosoma brucei rhodesiense, Tbg2 lacks the typical molecular markers associated with resistance to human serum. Only thirty-six strains of Tbg2 have been documented, and therefore, very limited research has been conducted despite its zoonotic nature. Some of these strains are only available in their procyclic form which hinders human serum resistance assays and mechanistic studies. Furthermore, the understanding of Tbg2s potential to infect tsetse flies and mammalian hosts is limited. In this study, 165 Glossina palpalis gambiensis flies were experimentally infected with procyclic Tbg2 parasites. 35 days post-infection, 43 flies out of the 80 still alive flies were found Tbg2 PCR-positive in the saliva. These flies were able to infect 3 out of the 4 mice used for blood-feeding. Dissection revealed that only six flies really carried mature infections in their midguts and salivary glands. Importantly, a single fly with a mature infection was sufficient to infect a mammalian host. This Tbg2 transmission success confirms that Tbg2 strains can establish in tsetse flies and infect mammalian hosts. The study describes an effective in vivo protocol for transforming Tbg2 from procyclic to bloodstream form, reproducing the complete Tbg2 cycle from G. p. gambiensis to mice. These findings provide valuable insights into Tbg2s host infectivity, and will facilitate further research on mechanisms of human serum resistance.

microbiology↗

bioRxiv2023

Population genetics of Glossina palpalis gambiensis in the sleeping sickness focus of Boffa (Guinea) before and after eight years of vector control: no effect of control despite a significant decrease of human exposure to the disease

Human African trypanosomosis (HAT), also known as sleeping sickness, is still a major concern in endemic countries. Its cyclical vector are biting insects of the genus Glossina or tsetse flies. In Guinea, the mangrove ecosystem contains the main HAT foci of Western Africa. There, the cyclical vector is Glossina palpalis gambiensis. A still ongoing vector control campaign (VCC) started in 2011 in the focus of Boffa, using tiny targets, with a 79% tsetse density reduction in 2016 and significant impact on the prevalence of the disease (from 0.3% in 2011 to 0.11% in 2013, 0.0352% in 2016 and 0.0097% in 2019). To assess the sustainability of these results, we have studied the impact of this VCC on the population biology of G. p. gambiensis in Boffa. We used the genotyping at 11 microsatellite markers and population genetic tools of tsetse flies from different sites and at different dates before and after the beginning of the VCC. In variance with a significant impact of VCC on the apparent densities of flies captured in the traps deployed, the global population of G. p. gambiensis displayed no variation of the sex-ratio, no genetic signature of control, and behaved as a very large population occupying the entire zone. This implies that targets deployment efficiently protected the human populations locally, but did not impact tsetse flies where targets cannot be deployed and where the main tsetse population exploits available resources. We thus recommend the pursuit of vector control measures with the same strategy, through the joint effect of VCC and medical surveys and treatments, in order to protect human populations from HAT infections until the disease can be considered as entirely eradicated from the focus.

evolutionary biology↗

bioRxiv2023

Adaptive evolution in virulence effectors of the rice blast fungus Pyricularia oryzae

Plant pathogens secrete proteins called effectors that target host cellular processes to promote disease. Recently, structural genomics has identified several families of fungal effectors that share a similar three-dimensional structure despite remarkably variable amino-acid sequences and surface properties. To explore the selective forces that underlie the sequence variability of structurally-analogous effectors, we focused on MAX effectors, a structural family of effectors that are major determinants of virulence in the rice blast fungus Pyricularia oryzae. Using structure-informed gene annotation, we identified 58 to 78 MAX effector genes per genome in a set of 120 isolates representing seven host-associated lineages. The expression of MAX effector genes was primarily restricted to the early biotrophic phase of infection and strongly influenced by the host plant. Pangenome analyses of MAX effectors demonstrated extensive presence/absence polymorphism and identified gene loss events possibly involved in host range adaptation. However, gene knock-in experiments did not reveal a strong effect on virulence phenotypes suggesting that other evolutionary mechanisms are the main drivers of MAX effector losses. MAX effectors displayed high levels of standing variation and high rates of non-synonymous substitutions, pointing to widespread positive selection shaping the molecular diversity of MAX effectors. The combination of these analyses with structural data revealed that positive selection acts mostly on residues located in particular structural elements and at specific positions. By providing a comprehensive catalog of amino acid polymorphism, and by identifying the structural determinants of the sequence diversity, our work will inform future studies aimed at elucidating the function and mode of action of MAX effectors. AUTHOR SUMMARYFungal plant pathogens use small secreted proteins, called effectors, to manipulate to their own advantage their hosts physiology and immunity. The evolution of these effectors, whether spontaneously or in response to human actions, can lead to epidemics or the emergence of new diseases. It is therefore crucial to understand the mechanisms underlying this evolution. In this article, we report on the evolution of effectors in one of the prime experimental model systems of plant pathology, Pyricularia oryzae, the fungus causing blast diseases in rice, wheat, and other cereals or grasses. We further characterize in this fungus a particular class of effectors, called MAX effectors, using structural models based on experimental protein structures of effectors. We show that this class of effector is produced by the pathogen during the early stages of infection, when plant cells are still alive. By comparing the gene content of isolates infecting different plant species, we show that the MAX effector arsenal is highly variable from one isolate to another. Finally, using the inferential framework of population genetics, we demonstrate that MAX effectors exhibit very high genetic variability and that this results from the action of natural selection.

evolutionary biology↗

bioRxiv2022

Extensive immune receptor repertoire diversity in disease-resistant rice landraces

Plants have powerful defence mechanisms, and extensive immune receptor repertoires, yet crop monocultures are prone to epidemic diseases. Rice is susceptible to many diseases, such as rice blast caused by Magnaporthe oryzae. Varietal resistance of rice to blast relies on intracellular nucleotide binding, leucine-rich repeat (NLR) receptors that recognize specific pathogen molecules and trigger immune responses. In the Yuanyang terraces in south-west China, rice landraces rarely show severe losses to disease whereas commercial inbred lines show pronounced field susceptibility. Here, we investigate within-landrace NLR sequence diversity of nine rice landraces and eleven modern varieties of indica, japonica and aus using complexity reduction techniques. We find that NLRs display high sequence diversity in landraces, consistent with balancing selection, and that balancing selection at NLRs is more pervasive in landraces than modern varieties. Notably, modern varieties lack many ancient NLR haplotypes that are retained in some landraces. Our study emphasises the value of standing genetic variation that is maintained in farmer landraces as resource to make modern crops and agroecosystems less prone to disease.

evolutionary biology↗

bioRxiv2021

COEVOLUTION WITH SPATIALLY STRUCTURED RICE LANDRACES MAINTAINS MULTIPLE GENERALIST LINEAGES IN THE RICE BLAST PATHOGEN

Traditional agrosystems, where humans, crops and microbes have coevolved over long periods, can serve as models to understand the eco-evolutionary determinants of disease dynamics and help the engineering of durably resistant agrosystems. Here, we investigated the genetic and phenotypic relationship between rice (Oryza sativa) landraces and their rice blast pathogen (Magnaporthe oryzae) in the traditional Yuanyang terraces of flooded rice paddies in China, where rice landraces have been grown and bred over centuries without significant disease outbreaks. Analyses of genetic subdivision revealed that indica rice plants clustered according to landrace names. Three new diverse lineages of rice blast specific to the Yuanyang terraces coexisted with lineages previously detected at the worldwide scale. Population subdivision in the pathogen population did not mirror pattern of population subdivision in the host. Measuring the pathogenicity of rice blast isolates on landraces revealed generalist life histories. Our results suggest that the implementation of disease control strategies based on the emergence or maintenance of a generalist lifestyle in pathogens may sustainably reduce the burden of disease in crops.

evolutionary biology↗

bioRxiv2021

CulebrONT: a streamlined long reads multi-assembler pipeline for prokaryotic and eukaryotic genomes

Using long reads provides higher contiguity and better genome assemblies. However, producing such high quality sequences from raw reads requires to chain a growing set of tools, and determining the best workflow is a complex task. To tackle this challenge, we developed CulebrONT, an open-source, scalable, modular and traceable Snakemake pipeline for assembling long reads data. CulebrONT enables to perform tests on multiple samples and multiple long reads assemblers in parallel, and can optionally perform, downstream circularization and polishing. It further provides a range of assembly quality metrics summarized in a final user-friendly report. CulebrONT alleviates the difficulties of assembly pipelines development, and allow users to identify the best assembly options.

bioinformatics↗

bioRxiv2021

Intrinsic Timescales Across the Basal Ganglia

Recent studies have shown that neuronal stability over time can be estimated by the structure of the spike-count autocorrelation of neuronal populations. This estimation, called the intrinsic timescale, has been computed for several cortical areas and can be used to propose a cortical hierarchy reflecting a scale of temporal receptive windows between areas. In this study, we performed an autocorrelation analysis on neuronal populations of three basal ganglia (BG) nuclei, including the striatum and the subthalamic nucleus (STN), the input structures of the BG, and the external globus pallidus (GPe). The analysis was performed during the baseline period of a motivational visuomotor task in which monkeys had to apply different amounts of force to receive a different amount of reward. We found that the striatum and the STN have longer intrinsic timescales than the GPe. Moreover, our results allow for the placement of these subcortical structures within the already-defined scale of cortical temporal receptive windows. Estimates of intrinsic timescales are important in adding further constraints in the development of computational models of the complex dynamics among these nuclei and throughout cortico-BG-thalamo-cortical loops.

neuroscience↗

bioRxiv2020

Ecological differentiation and incipient speciation in the fungal pathogen causing rice blast

Many invasive fungal species coexist as multiple lineages on the same host, but the factors underlying the origin and maintenance of population structure remain largely unknown. Here, we analyzed genetic and phenotypic diversity in isolates of the rice blast fungus (Pyricularia oryzae) covering a broad geographical range. We showed that the four lineages of P. oryzae were found in areas with different prevailing environmental conditions and types of rice grown, indicating niche separation. Pathogenicity tests revealed that specialization to rice subspecies contributed to niche separation between lineages, and differences in repertoires of putative virulence effectors were consistent with differences in host range. Experimental crosses revealed that female sterility and early post-mating genetic incompatibilities acted as strong barriers to gene flow between these lineages. Our results demonstrate that the spread of a pathogen across heterogeneous habitats and divergent populations of a crop species can lead to niche separation and reproductive isolation between distinct invasive lineages.

evolutionary biology↗

bioRxiv2018

TOGGLe, a flexible framework for easily building complex workflows and performing robust large-scale NGS analyses

The advent of NGS has intensified the need for robust pipelines to perform high-performance automated analyses. The required softwares depend on the sequencing method used to produce raw data (e.g. Whole genome sequencing, Genotyping By Sequencing, RNASeq) as well as the kind of analyses to carry on (GWAS, population structure, differential expression). These tools have to be generic and scalable, and should meet the biologists needs.\n\nHere, we present the new version of TOGGLe (Toolbox for Generic NGS Analyses), a simple and highly flexible framework to easily and quickly generate pipelines for large-scale second-and third-generation sequencing analyses, including multi-threading support. TOGGLe comprises a workflow manager designed to be as effortless as possible to use for biologists, so the focus can remain on the analyses. Embedded pipelines are easily customizable and supported analyses are reproducible and shareable. TOGGLe is designed as a generic, adaptable and fast evolutive solution, and has been tested and used in large-scale projects with numerous samples and organisms. It is freely available at http://toggle.southgreen.fr/ under the GNU GPLv3/CeCill-C licenses) and can be deployed onto HPC clusters as well as on local machines.

bioinformatics↗

bioRxiv2017

Coexistence of multiple endemic and pandemic lineages of the rice blast pathogen

The rice blast fungus Magnaporthe oryzae (syn. Pyricularia oryzae) is both a threat to global food security and a model for plant pathology. Molecular pathologists need an accurate understanding of the origins and line of descent of M. oryzae populations, to identify the genetic and functional bases of pathogen adaptation, and to guide the development of more effective control strategies. We used a whole-genome sequence analysis of samples from different times and places to infer details about the genetic makeup of M. oryzae from a global collection of isolates. Analyses of population structure identified six lineages within M. oryzae, including two pandemic on japonica and indica rice, respectively, and four lineages with more restricted distributions. Tip-dating calibration indicated that M. oryzae lineages separated about a millenium ago, long after the initial domestication of rice. The major lineage endemic to continental Southeast Asia displayed signatures of sexual recombination and evidence of DNA acquisition from multiple lineages. Tests for weak natural selection revealed that the pandemic spread of clonal lineages entailed an evolutionary cost, in terms of the accumulation of deleterious mutations. Our findings reveal the coexistence of multiple endemic and pandemic lineages with contrasting population and genetic characteristics within a widely distributed pathogen.\n\nImportanceThe rice blast fungus Magnaporthe oryzae (syn. Pyricularia oryzae) is a textbook example of a rapidly adapting pathogen, and is responsible for one of the most damaging diseases of rice. Improvements in our understanding of Magnaporthe oryzae diversity and evolution are required, to guide the development of more effective control strategies. We used genome sequencing data for samples from around the world to infer the evolutionary history of M. oryzae. We found that M. oryzae diversified about a thousand years ago ago, separating into six main lineages: two pandemic on japonica and indica rice, respectively, and four with more restricted distributions. We also found that a lineage endemic to continental Southeast Asia displayed signatures of sexual recombination and the acquisition of genetic material from multiple lineages. This work provides a population-level genomic framework for defining molecular markers for the control of rice blast and investigations of the molecular basis of differences in pathogenicity between M. oryzae lineages.

evolutionary biology↗

bioRxiv2017

Gene flow between divergent cereal- and grass-specific lineages of the rice blast fungus Magnaporthe oryzae

Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity, and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multi-host pathogen that infects multiple grasses and cereals, is responsible for the most damaging rice disease (rice blast), and of growing concern due to the recent introduction of wheat blast to Bangladesh from South America. However, the genetic structure and evolutionary history of M. oryzae, including the possible existence of cryptic phylogenetic species, remain poorly defined. Here, we use whole-genome sequence information for 76 M. oryzae isolates sampled from 12 grass and cereal genera to infer the population structure of M. oryzae, and to reassess the species status of wheat-infecting populations of the fungus. Species recognition based on genealogical concordance, using published data or extracting previously-used loci from genome assemblies, failed to confirm a prior assignment of wheat blast isolates to a new species (Pyricularia graminis tritici). Inference of population subdivisions revealed multiple divergent lineages within M. oryzae, each preferentially associated with one host genus, suggesting incipient speciation following host shift or host range expansion. Analyses of gene flow, taking into account the possibility of incomplete lineage sorting, revealed that genetic exchanges have contributed to the makeup of multiple lineages within M. oryzae. These findings provide greater understanding of the eco-evolutionary factors that underlie the diversification of M. oryzae and highlight the practicality of genomic data for epidemiological surveillance in this important multi-host pathogen.\n\nImportanceInfection of novel hosts is a major route for disease emergence by pathogenic micro-organisms. Understanding the evolutionary history of multi-host pathogens is therefore important to better predict the likely spread and emergence of new diseases. Magnaporthe oryzae is a multi-host fungus that causes serious cereal diseases, including the devastating rice blast disease, and wheat blast, a cause of growing concern due to its recent spread from South America to Asia. Using whole genome analysis of 76 fungal strains from different hosts, we have documented the divergence of M. oryzae into numerous lineages, each infecting a limited number of host species. Our analyses provide evidence that inter-lineage gene flow has contributed to the genetic makeup of multiple M. oryzae lineages within the same species. Plant health surveillance is therefore warranted to safeguard against disease emergence in regions where multiple lineages of the fungus are in contact with one another.

microbiology↗