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Adaptive evolution in virulence effectors of the rice blast fungus Pyricularia oryzae
No full textABSTRACT 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 SUMMARY Fungal plant pathogens use small secreted proteins, called effectors, to manipulate to their own advantage their host’s 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
L’intensification écologique et la déforestation au Brésil
No full textInternational audienceCet article explore les fondements et les contradictions d’un discours de réconciliation entre production agro-industrielle et conservation au Brésil. A partir d’une révision bibliographique et d’une étude de cas dans l’état de Roraima, j’analyse le décalage entre, d’un côté, le discours porté par des acteurs de l’agrobusiness sur le déboisement et, de l’autre, la réalité des pratiques agricoles et territoriales des producteurs. L'intensification écologique constitue un discours de solution technologique à la déforestation, peu remis en question dans les différentes sphères académiques et politiques, malgré l'absence de validation théorique et empirique. Pour l'agrobusiness, maintenir le mythe de l'intensification écologique est crucial pour cacher son rôle dans l'ouverture de nouveaux fronts de déforestation à travers l'Amérique du Sud
Identification and quantification of transposable element transcripts using Long-Read RNA-seq in Drosophila germline tissues
No full textInternational audienceTransposable elements (TEs) are repeated DNA sequences potentially able to move throughout the genome. In addition to their inherent mutagenic effects, TEs can disrupt nearby genes by donating their intrinsic regulatory sequences, for instance, promoting the ectopic expression of a cellular gene. TE transcription is therefore not only necessary for TE transposition per se but can also be associated with TE-gene fusion transcripts, and in some cases, be the product of pervasive transcription. Hence, correctly determining the transcription state of a TE copy is essential to apprehend the impact of the TE in the host genome. Methods to identify and quantify TE transcription have mostly relied on short RNA-seq reads to estimate TE expression at the family level while using specific algorithms to discriminate copy-specific transcription. However, assigning short reads to their correct genomic location, and genomic feature is not trivial. Here we retrieved full-length cDNA (TeloPrime, Lexogen) of Drosophila melanogaster gonads and sequenced them using Oxford Nanopore Technologies. We show that long-read RNA-seq can be used to identify and quantify transcribed TEs at the copy level. In particular, TE insertions overlapping annotated genes are better estimated using long reads than short reads. Nevertheless, long TE transcripts (> 4.5 kb) are not well captured. Most expressed TE insertions correspond to copies that have lost their ability to transpose, and within a family, only a few copies are indeed expressed. Long-read sequencing also allowed the identification of spliced transcripts for around 107 TE copies. Overall, this first comparison of TEs between testes and ovaries uncovers differences in their transcriptional landscape, at the subclass and insertion level
Impact of temperature and season on ant foraging activity of two invasive species in a Mediterranean urban area
No full textInternational audience1. Invasive species often have harmful effects on human activities and biodiversity. The Tapinoma nigerrimum complex includes three species that exhibit invasive traits and the ability to form supercolonies, including Tapinoma magnum and Tapinoma darioi. While these species are native to the Mediterranean basin, they have recently been reported as invasive in more northern regions of Europe. However, T. magnum and T. darioi show different invasion patterns in Europe, suggesting differences in thermal preferences between these species. We aimed to determine whether there was any difference in activity pattern depending on temperature or season between the two Tapinoma species and between Tapinoma and co-occurring native Mediterranean ants.2. We measured ambient temperature and ant foraging activity around the nest entrances of T. darioi and T. magnum in urbanised sites around Montpellier, southern France, over almost 1 year.3. We did not detect differences in activity between the two species according to temperature, but T. magnum was more active than T. darioi in winter. Compared to the co-occurring native species, the two Tapinoma species were more active at low temperatures and earlier in the year.4. These results suggest that the difference in invasion success between T. magnum and T. darioi may not be explained by temperature preference. The difference in activity between native Mediterranean species and invasive Tapinoma suggests a coexistence through niche partitioning. In addition, our results suggest that control measures against invasive Tapinoma species would be more effective if applied at the end of winter.1. Les espèces envahissantes ont souvent des effets néfastes sur les activités humaines et la biodiversité. Le complexe Tapinoma nigerrimum comprend trois espèces qui présentent des caractéristiques envahissantes et la capacité de former des supercolonies, notamment Tapinoma magnum et Tapinoma darioi. Bien que ces espèces soient originaires du bassin méditerranéen, elles ont récemment été reportées comme envahissantes dans des régions plus septentrionales d'Europe. Cependant, T. magnum et T. darioi présentent des schémas d'invasion différents en Europe, ce qui suggère des différences de préférences thermiques entre ces espèces. Nous avons donc cherché à déterminer s'il y avait des différences de modèles d'activité selon la température ou la saison entre les deux espèces de Tapinoma et entre les Tapinoma et les fourmis méditerranéennes natives concurrentes. 2. Nous avons mesuré la température et l'activité de recherche de nourriture des fourmis autour des entrées des nids de T. darioi et de T. magnum dans des sites urbanisés autour de Montpellier, dans le sud de la France, pendant près d'un an. 3. Nous n'avons pas détecté de différence d'activité entre les deux espèces en fonction de la température, mais T. magnum était plus active que T. darioi en hiver. Par rapport aux espèces indigènes concurrentes, les Tapinoma sont plus actives à basse température et plus tôt dans l'année. 4. Ces résultats suggèrent que la différence de succès d'invasion entre T. magnum et T. darioi peut ne pas être expliquée par des préférences thermiques. La différence d'activité entre les espèces méditerranéennes indigènes et les Tapinoma suggère une coexistence à travers le partage des niches. De plus, nos résultats suggèrent que les mesures de lutte contre les espèces envahissantes de Tapinoma seraient plus efficaces si elles étaient appliquées à la fin de l'hiver
Climate and management changes drove more stress-tolerant and less competitive plant communities in 40 years
No full textSpontaneous plant communities have undergone considerable constraints due to human-mediated changes. Understanding how plant communities are shifting in response to land management and climate changes is necessary to predict future ecosystem functioning and improve the resilience of managed ecosystems, such as agroecosystems. Using Mediterranean weed communities as models of managed plant communities in a climate change hotspot, we quantified to which extent they have shifted from the 1980s to the 2020s in response to climate and management changes in vineyards. In four decades, the annual range of temperatures ( i.e. the difference between the warmest month’s and the coldest month’s mean temperatures) increased by 1.2°C and the summer temperatures by 2°C. Weed management diversified over time with the adoption of mowing that replaced the chemical weeding of inter-rows. Current weed communities were 41% more abundant, 24% more diverse and with a less even distribution of abundance across species than the 1980s communities at the vineyard level. Modern communities were composed of more annual species (57% of annual species in the 1980s versus 80% in the 2020s) with lower lateral spreadability and seed mass and were composed of fewer C4 species. They had higher community-weighted specific leaf area, higher leaf dry matter content and lower leaf area than 1980s weed communities. At the community level, the onset of flowering was earlier and the duration of flowering was longer in the 2020s. Climate change induced more stress-tolerant communities in the 2020s while the diversification of weed management practices over time filtered less competitive communities. This study shows that plant communities are adapting to climate change and that land management is a strong lever for action to model more diverse and functional plant communities in the future
Primer pairs, PCR conditions, and peptide nucleic acid clamps affect fungal diversity assessment from plant root tissues
No full textRaw sequence data for this project have been submitted to NCBI’s SRA archive under accession no. SUB12918264.International audienceHigh-throughput sequencing has become a prominent tool to assess plant-associated microbial diversity. Still, some technical challenges remain in characterising these communities, notably due to plant and fungal DNA co-amplification. Fungal-specific primers, Peptide Nucleic Acid (PNA) clamps, or adjusting PCR conditions are approaches to limit plant DNA contamination. However, a systematic comparison of these factors and their interactions, which could limit plant DNA contamination in the study of plant mycobiota, is still lacking. Here, three primers targeting the ITS2 region were evaluated alone or in combination with PNA clamps both on nettle (Urtica dioica) root DNA and a mock community. PNA clamps did not improve the richness or diversity of the fungal communities but increased the number of fungal reads. Among the tested factors, the most significant was the primer pair. Specifically, the 5.8S-Fun/ITS4-Fun pair exhibited a higher OTU richness but fewer fungal reads. Our study demonstrates that the choice of primers is critical for limiting plant and fungal DNA co-amplification. PNA clamps increase the number of fungal reads when ITS2 is targeted but do not result in higher fungal diversity recovery at high sequencing depth. At lower read depths, PNA clamps might enhance microbial diversity quantification for primer pairs lacking fungal specificity
Allelic compatibility in plant immune receptors facilitates engineering of new effector recognition specificities
No full textInternational audienceEngineering the plant immune system offers genetic solutions to mitigate crop diseases caused by diverse agriculturally significant pathogens and pests. Modification of intracellular plant immune receptors of the nucleotide-binding leucine-rich repeat (NLR) receptor superfamily for expanded recognition of pathogen virulence proteins (effectors) is a promising approach for engineering disease resistance. However, engineering can cause NLR autoactivation, resulting in constitutive defense responses that are deleterious to the plant. This may be due to plant NLRs associating in highly complex signaling networks that coevolve together, and changes through breeding or genetic modification can generate incompatible combinations, resulting in autoimmune phenotypes. The sensor and helper NLRs of the rice (Oryza sativa) NLR pair Pik have coevolved, and mismatching between noncoevolved alleles triggers constitutive activation and cell death. This limits the extent to which protein modifications can be used to engineer pathogen recognition and enhance disease resistance mediated by these NLRs. Here, we dissected incompatibility determinants in the Pik pair in Nicotiana benthamiana and found that heavy metal-associated (HMA) domains integrated in Pik-1 not only evolved to bind pathogen effectors but also likely coevolved with other NLR domains to maintain immune homeostasis. This explains why changes in integrated domains can lead to autoactivation. We then used this knowledge to facilitate engineering of new effector recognition specificities, overcoming initial autoimmune penalties. We show that by mismatching alleles of the rice sensor and helper NLRs Pik-1 and Pik-2, we can enable the integration of synthetic domains with novel and enhanced recognition specificities. Taken together, our results reveal a strategy for engineering NLRs, which has the potential to allow an expanded set of integrations and therefore new disease resistance specificities in plants.</div
Unoccupied aerial system (UAS) Structure-from-Motion canopy fuel parameters: Multisite area-based modelling across forests in California, USA
No full textInternational audienceThere is a pressing need for well-informed management to reduce wildfire hazard and restore fire's beneficial ecological role in the Mediterranean- and temperate-climate forests of California, USA. These efforts rely upon the accessibility of high spatial and temporal resolution data on biomass and canopy fuel parameters such as canopy base height (CBH), mean canopy height, canopy bulk density (CBD), canopy cover, and leaf area index (LAI). Remote sensing using unoccupied aerial system Structure-from-Motion (UAS-SfM) presents a promising technology for this application due to its accessibility, relatively low cost, and possibility for high temporal cadence. However, to date, this method has not been studied in the complex mosaic of forest types found across California. In this study we examined the capacity of structural and multispectral information obtained from UAS-SfM, in conjunction with machine learning methods, to model aboveground biomass and forest canopy fuel structural parameters using an area-based approach across multiple sites representing a diversity of forest types in California. Based on correlations with field measurements, fuel parameters separated into vertical (biomass, CBH, and mean height) and horizontal (LAI, CBD, canopy cover) groups. UAS-SfM random forest models performed well for modelling the vertical structure canopy fuels parameters (R2 0.69–0.75). These models exhibited strong performance in comparison to ALS, as well as when transferred to a novel site. Vertical structure predictors were prominent in these models, and did not improve with the addition of spectral predictors. UAS-SfM random forest models of horizontal structure parameters mainly used raster-based spectral indices (primarily NDVI) and had relatively low performance (R2 0.49–0.59). In addition, these models underperformed ALS and had poor performance when applied to a novel site. When applied to a region with widespread UAS-SfM coverage, models from both groups successfully produced contiguous maps that could be used for modelling fire behavior or in management decision making and monitoring. These findings indicate that UAS-SfM, without the need for multispectral sensors, is well suited for mapping area-based vertical-structure canopy parameters across diverse landscapes supporting a wide range of forest types. In contrast, the identification of spectral mean variables for modelling horizontal structure canopy fuels suggests the potential of multi- or hyperspectral sensors or high-resolution satellite imagery for meeting management information needs
L’hybridation de la gouvernance des structures d’accompagnement pour construire des territoires entreprenants
No full textNational audienceIn this chapter, we consider hybrid governance of public incubators as a means of co-constructing an entrepreneurial territory.Based on a longitudinal study of 57 incubators in the Occitanie region, we show that within each structure there is a wide diversity of actors involved in the various stages of incubation. The incubator’s director is responsible for building a relevant governance that involves stakeholders whose expertise may be critical to the entrepreneurial project. As a result, incubator governance appears to be not only a hybrid process, but also a flexible governance with varying borders, implemented to meet the specific needs of project leaders and to create a favorable environment for business creation.L’hybridation de la gouvernance des structures d’accompagnement est considérée, dans ce chapitre, comme un moyen de co-construction d’un territoire entreprenant. Sur la base d’une étude longitudinale auprès de 57 incubateurs de la région Occitanie, nous montrons qu’au sein de chaque structure, il existe une grande diversité d’acteurs impliqués dans les différentes étapes de l’incubation. Le directeur de la structure est en charge de la construction d’une gouvernance pertinente qui implique des parties prenantes dont l’expertise peut être critique pour le projet entrepreneurial. En conséquence, la gouvernance de l’incubateur apparaît non seulement comme un processus hybride mais également flexible et à géométrie variable mis en œuvre pour répondre aux besoins spécifiques des porteurs de projet pour créer un environnement favorable à la création d’entreprise
Predictive modelling on Spatial–temporal Land Use and Land Cover changes at the Casablanca-Settat Region in Morocco
No full textInternational audienceUrban Population growth coupled with human activities are the main drivers inducing land use and land cover changes (LU/LCC), which impact earth’s landscapes dynamics. In the era of global challenges, a comprehensive modelling of past and future prediction of LU/LCC is therefore essential. In this regard, the current study aims to model LU/LCC and predict its changes by 2030, 2050 and 2100. Moreover, determine the main driver of these changes, and assess the impact of urbanization on natural ecosystems. For doing so, a three-decade times series (1992–2020) data have been used, including LU/LC, environmental, societal, and auxiliary data to conduct a statistical analysis and modelling using hybrid Multi-Layer-Perceptron Markov-Chain model (MLP-MC). The analyses results showed that urbanization has significantly increased between 1992 and 2020, mainly in the outskirts of the Casablanca metropolis, where economic dynamic, population growth, and territorial infrastructure takes place. This increase was at the expense of barren and agricultural land. Concerning the future projection, the MLP-MC model showed satisfactory results with an overall accuracy (OA) and Cohen’s Kappa greater than 0.98 Revealing that the model has batter reliability to predict LU/LC maps that are identical to observed ones. Consequently, the Future projection indicates that urban areas will persistently sprawl, especially in satellite cities of the economic capital which adversely affect biodiversity, local climate, water, and public health. These findings remain so promising that can guide decision-making and stakeholders to improve sustainable territorial and urban development