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Antibiotic resistance is an increasing threat to human health. A direct link has been established between antimicrobial self-resistance determinants of antibiotic producers, environmental bacteria, and clinical pathogens. Natural odilorhabdins (ODLs) constitute a new family of 10-mer linear cationic peptide antibiotics inhibiting bacterial translation by binding to the 30S subunit of the ribosome. These bioactive secondary metabolites are produced by entomopathogenic bacterial symbiont Xenorhabdus (Morganellaceae), vectored by the soil-dwelling nematodes. ODL-producing Xenorhabdus nematophila symbionts have mechanisms of self-protection. In this study, we cloned the 44.5-kb odl biosynthetic gene cluster (odl-BGC) of the symbiont by recombineering and showed that the N-acetyltransferase-encoding gene, oatA, is responsible for ODL resistance. In vitro acetylation and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analyses showed that OatA targeted the side chain amino group of ODL rare amino acids, leading to a loss of translation inhibition and antibacterial properties. Functional, genomic, and phylogenetic analyses of oatA revealed an exclusive cis-link to the odilorhabdin BGC, found only in X. nematophila and a specific phylogenetic clade of Photorhabdus. This work highlights the coevolution of antibiotic production and self-resistance as ancient features of this unique tripartite complex of host-vector-symbiont interactions without odl-BGC dissemination by lateral gene transfer.

Multipartite viruses have a genome divided into several nucleic acid segments, each encapsidated separately. An evident cost for these viral systems, particularly if some segments are rare, is the difficulty of gathering one copy of each segment to ensure infection. Here, we investigate the segment frequency-related cost by monitoring the copy number of the eight single-gene segments composing the genome of a plant nanovirus. We show that some viral genes accumulate at low frequency, whereas others dominate. We further show that the relative frequency of viral genes impacts both viral accumulation and symptom expression, and changes specifically in different hosts. Earlier proposed benefits of viral genome segmentation do not depend on the segments' frequency and cannot explain our observations. We propose that the differential control of gene/segment copy number may represent an unforeseen benefit for multipartite viruses, which may compensate for the extra costs induced by the low-frequency segments.

Understanding how pathogens evolve according to pressures exerted by their plant hosts is essential for the derivation of strategies aimed at the durable management of resistant cultivars. The spectrum of action of the resistance factors in the partially resistant cultivars is thought to be an important determinant of resistance durability. However, it has not yet been demonstrated whether the pressures exerted by quantitative resistance are different according to their spectrum of action. * To investigate selection pressures exerted by apple genotypes harbouring various resistance quantitative trait loci (QTLs) on a mixed inoculum of the scab disease agent, Venturia inaequalis, we monitored V. inaequalis isolate proportions on diseased apple leaves of an F1 progeny using quantitative pyrosequencing technology and QTL mapping. * Broad-spectrum resistances did not exert any differential selection pressures on the mixed inoculum, whereas narrow-spectrum resistances decreased the frequencies of some isolates in the mixture relative to the susceptible host genotypes. * Our results suggest that the management of resistant cultivars should be different according to the spectrum of action of their resistance factors. The pyramiding of broad-spectrum factors or the use of a mixture of apple genotypes that carry narrow-spectrum resistance factors are two possible strategies for the minimization of resistance erosion.

Seasonality, or periodic host absence, is a central feature in plant epidemiology. In this respect, seasonal plant epidemic models take into account the way the parasite overwinters and generates new infections. These are termed primary infections. In the literature, one finds two classes of models: high-dimensional elaborate models and low-dimensional compact models, where primary infection dynamics are explicit and implicit, respectively. Investigating a compact model allowed previous authors to show the existence of a competitive exclusion principle. However, the way compact models derive from elaborate models has not been made explicit yet. This makes it unclear whether results such as competitive exclusion extend to elaborate models as well. Here, we show that assuming primary infection dynamics are fast in a standard elaborate model translates into a compact form. Yet, it is not that usually found in the literature. Moreover, we numerically show that coexistence is possible in this original compact form. Reversing the question, we show that the usual compact form approximates an alternate elaborate model, which differs from the earlier one in that primary infection dynamics are density dependent. We discuss to which extent these results shed light on coexistence within soil- and air-borne plant parasites, such as within the take-all disease of wheat and the grapevine powdery mildew cryptic species complexes, respectively.

The legume-Rhizobium symbiosis leads to the formation of a new organ, the root nodule, involving coordinated and massive induction of specific genes. Several genes controlling DNA methylation are spatially regulated within the Medicago truncatula nodule, notably the demethylase gene, DEMETER (DME), which is mostly expressed in the differentiation zone. Here, we show that MtDME is essential for nodule development and regulates the expression of 1,425 genes, some of which are critical for plant and bacterial cell differentiation. Bisulphite sequencing coupled to genomic capture enabled the identification of 474 regions that are differentially methylated during nodule development, including nodule-specific cysteine-rich peptide genes. Decreasing DME expression by RNA interference led to hypermethylation and concomitant downregulation of 400 genes, most of them associated with nodule differentiation. Massive reprogramming of gene expression through DNA demethylation is a new epigenetic mechanism controlling a key stage of indeterminate nodule organogenesis during symbiotic interactions.

Despite the ubiquity of complex life cycles, we know little of the evolutionary constraints exerted by metamorphosis. Here, we present pitfalls and methods to answer whether animals with a complex life cycle can independently adapt to the environments encountered at each life stage, with a specific focus on the microevolution of quantitative characters. We first discuss challenges associated with study traits and populations. We further emphasize the benefits of using a combination of approaches. We then develop how multivariate methods can limit several issues by revealing genetic patterns that are invisible when only considering trait-by-trait genetic correlations. Finally, we detail how Lande's work on sexual dimorphism can be applied in measuring G matrices across life stages. The methods and tools described here will contribute towards building a predictive framework for trait evolution across life stages.

Background The process of speciation involves differentiation of whole genome sequences between a pair of diverging taxa. In the absence of a geographic barrier and in the presence of gene flow, genomic differentiation may occur when the homogenizing effect of recombination is overcome across the whole genome. The fall armyworm is observed as two sympatric strains with different host–plant preferences across the entire habitat. These two strains exhibit a very low level of genetic differentiation across the whole genome, suggesting that genomic differentiation occurred at an early stage of speciation. In this study, we aim at identifying critical evolutionary forces responsible for genomic differentiation in the fall armyworm. Results These two strains exhibit a low level of genomic differentiation (FST = 0.0174), while 99.2% of 200 kb windows have genetically differentiated sequences (FST > 0). We found that the combined effect of mild positive selection and genetic linkage to selectively targeted loci are responsible for the genomic differentiation. However, a single event of very strong positive selection appears not to be responsible for genomic differentiation. The contribution of chromosomal inversions or tight genetic linkage among positively selected loci causing reproductive barriers is not supported by our data. Phylogenetic analysis shows that the genomic differentiation occurred by sub-setting of genetic variants in one strain from the other. Conclusions From these results, we concluded that genomic differentiation may occur at the early stage of a speciation process in the fall armyworm and that mild positive selection targeting many loci alone is sufficient evolutionary force for generating the pattern of genomic differentiation. This genomic differentiation may provide a condition for accelerated genomic differentiation by synergistic effects among linkage disequilibrium generated by following events of positive selection. Our study highlights genomic differentiation as a key evolutionary factor connecting positive selection to divergent selection.

. Lipo-chitooligosaccharides (LCOs) are microbial symbiotic signals that also influence root growth. In Medicago truncatula, LCOs stimulate lateral root formation (LRF) synergistically with auxin. However, the molecular mechanisms of this phenomenon and whether it is restricted to legume plants are not known. . We have addressed the capacity of the model monocot Brachypodium distachyon (Brachypodium) to respond to LCOs and auxin for LRF. For this, we used a combination of root phenotyping assays, live-imaging and auxin quantification, and analysed the regulation of auxin homeostasis genes. We show that LCOs and a low dose of the auxin precursor indole-3-butyric acid (IBA) stimulated LRF in Brachypodium, while a combination of LCOs and IBA led to different regulations. Both LCO and IBA treatments locally increased endogenous indole-3-acetic acid (IAA) content, whereas the combination of LCO and IBA locally increased the endogenous concentration of a conjugated form of IAA (IAA-Ala). LCOs, IBA and the combination differentially controlled expression of auxin homeostasis genes. . These results demonstrate that LCOs are active on Brachypodium roots and stimulate LRF probably through regulation of auxin homeostasis. The interaction between LCO and auxin treatments observed in Brachypodium on root architecture opens interesting avenues regarding their possible combined effects during the arbuscular mycorrhizal symbiosis.

The split GFP technique is based on the auto-assembly of GFP when two polypeptides-GFP1-10 (residues 1-214; the detector) and GFP11 (residues 215-230; the tag)-both non-fluorescing on their own, associate spontaneously to form a fluorescent molecule. We evaluated this technique for its efficacy in contributing to the characterization of Cauliflower mosaic virus (CaMV) infection. A recombinant CaMV with GFP11 fused to the viral protein P6 (a key player in CaMV infection and major constituent of viral factory inclusions that arise during infection) was constructed and used to inoculate transgenic Arabidopsis thaliana expressing GFP1-10. The mutant virus (CaMV 11P6) was infectious, aphid-transmissible and the insertion was stable over many passages. Symptoms on infected plants were delayed and milder. Viral protein accumulation, especially of recombinant 11P6, was greatly decreased, impeding its detection early in infection. Nonetheless, spread of infection from the inoculated leaf to other leaves was followed by whole plant imaging. Infected cells displayed in real time confocal laser scanning microscopy fluorescence in wild type-looking virus factories. Thus, it allowed for the first time to track a CaMV protein in vivo in the context of an authentic infection. 11P6 was immunoprecipitated with anti-GFP nanobodies, presenting a new application for the split GFP system in protein-protein interaction assays and pro-teomics. Taken together, split GFP can be an attractive alternative to using the entire GFP for protein tagging.

Abstract Within the optimal foraging theory framework, parasitoids constitute ideal models to elucidate combined physiological and environmental determinism of foraging behavior between current and future fitness gains. Parasitoid females need hosts to lay eggs for their reproduction (immediate gain), but also sugar food resources for their survival (future gain). According to theoretical models and previous empirical studies, fed females should favor host foraging, whereas females with lower energetic reserves should search for food. Surprisingly, the influence of mating status and food quality has not been considered, whereas they may both constitute major factors altering animals’ choices between reproducing and feeding. We tested decision-making on Aphidius rhopalosiphi parasitoid females with different life expectancy levels (as set by recent feeding history) and mating status, using two flower species with contrasted attractiveness and nectar suitability. Interestingly, all fed and unfed females with different expected lifetime levels favored reproduction over nutrition since they are mated. This could be explained by their reproductive status that appeared to be the main determinant of their foraging decisions. For a given expected lifetime, mated females favored more reproduction whereas unmated ones favored food. Physiological status of females (mating and lifetime expectancy) did not interact with flower species on their foraging decisions nor did it modify their preferences, as they always favored the most attractive flower, which does not have the best nectar. These results highlight the need for more empirical studies to evaluate the interactions between different intrinsic factors and to carefully consider the mating status in model assumptions, as it influences foraging behavior between immediate and future fitness gains. Significance statement Parasitic wasps need hosts to lay eggs for their reproduction (immediate fitness gain) and sugar resources for their survival (future fitness gain). Empirical studies and related theoretical models about foraging decisions of parasitic wasps between current and future gains included influences of energetic and resource availability constrains. We examined assumptions used by those mathematical models by empirically testing two new factors, food qualities provided by two nectar provisioning flower species with contrasted functional traits, which had surprisingly no impact on decision-making, and mating status which we showed to play a decisive role on decision-making between food or host resources. These factors should henceforth be considered in model assumptions or in models themselves to realize accurate predictions and to provide a better understanding of foraging decisions made by female parasitic wasps.