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Additional file 3: Supplementary Figure 1. Base composition of known or novel mature miRNAs using weblogo [79, 80].

Additional file 5: Supplementary Figure 3. Variation between samples (treatments, replicates) of larvae exposed to different plants displayed by Principal Component Analysis (PCA). Top panel: On, bottom panel: Os. OnCor: On on corn, OnMug: On on mugwort, OsCor: Os on corn, OsMug: Os on mugwort.

Additional file 1: Supplementary Table S1. Number of sequence reads in each small non coding RNAs library.

Additional file 4: Supplementary Figure 2. MA-plots showing the relative expression of known or novel miR according to the host-plant (Mugwort compared to corn) in each sibling species. Top panel, in On, bottom panel In Os.

Additional file 9: Supplementary Figure 5. Variation between samples (treatments, replicates) of larvae exposed to different plants displayed by Principal Component Analysis (PCA). Os compared to On on corn. OnCor: On on corn, OnMug: On on mugwort, OsCor: Os on corn, OsMug: Os on mugwort.

Additional file 7: Supplementary Figure 4. MA-plots showing the relative expression of known or novel miR according to the genetic background. Relative expression analyzed by DESEQ2 in Os compared to On on corn.

International audience; We present an assembly and annotation of the mitogenome of a European specimen of the Adzuki bean borer, Ostrinia scapulalis (Walker, 1859). The present data were obtained by combining WGS data issue of a de novo and a previously published sequence library [1]. We also provide the phylogenetic positioning of the mitogenome within the Ostrinia genus, the Crambidae family and with more distant Lepidoptera species.

International audience; Puumala virus (PUUV) in Europe causes nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS). The incidence of NE is highly heterogeneous spatially, whereas the geographic distribution of the wild reservoir of PUUV, the bank vole, is essentially homogeneous. Our understanding of the processes driving this heterogeneity remains incomplete due to gaps in knowledge. Little is known about the current distribution and genetic variation of PUUV in the areas outside the well-identified zones of NE endemicity. We trapped bank voles in four forests in French regions in which NE is considered non-endemic, but sporadic NE cases have been reported recently. We tested bank voles for anti-PUUV IgG and characterized the S segment sequences of PUUV from seropositive animals. Phylogenetic analyses revealed specific amino-acid signatures and genetic differences between PUUV circulating in non-endemic and nearby NE-endemic areas. We also showed, in temporal surveys, that the amino-acid sequences of PUUV had undergone fewer recent changes in areas non-endemic for NE than in endemic areas. The evolutionary history of the current French PUUV clusters was investigated by phylogeographic approaches, and the results were considered in the context of the history of French forests. Our findings highlight the need to monitor the circulation and genetics of PUUV in a larger array of bank vole populations, to improve our understanding of the risk of NE.

International audience

Hyposoter didymator (Hymenoptera, Ichneumonidae) is a generalist solitary endoparasitoid of noctuid larvae. In the present work, we tested whether populations of H. didymator were divided in several genetically distinct taxa as described for many other generalist parasitoid species, and whether differences in H. didymator parasitism rates were explained by the insect host species and/or by the plant on which these hosts were feeding on. The genetic analysis of natural populations collected in different regions in France and Spain on seven different insect hosts and seven different host plants (775 individuals) showed that H. didymator populations belong to a unique single taxon. However, H. didymator seems to be somewhat specialized. Indeed, in the fields it more often parasitized Helicoverpa armigera compared to the other host species collected in the present work. Also, H. didymator parasitism rates in field conditions and semi-field experimental studies were dependent on the host plants on which H. armigera larvae are feeding. Still, H. didymator can occur occasionally on non-preferred noctuid species. One hypothesis explaining the ability of H. didymator to switch hosts in natura could be related to fluctuating densities of the preferred host over the year; this strategy would allow the parasitoid to avoid seasonal population collapses.

Spodoptera frugiperda , the fall armyworm (FAW), is an important agricultural pest in the Americas and an emerging pest in sub-Saharan Africa, causing damage to major crops such as corn, sorghum and soybean. While FAW larvae are considered polyphagous, differences in diet preference have been described between two genetic variants: the Corn strain (sf-C) and the Rice strain (sf-R). These two strains are sometimes considered as distinct species, raising the hypothesis that host plant specialization might have driven their divergence. Ecological speciation takes place when adaptations to different ecological niches lead to the reproductive isolation of two populations. Under this hypothesis, we expect that the transcriptional response to the host plants should affect differently the fitness of the two FAW strains. We also expect that these genes should also be linked to a reproductive isolation mechanism between the strains. In this study, we performed controlled reciprocal transplant (RT) experiments to address the impact of plant diet on several traits linked to the fitness of the sf-C and sf-R strains. The phenotypical data suggest that sf-C is specialized to corn. We then used RNA-Seq to analyze the gene expression of FAW larvae from RT experiments. We show that each strain has a different response to the same plant diets. However, we also found constitutive transcriptional differences between strains in laboratory and in natural populations. In particular, we show that mitochondrial transcription is the main difference between strains. A difference in mitochondrial function may be the basis for a shift in host plant and could be involved in hybrid incompatibility, raising the hypothesis that mitochondrial genome is the main target of selection between the two strains.

Background Divergent selection has been shown to promote speciation in many taxa and especially in phytophagous insects. In the Ostrinia species complex, the European corn borer (ECB) and adzuki bean borer (ABB) are two sibling species specialized to different host plants. The first is a well-known maize pest, whereas the second is a polyphagous species associated with various dicotyledons. Their specialization to host plants is driven by morphological, behavioral and physiological adaptations. In particular, previous studies have shown that ECB and ABB display marked behavior with regard to plant choice during oviposition, involving specific preference and avoidance mechanisms. In this study, our goal was to identify the mechanisms underlying this host-plant specialization in adult females through an analysis of their gene expression. We assembled and annotated a de novo reference transcriptome and measured differences in gene expression between ECB and ABB females, and between environments. We related differentially expressed genes to host preference behavior, and highlighted the functional categories involved. We also conducted a specific analysis of chemosensory genes, which are considered to be good candidates for host recognition before oviposition. Results We recorded more differentially expressed genes in ECB than in ABB samples, and noticed that the majority of genes potentially involved in the host preference were different between the two species. At the functional level, the response to plant environment in adult females involved many processes, including the metabolism of carbohydrates, lipids, proteins, and amino acids; detoxification mechanisms and immunity; and the chemosensory repertoire (as expected). Until now, most of the olfactory receptors described in Ostrinia spp. had been tested for their putative role in pheromone recognition by males. Here we observed that one specific olfactory receptor was clearly associated with ECB’s discrimination between maize and mugwort conditions, highlighting a potential new candidate involved in plant odor discrimination in adult females. Conclusions Our results are a first step toward the identification of candidate genes and functions involved in chemosensory processes, carbohydrate metabolism, and virus and retrovirus dynamics. These candidates provide new avenues for research into understanding the role of divergent selection between different environments in species diversification.

article in press; Maize was introduced into opposite sides of Eurasia 500 years ago, in Western Europe and in Asia. This caused two host-shifts in the phytophagous genus Ostrinia, O. nubilalis (the European corn borer; ECB) and O. furnacalis (the Asian corn borer; ACB) are now major pests of maize worldwide. They originated independently from Dicot-feeding ancestors, similar to O. scapulalis (the Adzuki bean borer; ABB). Unlike other host-plants, maize is yearly harvested, and harvesting practices impose severe mortality on larvae found above the cut-off line. Positive geotaxis in the ECB has been proposed as a behavioural adaptation to harvesting practices, allowing larvae to move below the cut-off line and thus escape harvest-mortality. Here we test whether the same behavioural adaptation evolved independently in Europe and in Asia. We sampled eight genetically differentiated ECB, ACB and ABB populations in France and China and monitored geotaxis through the entire larval development in artificial stacks mimicking maize stems. We find that all ECB and ACB populations show a similar tendency to move down during the latest larval stages, a behaviour not observed in any European or Asian ABB population. The behaviour is robustly expressed regardless of larval density, development mode or environmental conditions. Our results indicate that maize introduction triggered parallel behavioural adaptations in Europe and Asia, harvest selection presumably being the main driver.

Background: This study aimed at enhancing the transcriptomic resources for two sibling species of moths, Ostrinia scapulalis (Adzuki bean borer) and Ostrinia nubilalis (European corn borer), as a foundation for future researches on their divergence history. Previous works on these species had shown that their genetic divergence was low, while they were reproductively isolated in natura and specialized on different host plants. Comparative genomic resources will help facilitate the understanding of the mechanisms involved in this isolation and adaptation to the host plants. Despite their fundamental interest, these species still lack the genomic resources to thoroughly identify candidate genes for functions of interest. We present here a high throughput sequencing and de novo transcriptome assembly for these two sibling species in line with this objective of comparative genomics. Results: Based on 322,504 and 307,622 reads of 454 sequencing for O. scapulalis and O. nubilalis respectively, we reconstructed 11,231 and 10,773 transcripts, of which 40% were functionally annotated by BLAST analyzes. We determined the level of completeness of both assemblies as well as the recovery level of published Ostrinia genomic resources. Gene ontology (GO) of common and species-specific de novo transcripts did not reveal GO terms significantly enriched in one or the other species. By applying stringent homology searches on transcripts common to O. scapulalis and O. nubilalis, we identified a set of homologous transcripts, with a mean nucleotide identity value of 98.1%. In this set, the most divergent transcripts revealed candidate genes involved in developmental, sensorial and pathogen defense processes. Conclusions: This data greatly increases the genomic resources of Ostrinia species and constitute a solid skeleton for future comparative analyzes of expression or diversity, despite we show that the transcriptomes for both species have not been assembled at full completion. In addition, we provide a set of homologous transcripts together with their annotation as a source of candidate genes for comparative analyzes. Keywords: NGS, 454 sequencing, Tanscriptome, Moth, European corn borer, Adzuki bean borer, Sibling species, Ostrinia nubilalis, Ostrinia scapulalis

Correspondance: streiff@supagro.inra.fr; International audience; The evolutionary importance of hybridization in wild plants and animals has become increasingly widely recognized in the last decade. In practical terms, hybridization provides an exceptionally tough set of problems for conservation biologists. We illustrate this in a case study of two Carabidae species widely used to evaluate the impact of human activities on biodiversity. These two species live in a complex mosaic of sympatry/allopatry and are known to hybridize in controlled conditions. Hybridization has not been quantified in natural populations to date due to the lack of a simple set of phenotypic traits for identifying hybrids. We thus screened for hybrids in natural populations, by multilocus genotyping at nine microsatellite loci. A high level of genetic differentiation between these two taxa was observed, as shown by allelic frequency distributions. Two Bayesian assignment procedures without obligatory pure taxon references were used to infer different classes of hybrids (F(1), F(2) and backcrosses) and mixture proportions between the two species. A low level of hybridization (F(1) genotypes) was observed in natural populations, contrasting with results obtained in controlled conditions. A high level of introgression was, however, detected at three of 12 sites, as revealed by the detection of backcrossed genotypes. This interspecific gene flow was detected in a limited zone of the common geographical range of the two species and was not related to the pattern of sympatry/allopatry. We then considered the origin and repercussions of this introgression, based on intraspecific genetic diversity and geographical structure

Le volet 'acridiens' du projet de recherche concerne l'impact de la fragmentation et de la réduction de surface d'habitat sur une espèce d'orthoptère protégée sur le territoire national (J.O. du 23/09/1993). La plaine de Crau (Bouches du Rhône) est un habitat unique en France, soumis à une forte pression anthropique. Ce paléodelta de la Durance se caractérise par une formation steppique dont le maintien résulte de 4000 ans de pastoralisme. Depuis plus d'un siècle, l'irrigation a entraîné le développement des prairies de fauche et de l'arboriculture intensive. L'implantation de complexes industriels et militaires ont conjointement réduit l'espace pastoral original. Cette plaine est caractérisée par des espèces endémiques (strictes ou au sens plus large, lorsque une partie du cycle est inféodée à cette localité), pour la plupart en danger d'extinction. La protection de cet habitat, sollicitée au niveau national (réserve nationale depuis 2002, figure (1), et européen (mesures agri-environnementale depuis 1993), vise à (i) appréhender les objectifs prioritaires de conservation, (ii) caractériser l'impact de la fragmentation sur les processus écologiques afin de définir une gestion conservatoire des espèces et des espaces, (iii) intégrer les activités économiques dans les mesures de gestion. Le criquet rhodanien, Prionotropis hystrix rhodanica, objet des présents travaux, est une espèce modèle dans une optique de préservation et de conservation: son endémisme strict, son cycle annuel et l'absence de vol, le rendent potentiellement sensible aux dégradations de son habitat. Cette espèce présente le double intérêt de fournir un modèle d'étude typique d'organisme à faible pouvoir de dispersion (à comparer à d'autres organismes du projet aux capacités de dispersion contrastées, i.e. avifaune et végétation), et de représenter un enjeu de conservation patrimonial. Le projet de recherche se base sur une double approche génétique et démographique pour décrire le fonctionnement des populations du criquet rhodanien, estimer leur risque d'extinction et cerner l'impact des modifications de son habitat sur ses potentialités évolutives. Seront présentés dans le présent rapport d'activité, les différentes approches et échantillonnages réalisés à ce jour ainsi que des résultats préliminaires. Les perspectives jusqu'au terme du projet seront proposées à leur suite.

"Dans le cadre de mon stage, je me suis initié aux différentes techniques de base de biologie moléculaire, s'inscrivant dans les deux axes de recherches déve loppés à l'URPIGM sur la stratégie anti-virale et la mise au point de méthodes de diagnostic des maladies virales des invertébrés marins".

"Dans le cadre de mon stage, effectué à l'Unité de Recherche en Pathologie, Immunologie et Génétique Moléculaire des invertébrés marins à la Tremblade (URPIGM, station IFREMER), je me suis initié aux techniques d'hybridation lymphocytaire et d'immunodosages. Des anticorps monoclonaux ont été produit d'une part contre une souche bactérienne de genre Vibrio sp. associée au symdrome de la nécrose du tube digestif et d'autre part contre le Baculovirus, agents patogènes affectant les élevages de crevettes Penaeus vannamei en Equateur"