CNRS Institute of Genetics, Environment and Plant Protection

Rennes, France

CNRS Institute of Genetics, Environment and Plant Protection

Rennes, France
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Manzano-Marin A.,University of Valencia | Szabo G.,University of Vienna | Simon J.-C.,CNRS Institute of Genetics, Environment and Plant Protection | Horn M.,University of Vienna | Latorre A.,University of Valencia
Environmental Microbiology | Year: 2017

Virtually all aphids maintain an obligate mutualistic symbiosis with bacteria from the Buchnera genus, which produce essential nutrients for their aphid hosts. Most aphids from the Lachninae subfamily have been consistently found to house additional endosymbionts, mainly Serratia symbiotica. This apparent dependence on secondary endosymbionts was proposed to have been triggered by the loss of the riboflavin biosynthetic capability by Buchnera in the Lachninae last common ancestor. However, an integral large-scale analysis of secondary endosymbionts in the Lachninae is still missing, hampering the interpretation of the evolutionary and genomic analyses of these endosymbionts. Here, we analysed the endosymbionts of selected representatives from seven different Lachninae genera and nineteen species, spanning four tribes, both by FISH (exploring the symbionts’ morphology and tissue tropism) and 16S rRNA gene sequencing. We demonstrate that all analysed aphids possess dual symbiotic systems, and while most harbour S. symbiotica, some have undergone symbiont replacement by other phylogenetically-distinct bacterial taxa. We found that these secondary associates display contrasting cell shapes and tissue tropism, and some appear to be lineage-specific. We propose a scenario for symbiont establishment in the Lachninae, followed by changes in the symbiont's tissue tropism and symbiont replacement events, thereby highlighting the extraordinary versatility of host-symbiont interactions. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd

Traugott M.,University of Innsbruck | Kamenova S.,CNRS Chizé Center for Biological Studies | Kamenova S.,CNRS Institute of Genetics, Environment and Plant Protection | Ruess L.,Humboldt University of Berlin | And 2 more authors.
Advances in Ecological Research | Year: 2013

Food webs in agricultural systems are complex and trophic linkages are difficult to track using conventional methodologies. Here, we review three alternative approaches that allow empirical assessment of feeding interactions: DNA-based techniques, and stable isotope and fatty acid analyses. DNA-based methods, namely multiplex PCR and next-generation sequencing, allow identification of food types and host-parasitoid linkages, resulting in taxonomically highly resolved feeding networks. Stable isotopes and fatty acids reflect the assimilation of broader categories of resources, as metabolised into the consumers' tissue, together with the associated energy and nutrient fluxes in the food web. We discuss the strengths of the approaches but also highlight their limitations, providing practical advice on which technique is best suited to answer specific questions in examining food web interactions in agroecosystems. Future refinements of these techniques, especially when used in combination, could herald a new era in agricultural food web ecology, enabling management and environmental impact to be placed in the mechanistic context of trophic networks. © 2013 Elsevier Ltd.

Xhaard C.,University of Lorraine | Xhaard C.,French National Institute for Agricultural Research | Barres B.,French National Institute for Agricultural Research | Andrieux A.,University of Lorraine | And 3 more authors.
Molecular Ecology | Year: 2012

The advent of molecular epidemiology has greatly improved our ability to identify the population sources and track the pathogen movement. Yet the wide spatial and temporal scales usually considered are useful only to infer historical migration pathways. In this study, Bayesian genetic assignments and a landscape epidemiology approach were combined to unravel genetic origin and annual spread during a single epidemic of a plant pathogen: the poplar rust fungus Melampsora larici-populina. The study focused on a particular area - the Durance River valley - which enabled inoculum sources to be identified and channelled spread of the epidemic along a one-dimensional corridor. Spatio-temporal monitoring of disease showed that the epidemic began in the upstream part of the valley and spread out downstream. Using genetic assignment tests, individuals collected at the end of the epidemic were sorted into two genetic groups; very few hybrids were detected, although individuals from both groups coexisted locally downstream in the valley. The epidemic originated from two genetically distinct inoculum sources. Individuals of each group then dispersed southwards along the Durance River and became mixed in poplar riparian stands. These two genetic groups were found previously at a wider spatial scale and proved to result from distinct evolutionary histories on either wild or cultivated poplars. This study showed that the two groups can mix during an epidemic but do not hybridize because they then reproduce asexually. In general, the methods employed here could be useful for elucidating the genetic origin and retracing the colonization history and migration pathways of recent epidemics. © 2012 Blackwell Publishing Ltd.

Nicolas S.D.,CNRS Institute of Genetics, Environment and Plant Protection | Monod H.,French National Institute for Agricultural Research | Eber F.,CNRS Institute of Genetics, Environment and Plant Protection | Chevre A.-M.,CNRS Institute of Genetics, Environment and Plant Protection | And 2 more authors.
Plant Journal | Year: 2012

Summary Chromosome rearrangements are common, but their dynamics over time, mechanisms of occurrence and the genomic features that shape their distribution and rate are still poorly understood. We used allohaploid Brassica napus (AC, n = 19) as a model to analyze the effect of genomic features on the formation and diversity of meiotically driven chromosome rearrangements. We showed that allohaploid B. napus meiosis leads to extensive new structural diversity. Almost every allohaploid offspring carried a unique combination of multiple rearrangements throughout the genome, and was thus structurally differentiated from both its haploid parent and its sister plants. This large amount of genome reshuffling was remarkably well-tolerated in the heterozygous state, as neither male nor female fertility were strongly reduced, and meiosis behavior was normal in most cases. We also used a quantitative statistical model, which accounted for 75% of the observed variation in rearrangement rates, to show that the distribution of meiotically driven chromosome rearrangements was not random but was shaped by three principal genomic features. In descending order of importance, the rate of marker loss increased strongly with genetic distance from the centromere, the degree of collinearity between chromosomes, and the genome of origin (A < C). Overall, our results demonstrate that B. napus accumulates a large number of genetic changes, but these rearrangements are not randomly distributed in the genome. The structural genetic diversity produced by the allohaploid pathway and its role in the evolution of polyploid species compared to diploid meiosis are discussed. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

Carter M.J.,University of Sheffield | Simon J.-C.,CNRS Institute of Genetics, Environment and Plant Protection | Nespolo R.F.,Austral University of Chile
Ecology and Evolution | Year: 2012

Organisms with coexisting sexual and asexual populations are ideal models for studying the consequences of either reproductive mode on the quantitative genetic architecture of life-history traits. In the aphid Rhopalosiphum padi, lineages differing in their sex investment coexist but all share a common parthenogenetic phase. Here, we studied multiple genotypes of R. padi specialized either for sexual and asexual reproduction and compared their genetic variation in fitness during the parthenogenetic phase. Specifically, we estimated maintenance costs as standard metabolic rate (SMR), together with fitness (measured as the intrinsic rate of increase and the net reproductive rate). We found that genetic variation (in terms of broad-sense heritability) in fitness was higher in asexual genotypes compared with sexual genotypes. Also, we found that asexual genotypes exhibited several positive genetic correlations indicating that body mass, whole-animal SMR, and apterous individuals production are contributing to fitness.Hence, it appears that in asexual genotypes, energy is fully allocated to maximize the production of parthenogenetic individuals, the simplest possible form of aphid repertoire of life-histories strategies. © 2012 The Authors.

Gallot A.,CNRS Institute of Genetics, Environment and Plant Protection | Shigenobu S.,Japan National Institute for Basic Biology | Hashiyama T.,Japan National Institute for Basic Biology | Jaubert-Possamai S.,CNRS Institute of Genetics, Environment and Plant Protection | Tagu D.,CNRS Institute of Genetics, Environment and Plant Protection
BMC Genomics | Year: 2012

Background: Although sexual reproduction is dominant within eukaryotes, asexual reproduction is widespread and has evolved independently as a derived trait in almost all major taxa. How asexuality evolved in sexual organisms is unclear. Aphids, such as Acyrthosiphon pisum, alternate between asexual and sexual reproductive means, as the production of parthenogenetic viviparous females or sexual oviparous females and males varies in response to seasonal photoperiodism. Consequently, sexual and asexual development in aphids can be analyzed simultaneously in genetically identical individuals.Results: We compared the transcriptomes of aphid embryos in the stages of development during which the trajectory of oogenesis is determined for producing sexual or asexual gametes. This study design aimed at identifying genes involved in the onset of the divergent mechanisms that result in the sexual or asexual phenotype. We detected 33 genes that were differentially transcribed in sexual and asexual embryos. Functional annotation by gene ontology (GO) showed a biological signature of oogenesis, cell cycle regulation, epigenetic regulation and RNA maturation. In situ hybridizations demonstrated that 16 of the differentially-transcribed genes were specifically expressed in germ cells and/or oocytes of asexual and/or sexual ovaries, and therefore may contribute to aphid oogenesis. We categorized these 16 genes by their transcription patterns in the two types of ovaries; they were: i) expressed during sexual and asexual oogenesis; ii) expressed during sexual and asexual oogenesis but with different localizations; or iii) expressed only during sexual or asexual oogenesis.Conclusions: Our results show that asexual and sexual oogenesis in aphids share common genetic programs but diverge by adapting specificities in their respective gene expression profiles in germ cells and oocytes. © 2012 Gallot et al; licensee BioMed Central Ltd.

Manzano-Marin A.,University of Valencia | Simon J.-C.,CNRS Institute of Genetics, Environment and Plant Protection | Latorre A.,University of Valencia
Genome Biology and Evolution | Year: 2016

Virtually all aphids (Aphididae) harbor Buchnera aphidicola as an obligate endosymbiont to compensate nutritional deficiencies arising from their phloem diet. Many species within the Lachninae subfamily seem to be consistently associated also with Serratia symbiotica. We have previously shown that both Cinara (Cinara) cedri and Cinara (Cupressobium) tujafilina (Lachninae: Eulachnini tribe) have indeed established co-obligate associations with both Buchnera and S. symbiotica. However, while Buchnera genomes of both Cinara species are similar, genome degradation differs greatly between the two S. symbiotica strains. To gain insight into the essentiality and degree of integration of S. symbiotica within the Lachninae, we sequenced the genome of both Buchnera and S. symbiotica endo-symbionts from the distantly related aphid Tuberolachnus salignus (Lachninae: Tuberolachnini tribe). We found a striking level of similarity between the endosymbiotic system of this aphid and that of C. cedri. In both aphid hosts, S. symbiotica possesses a highly reduced genome and is found exclusively intracellularly inside bacteriocytes. Interestingly, T. salignus' endosymbionts present the same tryptophan biosynthetic metabolic complementation as C. cedri's, which is not present in C. tujafilina's. Moreover, we corroborate the riboflavin-biosynthetic-role take-over/rescue by S. symbiotica in T. salignus, and therefore, provide further evidence for the previously proposed establishment of a secondary co-obligate endosymbiont in the common ancestor of the Lachninae aphids. Finally, we propose that the putative convergent split of the tryptophan biosynthetic role between Buchnera and S. symbiotica could be behind the establishment of S. symbiotica as an obligate intracellular symbiont and the triggering of further genome degradation. © The Author 2016.

Bilodeau E.,Laval University | Simon J.-C.,CNRS Institute of Genetics, Environment and Plant Protection | Guay J.-F.,Laval University | Turgeon J.,Laval University | Cloutier C.,Laval University
Evolutionary Ecology | Year: 2013

The host-associated differentiation (HAD) hypothesis states that higher trophic levels in parasitic associations should exhibit similar divergence in case of host sympatric speciation. We tested HAD on populations of Aphidius ervi the main parasitoid of the pea aphid Acyrthosiphon pisum, emerging from host populations specialized on either alfalfa or red clover. Host and parasitoid populations were assessed for genetic variation and structure, while considering geography, host plant and host aphid protective symbionts Regiella insecticola and Hamiltonella defensa as potential covariables. Cluster and hierarchical analyses were used to assess the contribution of these variables to population structure, based on genotyping pea aphids and associated A. ervi with microsatellites, and host aphid facultative symbionts with 16S rDNA markers. Pea aphid genotypes were clearly distributed in two groups closely corresponding with their plant origins, confirming strong plant associated differentiation of this aphid in North America. Overall parasitism by A. ervi averaged 21. 5 % across samples, and many parasitized aphids producing a wasp hosted defensive bacteria, indicating partial or ineffective protective efficacy of these symbionts in the field. The A. ervi population genetic data failed to support differentiation according to the host plant association of their pea aphid host. Potential for parasitoid specialization was also explored in experiments where wasps from alfalfa and clover aphids were reciprocally transplanted on alternate hosts, the hypothesis being that wasp behaviour and parasitic stages should be most adapted to their host of origin. Results revealed higher probability of oviposition on the alfalfa aphids, but higher adult emergence success on red clover aphids, with no interaction as expected under HAD. We conclude that our study provides no support for the HAD in this system. We discuss factors that might impair A. ervi specialization on its divergent aphid hosts on alfalfa and clover. © 2012 Springer Science+Business Media B.V.

Rizk G.,French Institute for Research in Computer Science and Automation | Gouin A.,CNRS Institute of Genetics, Environment and Plant Protection | Chikhi R.,Pennsylvania State University | Lemaitre C.,French Institute for Research in Computer Science and Automation
Bioinformatics | Year: 2014

Motivation: Insertions play an important role in genome evolution. However, such variants are difficult to detect from short-read sequencing data, especially when they exceed the paired-end insert size. Many approaches have been proposed to call short insertion variants based on paired-end mapping. However, there remains a lack of practical methods to detect and assemble long variants. Results: We propose here an original method, called MindTheGap, for the integrated detection and assembly of insertion variants from re-sequencing data. Importantly, it is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. MINDTHEGAP uses an efficient k-mer-based method to detect insertion sites in a reference genome, and subsequently assemble them from the donor reads. MINDTHEGAP showed high recall and precision on simulated datasets of various genome complexities. When applied to real Caenorhabditis elegans and human NA12878 datasets, MINDTHEGAP detected and correctly assembled insertions>1kb, using at most 14GB of memory. © The Author 2014. Published by Oxford University Press. All rights reserved.

Henry L.M.,University of Oxford | Peccoud J.,CNRS Institute of Genetics, Environment and Plant Protection | Simon J.-C.,CNRS Institute of Genetics, Environment and Plant Protection | Hadfield J.D.,University of Oxford | And 3 more authors.
Current Biology | Year: 2013

Facultative or "secondary" symbionts are common in eukaryotes, particularly insects. While not essential for host survival, they often provide significant fitness benefits [1-5]. It has been hypothesized that secondary symbionts form a "horizontal gene pool" shuttling adaptive genes among host lineages in an analogous manner to plasmids and other mobile genetic elements in bacteria [6, 7]. However, we do not know whether the distributions of symbionts across host populations reflect random acquisitions followed by vertical inheritance or whether the associations have occurred repeatedly in a manner consistent with a dynamic horizontal gene pool. Here we explore these questions using the phylogenetic and ecological distributions of secondary symbionts carried by 1,104 pea aphids, Acyrthosiphon pisum. We find that not only is horizontal transfer common, but it is also associated with aphid lineages colonizing new ecological niches, including novel plant species and climatic regions. Moreover, aphids that share the same ecologies worldwide have independently acquired related symbiont genotypes, suggesting significant involvement of symbionts in their host's adaptation to different niches. We conclude that the secondary symbiont community forms a horizontal gene pool that influences the adaptation and distribution of their insect hosts. These findings highlight the importance of symbiotic microorganisms in the radiation of eukaryotes. © 2013 Elsevier Ltd.

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