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Introduction
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September 2013 - present
November 1994 - August 2013
Publications
Publications (137)
Ticks represent a major health issue for humans and domesticated animals. Assessing the expression patterns of the tick's central nervous system, known as the synganglion, is an important step in understanding tick physiology and in managing tick-borne diseases. Neuron-specific genes like the cys-loop ligand-gated ion channels (cys-loop LGICs) are...
We studied a group of tick-associated viruses with characteristics of members of the family Iflaviridae , a family of viruses frequently found in arthropods. Our aim was to gain insight into the evolutionary dynamics of this group of viruses, which may be linked to the biology of ticks. We explored assembled RNA-Seq data sets for different species...
Many developmental processes in the life sciences, ecology and even in economics depend strongly on the environmental conditions occurring in a bounded time interval, the results occurring often far later. Examples are as diverse as plant phenology, grapewine maturation, diapause induction and so on. The method proposed here, aims at detecting quic...
Nicotinic acetylcholine receptors are an important class of excitatory receptors in the central nervous system of arthropods. In the ticks Ixodes ricinus, the functional and pharmacological properties of nicotinic receptors located in their neurons are still unknown. The objective of this study was to characterize the pharmacological properties of...
Tick-borne diseases have a complex epidemiology that depends on different ecological communities, associating several species of vertebrate hosts, vectors and pathogens. While most studies in Europe are focused on Ixodes ricinus, other Ixodes species may also be involved in the transmission or maintenance of pathogens. This is the case of Ixodes fr...
An amendment to this paper has been published and can be accessed via the original article.
Background: Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors suc...
We studied a family of iflaviruses, a group of RNA viruses frequently found in arthropods, focusing on viruses associated with ticks. Our aim was to bring insight on the evolutionary dynamics of this group of viruses, which may interact with the biology of ticks. We explored systematically de novo RNA-Seq assemblies available for species of ticks w...
Background:
All eukaryotes share a conserved network of processes regulated by the proteasome and fundamental to growth, development, or perception of the environment, leading to complex but often predictable responses to stress. As a specialized component of the ubiquitin-proteasome system (UPS), the RING finger domain mediates protein-protein in...
Hard ticks are widely distributed across temperate regions, show strong variation in host associations, and are potential vectors of a diversity of medically important zoonoses, such as Lyme disease. To address unresolved issues with respect to the evolutionary relationships among certain species or genera, we produced novel RNA-Seq data sets for n...
Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high conti...
Supplementary material for "A high-quality grapevine downy mildew genome assembly reveals rapidly evolving and lineage-specific putative host adaptation genes"
1. Introduction
2. The need for tick genome resources
3. Data-driven solutions for tick and tick-borne disease control
3.1. The systems biology of tick-host-pathogen interactions
3.2. The link between tick genetics, vector competence and disease
transmission
3.3. Genetic frameworks for Ixodes control
4. The Ix1000G roadmap
4.1. Priority area 1: Hig...
Background:
Ixodes ricinus is the most important vector of tick-borne diseases in Europe. A better knowledge of its genome and transcriptome is important for developing control strategies. Previous transcriptomic studies of I. ricinus have focused on gene expression during the blood meal in specific tissues. To obtain a broader picture of changes...
Downy mildews are obligate biotrophic oomycete pathogens that cause devastating plant diseases on economically important crops. Plasmopara viticola is the causal agent of grapevine downy mildew, a major disease in vineyards worldwide. We sequenced the genome of Pl. viticola with PacBio long reads and obtained a new 92.94 Mb assembly with high conti...
The faster evolution of X chromosomes has been documented in several species, and results from the increased efficiency of selection on recessive alleles in hemizygous males and/or from increased drift due to the smaller effective population size of X chromosomes. Aphids are excellent models for evaluating the importance of selection in faster-X ev...
Background
Ixodes ricinus is the most important vector of tick-borne-diseases in Europe. A better knowledge of its genome and transcriptome is important for developing control strategies. Previous transcriptomic studies of I. ricinus have focused on gene expression during the blood meal in specific tissues. To obtain a broader picture of changes in...
Faster evolution of X chromosomes has been documented in several species and results from the increased efficiency of selection on recessive alleles in hemizygous males and/or from increased drift due to the smaller effective population size of X chromosomes. Aphids are excellent models for evaluating the importance of selection in faster-X evoluti...
Grapevine phylloxera, an insect related to true aphids, is a major historic pest of viticulture only controlled through the selection of resistant rootstocks or through quarantine regulations where grapevine is cultivated own-rooted. Transcriptomic data could help understand the bases of its original life-traits, including a striking case of polyph...
Although evolutionary transitions from sexual to asexual reproduction are frequent in eukaryotes, the genetic bases of such shifts toward asexuality remain largely unknown. We addressed this issue in an aphid species where both sexual and obligate asexual lineages coexist in natural populations. These sexual and asexual lineages may occasionally in...
Phenotypic plasticity, the production of alternative phenotypes (or morphs) from the same genotype due to environmental factors,
results in some genes being expressed in a morph-biased manner. Theoretically, these morph-biased genes experience relaxed
selection, the consequence of which is the buildup of slightly deleterious mutations at these gene...
In the framework of the International Aphid Genomics Consortium (IAGC) and the i5K initative, the Phylloxera Genomics Initiative proposes the sequencing of the grape phylloxera (Daktulosphaira vitifoliae Fitch) genome through an integrated approach. Currently, DNA sequencing and pre-assembly of an Australian lineage have been obtained by performing...
Patterns of invasion of the X chromosome and autosomes by mutations that may differentially affect fitness of males, sexual females and asexual females, derived from stochastic individual-based simulations. These results are based on a set of 200'000 simulations for each scenario (A to F) (see Methods for additional details). The selective coeffici...
Characteristics of mutations (in terms of their selection coefficients in males [sm] and in females [sf]) that rise in frequency on the X but not on autosomes (panel A) and autosomes but not X (panel B) as a function of the dominance coefficient h in standard XX/XY sex-determining systems (e.g. Drosophila, mammals). As predicted [2], the X chromoso...
Description of the RNA-Seq libraries used for the three different types of reproductive morphs (males, sexual females and asexual females).
(DOC)
Characteristics of mutations (in terms of their selection coefficients in males [sm], sexual females [sf] and asexual females [sa]) that increase in frequency on the X but not on autosomes (panel A) and on autosomes but not on the X (panel B) when dominance is constant across sexes (hm = hf = ha) (Scenario A, see also Figure 2), when the dominance...
Genomic location (X-chromosome versus autosomes) for genes differentially expressed in males, sexual females or asexual females when considering different sizes of window around the microsatellite markers used to tag the genomic region as X-linked or autosomal. The number of autosomal and X-linked genes (as well as X-linkage frequency) is shown whe...
Primer sequences of the six additional X-linked microsatellite loci. See [51] for amplification conditions.
(DOC)
Evolutionary theory predicts that sexually antagonistic mutations accumulate differentially on the X chromosome and autosomes in species with an XY sex-determination system, with effects (masculinization or feminization of the X) depending on the dominance of mutations. Organisms with alternative modes of inheritance of sex chromosomes offer intere...
Several bacterial strains of the Pseudomonas genus provide plant growth stimulation, plant protection against pests or bioremediation. Among these bacteria, P. fluorescens Pf29Arp reduces the severity of take-all, a disease caused by the pathogenic fungus Gaeumannomyces graminis var. tritici (Ggt) on wheat roots. In this study, we obtained a draft...
Background
The sequencing of the genome of the pea aphid Acyrthosiphon pisum revealed an unusual expansion of the miRNA machinery, with two argonaute-1, two dicer-1 and four pasha gene copies. In this report, we have undertaken a deeper evolutionary analysis of the phylogenetic timing of these gene duplications and of the associated selective press...
Table S2. PCR primers used for semiquantitative RT-PCRs.
Figure S2. Further duplication of dcr-1 in Acyrthosiphon pisumLSR1.
Table S1. PCR primers used in this study, ordered in relative positions from 5’ to 3’ of the corresponding gene/region.
Figure S1. Further duplication of dcr-1 in Acyrthosiphon kondoi and Acyrthosiphon svalbardicum.
Figure S3. Test of alternative hypotheses for the phylogeny of dcr-1 in aphids.
Most aphids show reproductive polyphenism, i.e. they alternate their reproductive modes from parthenogenesis to sexual reproduction in response to short photoperiods. Although juvenile hormone (JH) has been considered a likely candidate for regulating the transition from asexual to sexual reproduction after photoperiod sensing, there are few studie...
Sex chromosomes play a role in many important biological processes, including sex determination, genomic conflicts, imprinting, and speciation. In particular, they exhibit several unusual properties such as inheritance pattern, hemizygosity, and reduced recombination, which influence their response to evolutionary factors (e.g., drift, selection, a...
In theory, the loss of sexual reproduction is expected to result in the accumulation of deleterious mutations. In aphids, two main types of life cycle, cyclic and obligate parthenogenesis, represent respectively "sexual" and "asexual" reproductive modes. We used the complete pea aphid genome and previously published expressed sequence tags (ESTs) f...
Comparison of expressions of Api-ago3a and Api-ago3b in sexuparous and oviparous embryos. Dissected ovarioles were hybridised with DIG-labelled antisense riboprobes of Api-ago3a (A–H) and Api-ago3b (I–P), respectively. For orientation and morphological characteristics of embryos refer to Figure 3O. Early development: A, B, E, F, I, J, M, N; Mid dev...
Double in situ hybridisation of Api-piwi2 and vasa in virginoparous embryos. (A–D) Ovarioles hybridised with DIG-labelled antisense riboprobe of Api-piwi2; (E–H) Ovarioles hybridised with FL-labelled antisense riboprobes of vasa; (I–L) Ovarioles hybridised with both DIG-labelled Api-piwi2 and FL-labelled vasa riboprobes. Color keys indicating singl...
Double in situ hybridisation of Api-ago3a and vasa in virginoparous embryos. (A–D) Ovarioles hybridised with DIG-labelled antisense riboprobe of Api-ago3a; (E–H) Ovarioles hybridised with FL-labelled antisense riboprobes of vasa; (I–L) Ovarioles hybridised with both DIG-labelled Api-ago3a and FL-labelled vasa riboprobes. Color keys indicating singl...
Primer pairs used for the synthesis of sense and antisense riboprobes.
(DOC)
Expression levels of the Api-piwi and Api-ago3 genes in the four reproductive morphs. Expressions of the eight Api-piwi and the two Api-ago3 genes were quantified in the four reproductive morphs of the pea aphid by semi-quantitative RT-PCR. The figure shows agarose gels after electrophoresis of RT-PCR products. Quantification of gene expression was...
Double in situ hybridisation of Api-piwi6 and vasa in virginoparous embryos. (A–D) Ovarioles hybridised with DIG-labelled antisense riboprobe of Api-piwi6; (E–H) Ovarioles hybridised with FL-labelled antisense riboprobes of vasa; (I–L) Ovarioles hybridised with both DIG-labelled Api-piwi6 and FL-labelled vasa riboprobes. Color keys indicating singl...
Summary of in situ hybridisation of Api-piwi and Api-ago3 genes during embryogenesis.
(DOC)
Comparison of expressions of Api-piwi3 and Api-piwi6 in sexuparous and oviparous embryos. Dissected ovarioles were hybridised with DIG-labelled antisense riboprobes of Api-piwi3 (A–H) and Api-piwi6 (I–P), respectively. For orientations and morphological characteristics of embryos refer to Figure 3O. Early development: A, B, E, F, I, J, M, N; Mid de...
Primers used for semi quantitative RT-PCR.
(DOC)
Alignment of deduced protein sequences of the eight Api-piwi genes and the two Api-ago3 genes. Deduced protein sequence of the eight Api-Piwi and the two Api-Ago3 proteins were aligned with their D. melanogaster orthologues Dme-Piwi, Dme-Aub and Dme-Ago3 by using ClustalW2 (http://www.ebi.ac.uk/Tools/msa/clustalw2/). The PAZ and PIWI domains [47] o...
Piwi-interacting RNAs (piRNAs) are known to regulate transposon activity in germ cells of several animal models that propagate sexually. However, the role of piRNAs during asexual reproduction remains almost unknown. Aphids that can alternate sexual and asexual reproduction cycles in response to seasonal changes of photoperiod provide a unique oppo...
Aphids have a high adaptative potential and their capacity to adapt to various environments could be linked with specific
expansions in gene repertoires. A large scale acquisition of genomic data has been recently undertaken with the genome of
Acyrthosiphon pisum (reference gene set) and EST data from three other species: Myzus persicae, Aphis goss...
In 2009, the genome of the pea aphid (Acyrthosiphon pisum) was sequenced and partially annotated. This means that the scientific community has now access to the genetic material of aphids that are serious pests of plants. The description of an aphid genome is a first step to go deeper in the understanding of the biology of these insects. In this ar...
For poikilotherm animals such as insects, extreme temperatures can be a severe issue in continental regions. Aphids, which reproduce in spring and summer by viviparity, are prone to death in hard winter conditions. These species exhibit reproductive plasticity adapted to winter by producing oviparous females in autumn, which lay overwintering eggs....
AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source...
To study gene repertoires and their evolution within aphids, we compared the complete genome sequence of Acyrthosiphon pisum (reference gene set) and expressed sequence tag (EST) data from three other species: Myzus persicae, Aphis gossypii and Toxoptera citricida. We assembled ESTs, predicted coding sequences, and identified potential pairs of ort...
Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetab...
Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetab...
Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetab...
Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetab...
Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetab...
