Interferons and viruses: an interplay between induction, signalling, antiviral responses and virus countermeasures, J Gen Virol, vol.89, pp.1-47, 2008. ,
DOI : 10.1099/vir.0.83391-0
URL : http://jgv.microbiologyresearch.org/deliver/fulltext/jgv/89/1/1.pdf?itemId=/content/journal/jgv/10.1099/vir.0.83391-0&mimeType=pdf&isFastTrackArticle=
Viral modulation of antigen presentation: manipulation of cellular targets in the ER and beyond, Immunol Rev, vol.207, pp.126-144, 2005. ,
The host restriction factor APOBEC3G and retroviral Vif protein coevolve due to ongoing genetic conflict, Cell Host Microbe, vol.11, pp.91-98, 2012. ,
RNA-based antiviral immunity, Nat Rev Immunol, vol.10, pp.632-644, 2010. ,
DOI : 10.1038/nri2824
Natural and experimental infection of Caenorhabditis nematodes by novel viruses related to nodaviruses, PLoS Biol, vol.9, p.1000586, 2011. ,
URL : https://hal.archives-ouvertes.fr/hal-00566941
Loss and retention of RNA interference in fungi and parasites, PLoS Pathog, vol.9, p.1003089, 2013. ,
Defense and counterdefense in the RNAi-based antiviral immune system in insects, Methods Mol Biol, vol.721, pp.3-22, 2011. ,
RNA interference functions as an antiviral immunity mechanism in mammals, Science, vol.342, pp.231-234, 2013. ,
Antiviral RNA interference in mammalian cells, Science, vol.342, pp.235-238, 2013. ,
Doublestranded RNA is produced by positive-strand RNA viruses and DNA viruses but not in detectable amounts by negative-strand RNA viruses, J Virol, vol.80, pp.5059-5064, 2006. ,
Mechanism of induction and suppression of antiviral immunity directed by virus-derived small RNAs in Drosophila, Cell Host Microbe, vol.4, pp.387-397, 2008. ,
Dicing of viral replication intermediates during silencing of latent Drosophila viruses, Proc Natl Acad Sci U S A, vol.106, pp.5270-5275, 2009. ,
Dicer-2 processes diverse viral RNA species, PLoS One, vol.8, p.55458, 2013. ,
Convergent evolution of argonaute-2 slicer antagonism in two distinct insect RNA viruses, PLoS Pathogens, vol.8, p.1002872, 2012. ,
Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs, Proc Natl Acad Sci U S A, vol.107, pp.1606-1611, 2010. ,
RNAi targeting of West Nile virus in mosquito midguts promotes virus diversification, PLoS Pathog, vol.5, p.1000502, 2009. ,
The DNA virus Invertebrate iridescent virus 6 is a target of the Drosophila RNAi machinery, Proc Natl Acad Sci U S A, vol.109, pp.3604-3613, 2012. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01379102
Small RNA profiling of Dengue virus-mosquito interactions implicates the PIWI RNA pathway in anti-viral defense, BMC Microbiol, vol.11, p.45, 2011. ,
Dicer-2-and Piwi-mediated RNA interference in Rift Valley fever virus-infected mosquito cells, J Virol, vol.87, pp.1631-1648, 2013. ,
Origins of alphavirus-derived small RNAs in mosquitoes, RNA Biol, vol.6, pp.387-391, 2009. ,
Alphavirus-derived small RNAs modulate pathogenesis in disease vector mosquitoes, Proc Natl Acad Sci U S A, vol.105, pp.19938-19943, 2008. ,
Comparison of dengue virus type 2-specific small RNAs from RNA interferencecompetent and-incompetent mosquito cells, PLoS Negl Trop Dis, vol.4, p.848, 2010. ,
Antiviral RNA interference responses induced by Semliki Forest virus infection of mosquito cells: characterization, origin, and frequency-dependent functions of virus-derived small interfering RNAs, J Virol, vol.85, pp.2907-2917, 2011. ,
R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway, Science, vol.301, pp.1921-1925, 2003. ,
Hierarchical rules for Argonaute loading in Drosophila, Mol Cell, vol.36, pp.445-456, 2009. ,
Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes, Cell, vol.123, pp.607-620, 2005. ,
Slicer function of Drosophila Argonautes and its involvement in RISC formation, Genes Dev, vol.19, pp.2837-2848, 2005. ,
Argonaute2 cleaves the anti-guide strand of siRNA during RISC activation, Cell, vol.123, pp.621-629, 2005. ,
The long and short of antiviral defense: small RNA-based immunity in insects, Curr Opin Virol, vol.7, pp.19-28, 2014. ,
Dual modes of RNA-silencing suppression by Flock House virus protein B2, Nat Struct Mol Biol, vol.12, pp.952-957, 2005. ,
Cucumber mosaic virus 2b protein subcellular targets and interactions: their significance to RNA silencing suppressor activity, Mol Plant Microbe Interact, vol.23, pp.294-303, 2010. ,
Characterization of silencing suppressor 2b of cucumber mosaic virus based on examination of its small RNA-binding abilities, Plant Cell Physiol, vol.48, pp.1050-1060, 2007. ,
The NS3 protein of Rice hoja blanca tenuivirus suppresses RNA silencing in plant and insect hosts by efficiently binding both siRNAs and miRNAs, Rna, vol.13, pp.1079-1089, 2007. ,
Molecular mechanism of RNA silencing suppression mediated by p19 protein of tombusviruses, EMBO J, vol.23, pp.876-884, 2004. ,
Induction and suppression of RNA silencing by an animal virus, Science, vol.296, pp.1319-1321, 2002. ,
Doublestranded RNA binding may be a general plant RNA viral strategy to suppress RNA silencing, J Virol, vol.80, pp.5747-5756, 2006. ,
A viral protein suppresses RNA silencing and binds silencing-generated, 21-to 25nucleotide double-stranded RNAs, EMBO J, vol.21, pp.3070-3080, 2002. ,
The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster, Genes Dev, vol.20, pp.2985-2995, 2006. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01954329
Argonaute quenching and global changes in Dicer homeostasis caused by a pathogenencoded GW repeat protein, Genes Dev, vol.24, pp.904-915, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00788111
The Polerovirus silencing suppressor P0 targets Argonaute proteins for degradation, Curr Biol, vol.17, pp.1609-1614, 2007. ,
The Polerovirus F box protein P0 targets ARGONAUTE1 to suppress RNA silencing, Curr Biol, vol.17, pp.1615-1621, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00187898
Polerovirus protein P0 prevents the assembly of small RNA-containing RISC complexes and leads to degradation of ARGONAUTE1, Plant J, vol.62, pp.463-472, 2010. ,
Cricket paralysis virus antagonizes Argonaute 2 to modulate antiviral defense in Drosophila, Nat Struct Mol Biol, vol.17, pp.547-554, 2010. ,
Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense, Genes Dev, vol.20, pp.3255-3268, 2006. ,
Viral protein inhibits RISC activity by argonaute binding through conserved WG/ GW motifs, PLoS Pathog, vol.6, p.1000996, 2010. ,
Rules of engagement: molecular insights from host-virus arms races, Annu Rev Genet, vol.46, pp.677-700, 2012. ,
Natural selection drives extremely rapid evolution in antiviral RNAi genes, Curr Biol, vol.16, pp.580-585, 2006. ,
Recurrent adaptation in RNA interference genes across the Drosophila phylogeny, Mol Biol Evol, vol.28, pp.1033-1042, 2011. ,
Recent and recurrent selective sweeps of the antiviral RNAi gene Argonaute-2 in three species of Drosophila, Mol Biol Evol, vol.28, pp.1043-1056, 2011. ,
The evolution of RNAi as a defence against viruses and transposable elements, Philosophical Transactions of the Royal Society of London Series B: Biological Sciences, vol.364, pp.99-115, 2009. ,
Probing the microRNA and small interfering RNA pathways with virus-encoded suppressors of RNA silencing, Plant Cell, vol.16, pp.1235-1250, 2004. ,
The NS3 protein of rice hoja blanca virus suppresses RNA silencing in mammalian cells, J Gen Virol, vol.89, pp.336-340, 2008. ,
Small RNA binding is a common strategy to suppress RNA silencing by several viral suppressors, Embo J, vol.25, pp.2768-2780, 2006. ,
Interferon antagonist proteins of influenza and vaccinia viruses are suppressors of RNA silencing, Proc Natl Acad Sci U S A, vol.101, pp.1350-1355, 2004. ,
Double-stranded RNA-binding proteins could suppress RNA interference-mediated antiviral defences, J Gen Virol, vol.84, pp.975-980, 2003. ,
Nora virus, a persistent virus in Drosophila, defines a new picorna-like virus family, J Gen Virol, vol.87, pp.3045-3051, 2006. ,
Drosophila Nora virus capsid proteins differ from those of other picorna-like viruses, Virus Res, vol.160, pp.51-58, 2011. ,
Redefining chronic viral infection, Cell, vol.138, pp.30-50, 2009. ,
Identification of microorganisms in partially fed female horn flies, Haematobia irritans, Parasitol Res, vol.111, pp.1391-1395, 2012. ,
Data mining cDNAs reveals three new single stranded RNA viruses in Nasonia (Hymenoptera: Pteromalidae), Insect Mol Biol, vol.19, pp.99-107, 2010. ,
PAML 4: phylogenetic analysis by maximum likelihood, Mol Biol Evol, vol.24, pp.1586-1591, 2007. ,
Unbiased estimates of the number of nucleotide substitutions when substitution rate varies among different sites, J Mol Evol, vol.38, pp.295-299, 1994. ,
Synonymous nucleotide divergence: what is ''saturation''?, Genetics, vol.142, pp.1033-1036, 1996. ,
Analysis of gene content in sweet potato chlorotic stunt virus RNA1 reveals the presence of the p22 RNA silencing suppressor in only a few isolates: implications for viral evolution and synergism, J Gen Virol, vol.89, pp.573-582, 2008. ,
RNA silencing suppression by a second copy of the P1 serine protease of Cucumber vein yellowing ipomovirus, a member of the family Potyviridae that lacks the cysteine protease HCPro, J Virol, vol.80, pp.10055-10063, 2006. ,
Protease activity, self interaction, and small interfering RNA binding of the silencing suppressor p1b from cucumber vein yellowing ipomovirus, J Virol, vol.82, pp.974-986, 2008. ,
In vitro analysis of RNA interference in Drosophila melanogaster, Methods, vol.30, pp.330-336, 2003. ,
Natural variation of the amino-terminal glutamine-rich domain in Drosophila argonaute2 is not associated with developmental defects, PLoS One, vol.5, p.15264, 2010. ,
Antiviral immunity in Drosophila requires systemic RNA interference spread, Nature, vol.458, pp.346-350, 2009. ,
DOI : 10.1038/nature07712
URL : https://hal.archives-ouvertes.fr/pasteur-00460853
Dual hostvirus arms races shape an essential housekeeping protein, PLoS Biol, vol.11, p.1001571, 2013. ,
DOI : 10.1371/journal.pbio.1001571
URL : https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.1001571&type=printable
Adaptive evolution of relish, a Drosophila NFkappaB/IkappaB protein, Genetics, vol.154, pp.1231-1238, 2000. ,
Variation in positive selection in termite GNBPs and Relish, Mol Biol Evol, vol.23, pp.317-326, 2006. ,
DOI : 10.1093/molbev/msj037
URL : https://academic.oup.com/mbe/article-pdf/23/2/317/13433630/msj037.pdf
Molecular evolution of daphnia immunity genes: polymorphism in a gram-negative binding protein gene and an alpha-2-macroglobulin gene, J Mol Evol, vol.59, pp.498-506, 2004. ,
Hostswitching by a vertically transmitted rhabdovirus in Drosophila, Biol Lett, vol.7, pp.747-750, 2011. ,
DOI : 10.1098/rsbl.2011.0160
URL : http://rsbl.royalsocietypublishing.org/content/7/5/747.full.pdf
Virus counterdefense: diverse strategies for evading the RNA-silencing immunity, Annu Rev Microbiol, vol.60, pp.503-531, 2006. ,
DOI : 10.1146/annurev.micro.60.080805.142205
URL : http://europepmc.org/articles/pmc2693410?pdf=render
ConDeTri-a content dependent read trimmer for Illumina data, PLoS One, vol.6, p.26314, 2011. ,
DOI : 10.1371/journal.pone.0026314
URL : https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0026314&type=printable
Fulllength transcriptome assembly from RNA-Seq data without a reference genome, Nat Biotechnol, vol.29, pp.644-652, 2011. ,
DOI : 10.1038/nbt.1883
URL : http://europepmc.org/articles/pmc3571712?pdf=render
Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads, Genome Res, vol.21, pp.936-939, 2011. ,
DOI : 10.1101/gr.111120.110
URL : http://genome.cshlp.org/content/21/6/936.full.pdf
The transcriptome of Spodoptera exigua larvae exposed to different types of microbes, Insect Biochem Mol Biol, vol.42, pp.557-570, 2012. ,
First Transcriptome and Digital Gene Expression Analysis in Neuroptera with an Emphasis on Chemoreception Genes in (Rambur), PLoS One, vol.8, p.67151, 2013. ,
Integrative approach reveals composition of endoparasitoid wasp venoms, PLoS One, vol.8, p.64125, 2013. ,
DOI : 10.1371/journal.pone.0064125
URL : https://doi.org/10.1371/journal.pone.0064125
MRBAYES: Bayesian inference of phylogenetic trees, Bioinformatics, vol.17, pp.754-755, 2001. ,
DOI : 10.1093/bioinformatics/17.8.754
URL : https://academic.oup.com/bioinformatics/article-pdf/17/8/754/8201380/170754.pdf
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst Biol, vol.59, pp.307-321, 2010. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00511784
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach, Mol Biol Evol, vol.18, pp.691-699, 2001. ,
Unbiased estimation of the rates of synonymous and nonsynonymous substitution, J Mol Evol, vol.36, pp.96-99, 1993. ,
Hsc70/Hsp90 chaperone machinery mediates ATP-dependent RISC loading of small RNA duplexes, Molecular Cell, vol.39, pp.292-299, 2010. ,
DOI : 10.1016/j.molcel.2010.05.015
URL : https://doi.org/10.1016/j.molcel.2010.05.015
Comparative analysis of argonaute-dependent small RNA pathways in Drosophila, Mol Cell, vol.32, pp.592-599, 2008. ,
Identification of viral suppressors of RNAi by a reporter assay in Drosophila S2 cell culture, Methods in Molecular Biology, vol.721, pp.201-213, 2011. ,
Infectious Sindbis virus transient expression vectors for studying antigen processing and presentation, Proceedings of the National Academy of Sciences of the United States of America, vol.89, pp.2679-2683, 1992. ,
Arbovirus-derived piRNAs exhibit a ping-pong signature in mosquito cells, PLoS One, vol.7, p.30861, 2012. ,
URL : https://hal.archives-ouvertes.fr/pasteur-01379361
The bacterial symbiont Wolbachia induces resistance to RNA viral infections in Drosophila melanogaster, PLoS Biol, vol.6, p.2, 2008. ,
dsRNA uptake in adult Drosophila, Methods in Molecular Biology, vol.721, pp.253-263, 2011. ,
URL : https://hal.archives-ouvertes.fr/pasteur-00591080
Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method, Methods, vol.25, pp.402-408, 2001. ,