A. M. Powers, A. C. Brault, Y. Shirako, E. G. Strauss, W. Kang et al., Evolutionary relationships and systematics of the alphaviruses, J Virol, vol.75, issue.21, pp.10118-10149, 2001.

G. J. Atkins, The pathogenesis of alphaviruses, ISRN Virology, vol.2013, pp.1-22, 2013.

A. D. Labeaud, T. Banda, J. Brichard, E. M. Muchiri, P. L. Mungai et al., High rates of o'nyong nyong and chikungunya virus transmission in coastal Kenya, PLoS Negl Trop Dis, vol.9, issue.2, p.3436, 2015.

B. Wct, K. E. Bennett, N. Gorrochotegui-escalante, C. V. Barillas-mury, I. Fernandezsalas et al., Flavivirus susceptibility in Aedes aegypti, Arch Med Res, vol.33, issue.4, pp.379-88, 2002.

J. L. Hardy, E. J. Houk, L. D. Kramer, and W. C. Reeves, Intrinsic factors affecting vector competence of mosquitoes for arboviruses, Annu Rev Entomol, vol.28, pp.229-62, 1983.
DOI : 10.1146/annurev.en.28.010183.001305

G. Carissimo, E. Pondeville, M. Mcfarlane, I. Dietrich, C. Mitri et al., Antiviral immunity of Anopheles gambiae is highly compartmentalized, with distinct roles for RNA interference and gut microbiota, Proc Natl Acad Sci, vol.112, issue.2, pp.176-85, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01103895

K. M. Keene, B. D. Foy, I. Sanchez-vargas, B. J. Beaty, C. D. Blair et al., RNA interference acts as a natural antiviral response to O'nyong-nyong virus (alphavirus; Togaviridae) infection of Anopheles gambiae, Proc Natl Acad Sci U S A, vol.101, issue.49, pp.17240-17245, 2004.

C. Sim, Y. S. Hong, D. L. Vanlandingham, B. W. Harker, G. K. Christophides et al., Modulation of Anopheles gambiae gene expression in response to o'nyong-nyong virus infection, Insect Mol Biol, vol.14, issue.5, pp.475-81, 2005.

C. Sim, Y. S. Hong, K. A. Tsetsarkin, D. L. Vanlandingham, S. Higgs et al., Anopheles gambiae heat shock protein cognate 70B impedes o'nyongnyong virus replication, BMC Genomics, vol.8, p.231, 2007.
DOI : 10.1186/1471-2164-8-231

URL : https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-8-231

J. Waldock, K. E. Olson, and G. K. Christophides, Anopheles gambiae antiviral immune response to systemic O'nyong-nyong infection, PLoS Negl Trop Dis, vol.6, issue.3, p.1565, 2012.
DOI : 10.1371/journal.pntd.0001565

URL : https://journals.plos.org/plosntds/article/file?id=10.1371/journal.pntd.0001565&type=printable

T. Yoshiga, T. Georgieva, B. C. Dunkov, N. Harizanova, K. Ralchev et al., Drosophila melanogaster transferrin. Cloning, deduced protein sequence, expression during the life cycle, gene localization and up-regulation on bacterial infection, Eur J Biochem, vol.260, issue.2, pp.414-434, 1999.
DOI : 10.1046/j.1432-1327.1999.00173.x

URL : https://febs.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1432-1327.1999.00173.x

F. Levy, P. Bulet, and L. Ehret-sabatier, Proteomic analysis of the systemic immune response of Drosophila, Mol Cell Proteomics, vol.3, issue.2, pp.156-66, 2004.

N. Buchon, N. A. Broderick, M. Poidevin, S. Pradervand, and B. Lemaitre, Drosophila intestinal response to bacterial infection: activation of host defense and stem cell proliferation, Cell Host Microbe, vol.5, issue.2, pp.200-211, 2009.

M. Karlikow, B. Goic, and M. C. Saleh, RNAi and antiviral defense in Drosophila: setting up a systemic immune response, Dev Comp Immunol, vol.42, issue.1, pp.85-92, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01954297

Y. Dong, R. Aguilar, Z. Xi, E. Warr, E. Mongin et al., Anopheles gambiae immune responses to human and rodent Plasmodium parasite species, PLoS Pathog, vol.2, issue.6, p.52, 2006.

I. Biryukova, T. Ye, and E. Levashina, Transcriptome-wide analysis of microRNA expression in the malaria mosquito Anopheles gambiae, BMC Genomics, vol.15, p.557, 2014.

F. Winter, S. Edaye, A. Huttenhofer, and C. Brunel, Anopheles gambiae miRNAs as actors of defence reaction against Plasmodium invasion, Nucleic Acids Res, vol.35, issue.20, pp.6953-62, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00530321

N. J. Dennison, O. J. Benmarzouk-hidalgo, and G. Dimopoulos, MicroRNA-regulation of Anopheles gambiae immunity to Plasmodium falciparum infection and midgut microbiota, Dev Comp Immunol, vol.49, issue.1, pp.170-178, 2015.

M. Ghildiyal and P. D. Zamore, Small silencing RNAs: an expanding universe, Nat Rev Genet, vol.10, issue.2, pp.94-108, 2009.

W. Filipowicz, S. N. Bhattacharyya, and N. Sonenberg, Mechanisms of posttranscriptional regulation by microRNAs: are the answers in sight?, Nat Rev Genet, vol.9, issue.2, pp.102-116, 2008.

W. Ritchie, S. Flamant, and J. E. Rasko, Predicting microRNA targets and functions: traps for the unwary, Nat Methods, vol.6, issue.6, pp.397-405, 2009.

A. Muniategui, J. Pey, F. J. Planes, and A. Rubio, Joint analysis of miRNA and mRNA expression data, Brief Bioinform, vol.14, issue.3, pp.263-78, 2013.

A. S. Flynt and E. C. Lai, Biological principles of microRNA-mediated regulation: shared themes amid diversity, Nat Rev Genet, vol.9, issue.11, pp.831-873, 2008.

D. Didiano and O. Hobert, Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions, Nat Struct Mol Biol, vol.13, issue.9, pp.849-51, 2006.

H. C. Martin, S. Wani, A. L. Steptoe, K. Krishnan, K. Nones et al., Imperfect centered miRNA binding sites are common and can mediate repression of target mRNAs, Genome Biol, vol.15, issue.3, p.51, 2014.

G. Carissimo, K. Eiglmeier, J. Reveillaud, I. Holm, M. Diallo et al., Identification and characterization of two novel RNA viruses from Anopheles gambiae species complex mosquitoes, PLoS One, vol.11, issue.5, p.153881, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01316516

J. R. Fauver, N. D. Grubaugh, B. J. Krajacich, J. Weger-lucarelli, S. M. Lakin et al., West African Anopheles gambiae mosquitoes harbor a taxonomically diverse virome including new insect-specific flaviviruses, mononegaviruses, and totiviruses, Virology, vol.498, pp.288-99, 2016.

A. Colmant, K. Etebari, C. E. Webb, S. A. Ritchie, C. C. Jansen et al., Discovery of new orbiviruses and totivirus from Anopheles mosquitoes in eastern Australia, Arch Virol, vol.162, issue.11, pp.3529-3563, 2017.

N. Minkeu, F. Vernick, and K. D. , A systematic review of the natural Virome of Anopheles mosquitoes, Viruses, vol.10, issue.5, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01830169

X. Ren, G. L. Hughes, G. Niu, Y. Suzuki, and J. L. Rasgon, Anopheles gambiae densovirus (AgDNV) has negligible effects on adult survival and transcriptome of its mosquito host, PeerJ, vol.2, p.584, 2014.

T. K. Barik, Y. Suzuki, and J. L. Rasgon, Factors influencing infection and transmission of Anopheles gambiae densovirus (AgDNV) in mosquitoes, PeerJ, vol.4, p.2691, 2016.

N. Buchon, N. A. Broderick, and B. Lemaitre, Gut homeostasis in a microbial world: insights from Drosophila melanogaster, Nat Rev Microbiol, vol.11, issue.9, pp.615-641, 2013.

Z. Xi, J. L. Ramirez, and G. Dimopoulos, The Aedes aegypti toll pathway controls dengue virus infection, PLoS Pathog, vol.4, issue.7, p.1000098, 2008.

T. M. Colpitts, J. Cox, D. L. Vanlandingham, F. M. Feitosa, G. Cheng et al., Alterations in the Aedes aegypti transcriptome during infection with West Nile, dengue and yellow fever viruses, PLoS Pathog, vol.7, issue.9, p.1002189, 2011.

S. Dong, S. K. Behura, and A. Franz, The midgut transcriptome of Aedes aegypti fed with saline or protein meals containing chikungunya virus reveals genes potentially involved in viral midgut escape, BMC Genomics, vol.18, issue.1, p.382, 2017.

M. Bonizzoni, W. A. Dunn, C. L. Campbell, K. E. Olson, O. Marinotti et al., Complex modulation of the Aedes aegypti transcriptome in response to dengue virus infection, PLoS One, vol.7, issue.11, p.50512, 2012.

M. A. Saldana, K. Etebari, C. E. Hart, S. G. Widen, T. G. Wood et al., Zika virus alters the microRNA expression profile and elicits an RNAi response in Aedes aegypti mosquitoes, PLoS Negl Trop Dis, vol.11, issue.7, p.5760, 2017.

K. Etebari, S. Hegde, M. A. Saldana, S. G. Widen, T. G. Wood et al., Global transcriptome analysis of Aedes aegypti mosquitoes in response to Zika virus infection, mSphere, vol.2, issue.6, 2017.

R. H. Baxter, S. Steinert, Y. Chelliah, G. Volohonsky, E. A. Levashina et al., A heterodimeric complex of the LRR proteins LRIM1 and APL1C regulates complement-like immunity in Anopheles gambiae, Proc Natl Acad Sci, vol.107, issue.39, pp.16817-16839, 2010.

M. Povelones, R. M. Waterhouse, F. C. Kafatos, and G. K. Christophides, Leucine-rich repeat protein complex activates mosquito complement in defense against Plasmodium parasites, Science, vol.324, issue.5924, pp.258-61, 2009.

C. Mitri, E. Bischoff, E. Takashima, M. Williams, K. Eiglmeier et al., An evolutionbased screen for genetic differentiation between Anopheles sister taxa enriches for detection of functional immune factors, PLoS Pathog, vol.11, issue.12, p.1005306, 2015.
URL : https://hal.archives-ouvertes.fr/inserm-01247471

X. Zhang, C. An, K. Sprigg, and K. Michel, CLIPB8 is part of the prophenoloxidase activation system in Anopheles gambiae mosquitoes, Insect Biochem Mol Biol, vol.71, pp.106-121, 2016.

S. M. Paskewitz, O. Andreev, and L. Shi, Gene silencing of serine proteases affects melanization of Sephadex beads in Anopheles gambiae, Insect Biochem Mol Biol, vol.36, issue.9, pp.701-712, 2006.

J. Volz, H. M. Muller, A. Zdanowicz, F. C. Kafatos, and M. A. Osta, A genetic module regulates the melanization response of Anopheles to Plasmodium, Cell Microbiol, vol.8, issue.9, pp.1392-405, 2006.

M. Varjak, K. Maringer, M. Watson, V. B. Sreenu, A. C. Fredericks et al., Aedes aegypti Piwi4 is a noncanonical PIWI protein involved in antiviral responses, mSphere, vol.2, issue.3, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01573771

J. Shrinet, S. Jain, J. Jain, R. K. Bhatnagar, and S. Sunil, Next generation sequencing reveals regulation of distinct Aedes microRNAs during chikungunya virus development, PLoS Negl Trop Dis, vol.8, issue.1, p.2616, 2014.

H. Yan, Y. Zhou, Y. Liu, Y. Deng, and X. Chen, miR-252 of the Asian tiger mosquito Aedes albopictus regulates dengue virus replication by suppressing the expression of the dengue virus envelope protein, J Med Virol, vol.86, issue.8, pp.1428-1464, 2014.

A. Slonchak, M. Hussain, S. Torres, S. Asgari, and A. A. Khromykh, Expression of mosquito microRNA Aae-miR-2940-5p is downregulated in response to West Nile virus infection to restrict viral replication, J Virol, vol.88, issue.15, pp.8457-67, 2014.

R. L. Skalsky, D. L. Vanlandingham, F. Scholle, S. Higgs, and B. R. Cullen, Identification of microRNAs expressed in two mosquito vectors, Aedes albopictus and Culex quinquefasciatus, BMC Genomics, vol.11, p.119, 2010.

M. Hussain, S. Torres, E. Schnettler, A. Funk, A. Grundhoff et al., West Nile virus encodes a microRNA-like small RNA in the 3? untranslated region which up-regulates GATA4 mRNA and facilitates virus replication in mosquito cells, Nucleic Acids Res, vol.40, issue.5, pp.2210-2233, 2012.

M. Varjak, C. L. Donald, T. J. Mottram, V. B. Sreenu, A. Merits et al., Characterization of the Zika virus induced small RNA response in Aedes aegypti cells, PLoS Negl Trop Dis, vol.11, issue.10, p.6010, 2017.

C. Harris, L. Lambrechts, F. Rousset, L. Abate, S. E. Nsango et al., Polymorphisms in Anopheles gambiae immune genes associated with natural resistance to Plasmodium falciparum, PLoS Pathog, vol.6, issue.9, p.1001112, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-02011022

I. Holm, C. Lavazec, T. Garnier, C. Mitri, M. M. Riehle et al., Diverged alleles of the Anopheles gambiae leucine-rich repeat gene APL1A display distinct protective profiles against Plasmodium falciparum, PLoS One, vol.7, issue.12, p.52684, 2012.
URL : https://hal.archives-ouvertes.fr/pasteur-02008328

H. M. Muller, G. Dimopoulos, C. Blass, and F. C. Kafatos, A hemocyte-like cell line established from the malaria vector Anopheles gambiae expresses six prophenoloxidase genes, J Biol Chem, vol.274, issue.17, pp.11727-11762, 1999.

M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, vol.17, 2011.

H. Li, Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM, ARXIV, 2013.

S. Anders, P. T. Pyl, and W. Huber, HTSeq-a Python framework to work with highthroughput sequencing data, Bioinformatics, vol.31, issue.2, pp.166-175, 2015.

, R: A language and environment for statistical computing

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, issue.12, p.550, 2014.

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate-a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B-Methodological, vol.57, issue.1, pp.289-300, 1995.

A. Alexa and J. Rahnenfuhrer, topGO: enrichment analysis for gene ontology. R package version, p.2300, 2016.

A. Kozomara, S. Griffiths-jones, and . Mirbase, annotating high confidence microRNAs using deep sequencing data, Nucleic Acids Res, vol.42, pp.68-73, 2014.

L. Castellano, E. Rizzi, J. Krell, D. Cristina, M. Galizi et al., The germline of the malaria mosquito produces abundant miRNAs, endo-siRNAs, piRNAs and 29-nt small RNAs, BMC Genomics, vol.16, p.100, 2015.

A. R. Quinlan and I. M. Hall, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, vol.26, issue.6, pp.841-843, 2010.

S. D. Mackowiak, Identification of novel and known miRNAs in deepsequencing data with miRDeep2, Curr Protoc Bioinformatics, vol.12, p.10

A. Stark, J. Brennecke, R. B. Russell, and S. M. Cohen, Identification of Drosophila MicroRNA targets, PLoS Biol, vol.1, issue.3, p.60, 2003.