P. Rosenkranz, P. Aumeier, and B. Ziegelmann, Biology and control of Varroa destructor, J Invertebr Pathol, vol.103, pp.96-119, 2010.

L. Conte, Y. Ellis, M. Ritter, and W. , Varroa mites and honey bee health: can Varroa explain part of the colony losses?, Apidologie, vol.41, pp.353-63, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00892103

I. Fries, S. Camazine, and J. Sneyd, Population-dynamics of Varroa-Jacobsoni -a model and a review, Bee World, vol.75, issue.1, pp.5-28, 1994.

F. Nazzi, L. Conte, and Y. , Ecology of Varroa destructor, the major ectoparasite of the western honey bee, Apis mellifera, Annu Rev Entomol, vol.61, pp.417-449, 2016.

Y. P. Chen and R. Siede, Honey bee viruses, Adv Virus Res, vol.70, pp.33-80, 2007.

J. R. De-miranda and I. Fries, Venereal and vertical transmission of deformed wing virus in honeybees (Apis mellifera L.), J Invertebr Pathol, vol.98, issue.2, pp.184-193, 2008.

J. R. De-miranda, L. Gauthier, M. Ribiere, and Y. P. Chen, Honey bee colony health: challenges and sustainable solutions, Honey bee colony health: challenges and sustainable solutions, pp.71-102, 2012.

F. Nazzi, S. P. Brown, D. Annoscia, D. Piccolo, F. et al., Synergistic parasitepathogen interactions mediated by host immunity can drive the collapse of honeybee colonies, PLoS Pathog, vol.8, issue.6, p.1002735, 2012.

R. D. Kuster, H. F. Boncristiani, and O. Rueppell, Immunogene and viral transcript dynamics during parasitic Varroa destructor mite infection of developing honey bee (Apis mellifera) pupae, J Exp Biol, vol.217, issue.10, pp.1710-1718, 2014.

A. Gregorc, J. D. Evans, M. Scharf, and J. D. Ellis, Gene expression in honey bee (Apis mellifera) larvae exposed to pesticides and Varroa mites (Varroa destructor), J Insect Physiol, vol.58, issue.8, pp.1042-1051, 2012.
DOI : 10.1016/j.jinsphys.2012.03.015

P. J. Elzen, J. R. Baxter, M. Spivak, and W. T. Wilson, Control of Varroa jacobsoni oud. Resistant to fluvalinate and amitraz using coumaphos, Apidologie, vol.31, issue.3, pp.437-478, 2000.
URL : https://hal.archives-ouvertes.fr/hal-00891728

J. Gonzalez-cabrera, S. Rodriguez-vargas, T. G. Davies, L. M. Field, D. Schmehl et al., Novel mutations in the voltage-gated sodium channel of pyrethroid-resistant Varroa destructor populations from the southeastern USA, PLoS One, vol.11, issue.5, p.155332, 2016.

M. Spreafico, F. R. Eordegh, I. Bernardinelli, and M. Colombo, First detection of strains of Varroa destructor resistant to coumaphos. Results of laboratory tests and field trials, Apidologie, vol.32, issue.1, pp.49-55, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00891760

S. R. Cornman, M. C. Schatz, S. J. Johnston, Y. P. Chen, J. Pettis et al., Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera, BMC Genomics, vol.11, p.602, 2010.

E. M. Campbell, G. E. Budge, M. Watkins, and A. S. Bowman, Transcriptome analysis of the synganglion from the honey bee mite, Varroa destructor and RNAi knockdown of neural peptide targets, Insect Biochem Mol Biol, vol.70, pp.116-142, 2016.

N. Eliash, N. K. Singh, S. Thangarajan, N. Sela, D. Leshkowitz et al., Chemosensing of honeybee parasite, Varroa destructor: Transcriptomic analysis, Sci Rep, vol.7, p.13091, 2017.

A. Mcafee, Q. Chan, J. Evans, and L. J. Foster, A Varroa destructor protein atlas reveals molecular underpinnings of developmental transitions and sexual differentiation, Mol Cell Proteomics, vol.16, pp.2125-2162, 2017.

G. K. Andino, M. Gribskov, D. L. Anderson, J. D. Evans, and G. J. Hunt, Differential gene expression in Varroa jacobsoni mites following a host shift to European honey bees (Apis mellifera), BMC Genomics, vol.17, issue.1, p.926, 2016.

A. R. Cabrera, P. D. Shirk, A. J. Duehl, K. V. Donohue, C. M. Grozinger et al., Genomic organization and reproductive regulation of a large lipid transfer protein in the varroa mite, Varroa destructor (Anderson & Trueman), Insect Mol Biol, vol.22, issue.5, pp.505-527, 2013.

A. R. Cabrera, P. D. Shirk, J. D. Evans, K. Hung, J. Sims et al., Three Halloween genes from the Varroa mite, Varroa destructor (Anderson & Trueman) and their expression during reproduction, Insect Mol Biol, vol.24, issue.3, pp.277-92, 2015.

A. R. Cabrera-cordon, P. D. Shirk, A. J. Duehl, J. D. Evans, and P. E. Teal, Variable induction of vitellogenin genes in the varroa mite, Varroa destructor (Anderson & Trueman), by the honeybee, Apis mellifera L, host and its environment, Insect Mol Biol, vol.22, issue.1, pp.88-103, 2013.

A. R. Cabrera, P. D. Shirk, P. E. Teal, C. M. Grozinger, and J. D. Evans, Examining the role of foraging and malvolio in host-finding behavior in the honey bee parasite, Varroa destructor (Anderson & Trueman), Arch Insect Biochem Physiol, vol.85, issue.2, pp.61-75, 2014.

M. A. Hoy, R. M. Waterhouse, K. Wu, A. S. Estep, P. Ioannidis et al., Genome sequencing of the phytoseiid predatory mite Metaseiulus occidentalis reveals completely atomized Hox genes and superdynamic intron evolution, Genome Biol Evol, vol.8, issue.6, pp.1762-75, 2016.

F. A. Simao, R. M. Waterhouse, P. Ioannidis, E. V. Kriventseva, and E. M. Zdobnov, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, vol.31, pp.3210-3212, 2015.

A. R. Cabrera, K. V. Donohue, and R. M. Roe, Regulation of female reproduction in mites: a unifying model for the Acari, J Insect Physiol, vol.55, issue.12, pp.1079-90, 2009.

R. M. Roe, K. V. Donohue, S. Khalil, B. W. Bissinger, J. Zhu et al., Hormonal regulation of metamorphosis and reproduction in ticks, Biology of ticks, pp.416-448, 2014.

K. F. Rewitz, R. Rybczynski, J. T. Warren, and L. I. Gilbert, The Halloween genes code for cytochrome P450 enzymes mediating synthesis of the insect moulting hormone, Biochem Soc Trans, vol.34, issue.6, pp.1256-60, 2006.

M. Gulia-nuss, A. B. Nuss, J. M. Meyer, D. E. Sonenshine, R. M. Roe et al., Genomic insights into the Ixodes scapularis tick vector of Lyme disease, Nat Commun, vol.7, p.10507, 2016.

A. Garedew, E. Schmolz, and I. Lamprecht, The energy and nutritional demand of the parasitic life of the mite Varroa destructor, Apidologie, vol.35, pp.419-449, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00891839

F. Dittmann and J. Steiner, Intercellular connection between the lyrate organ and the growing oocyte in Varroa jacobsoni as revealed by Lucifer yellow dyecoupling, J Apic Res, vol.36, issue.3-4, pp.145-154, 1997.

J. Steiner, F. Dittmann, P. Rosenkranz, and W. Engels, The 1st gonocycle of the parasitic mite (Varroa-Jacobsoni) in relation to preimaginal development of its host, the honey-bee (Apis-Mellifera-Carnica), Invertebr Reprod Dev, vol.25, issue.3, pp.175-83, 1994.

N. C. Tewarson, Resorption of undigested proteins and their incorporation into the eggs of Varroa jacobsoni, Apidologie, vol.13, pp.95-101, 1982.

N. C. Tewarson, Immunocytochemical localization of host (Apis mellifera) proteins in growing oocytes of a hemophagous mite (Varroa jacobsoni) by the unlabeled antibody enzyme (PAP) method, Int J Invert Reprod, vol.5, pp.345-353, 1982.

N. C. Tewarson and W. Engels, Undigested uptake of non-host proteins by Varroa jacobsoni, J Apic Res, vol.21, pp.222-227, 1982.

C. Luo, E. M. Dewey, S. Sudo, J. Ewer, S. Y. Hsu et al., Bursicon, the insect cuticle-hardening hormone, is a heterodimeric cystine knot protein that activates G protein-coupled receptor LGR2, P Natl Acad Sci USA, vol.102, issue.8, pp.2820-2825, 2005.

B. T. Nganso, A. T. Fombong, A. A. Yusuf, C. Pirk, C. Stuhl et al., Hygienic and grooming behaviors in African and European honeybees-new damage categories in Varroa destructor, PLoS One, vol.12, issue.6, p.179329, 2017.

K. Mandilaras, T. Pathmanathan, and F. Missirlis, Iron absorption in Drosophila melanogaster, Nutrients, vol.5, issue.5, pp.1622-1669, 2013.

G. R. Braz, H. S. Coelho, H. Masuda, and P. L. Oliveira, A missing metabolic pathway in the cattle tick Boophilus microplus, Curr Biol, vol.9, issue.13, pp.703-709, 1999.

G. L. Zhou, P. Kohlhepp, D. Geiser, M. Frasquillo, L. Vazquez-moreno et al., Fate of blood meal iron in mosquitoes, J Insect Physiol, vol.53, issue.11, pp.1169-78, 2007.

C. Garrido, P. Rosenkranz, M. Sturmer, R. Rubsam, and J. Buning, Toluidine blue staining as a rapid measure for initiation of oocyte growth and fertility in Varroa jacobsoni oud, Apidologie, vol.31, issue.5, pp.559-66, 2000.
URL : https://hal.archives-ouvertes.fr/hal-00891740

S. A. Blatch, K. W. Meyer, and J. F. Harrison, Effects of dietary folic acid level and symbiotic folate production on fitness and development in the fruit fly Drosophila melanogaster, Fly, vol.4, issue.4, pp.312-321, 2010.

X. Dong, S. D. Armstrong, D. Xia, B. L. Makepeace, A. C. Darby et al., Draft genome of the honey bee ectoparasitic mite, Tropilaelaps mercedesae, is shaped by the parasitic life history, Gigascience, vol.6, issue.3, pp.1-17, 2017.

P. Georgiev, S. Chlamydas, and A. Akhtar, Drosophila dosage compensation males are from Mars, females are from Venus, Fly, vol.5, issue.2, pp.147-54, 2011.

C. I. Rodriguez and C. L. Stewart, Disruption of the ubiquitin ligase HERC4 causes defects in spermatozoon maturation and impaired fertility, Dev Biol, vol.312, issue.2, pp.501-509, 2007.

E. Bonilla and E. Y. Xu, Identification and characterization of novel mammalian spermatogenic genes conserved from fly to human, Mol Hum Reprod, vol.14, issue.3, pp.137-179, 2008.

L. Ge, T. Xia, B. Huang, Q. Song, H. Zhang et al., Suppressing male spermatogenesis-associated protein 5-like gene expression reduces vitellogenin gene expression and fecundity in Nilaparvata lugens, Sci Rep, vol.6, p.28111, 2016.

E. Frey, R. Odemer, T. Blum, and P. Rosenkranz, Activation and interruption of the reproduction of Varroa destructor is triggered by host signals

, J Invertebr Pathol, vol.113, issue.1, pp.56-62, 2013.

D. R. Nassel and M. J. Williams, Cholecystokinin-like peptide (DSK) in Drosophila Not Only for Satiety Signaling, Front Endocrinol, vol.5, p.219, 2014.

A. R. Cabrera, P. D. Shirk, and P. Teal, A feeding protocol for delivery of agents to assess development in Varroa mites, PLoS One, vol.12, issue.4, p.176097, 2017.

L. I. De-guzman, K. Khongphinitbunjong, T. E. Rinderer, M. R. Tarver, and A. M. Frake, A laboratory technique to study the effects of Varroa destructor and viruses on developing worker honey bees, J Apic Res, vol.52, pp.262-265, 2013.

F. Nazzi and N. Milani, A technique for reproduction of Varroa-Jacobsoni oud under laboratory conditions, Apidologie, vol.25, issue.6, pp.579-84, 1994.
URL : https://hal.archives-ouvertes.fr/hal-00891234

J. Tabart, M. E. Colin, J. L. Carayon, N. Tene, B. Payre et al., Artificial feeding of Varroa destructor through a chitosan membrane: a tool for studying the host-microparasite relationship, Exp App Acarol, vol.61, issue.1, pp.107-125, 2013.

T. Erban, K. Harant, M. Hubalek, P. Vitamvas, M. Kamler et al., In-depth proteomic analysis of Varroa destructor: detection of DWV-complex, ABPVV, dMLV and honeybee proteins in the mite, Sci Rep, vol.5, p.13907, 2015.

D. Nascimento, A. M. Cuvillier-hot, V. Barchuk, A. R. Simoes, Z. L. Hartfelder et al., Honey bee (Apis mellifera) transferrin-gene structure and the role of ecdysteroids in the developmental regulation of its expression, Insect Biochem Mol Biol, vol.34, issue.5, pp.415-439, 2004.

J. R. Martins, F. M. Nunes, A. S. Cristino, Z. L. Simoes, and M. M. Bitondi, The four hexamerin genes in the honey bee: structure, molecular evolution and function deduced from expression patterns in queens, workers and drones, BMC Mol Biol, vol.11, p.23, 2010.

Q. W. Chan, C. G. Howes, and L. J. Foster, Quantitative comparison of caste differences in honeybee hemolymph, Mol Cell Proteomics, vol.5, issue.12, pp.2252-62, 2006.

N. Agrawal, P. Dasaradhi, A. Mohmmed, P. Malhotra, R. K. Bhatnagar et al., RNA interference: biology, mechanism, and applications, Microbiol Mol Biol Rrv, vol.67, issue.4, pp.657-85, 2003.

E. Check, RNA interference -hitting the on switch, Nature, vol.448, issue.7156, pp.855-863, 2007.

D. J. Obbard, K. Gordon, A. H. Buck, and F. M. Jiggins, The evolution of RNAi as a defence against viruses and transposable elements, Philos T R Soc B, vol.364, pp.99-115, 1513.

R. A. Schwenke, B. P. Lazzaro, and M. F. Wolfner, Reproduction-immunity trade-offs in insects, Annu Rev Entomol, vol.61, pp.239-56, 2016.

J. Ribeiro, I. Martin-martin, B. Arca, and E. Calvo, A deep insight into the sialome of male and female Aedes aegypti mosquitoes, PLoS One, vol.11, issue.3, p.151400, 2016.

J. G. Valenzuela, I. Francischetti, V. M. Pham, M. K. Garfield, T. N. Mather et al., Exploring the sialome of the tick Ixodes scapularis, J Exp Biol, vol.205, issue.18, pp.2843-64, 2002.

H. Breer, Arthropod brain its evolution, development, sructure and functions, pp.415-452, 1987.

R. Rytz, V. Croset, and R. Benton, Ionotropic receptors (IRs): chemosensory ionotropic glutamate receptors in Drosophila and beyond, Insect Biochem Mol Biol, vol.43, issue.9, pp.888-97, 2013.

N. Eliash, N. K. Singh, Y. Kamer, G. R. Pinnelli, and E. Plettner, Can we disrupt the sensing of honey bees by the bee parasite Varroa destructor?, PLoS One, vol.9, issue.12, p.106889, 2014.

J. Caers, H. Verlinden, S. Zels, H. P. Vandersmissen, K. Vuerinckx et al., More than two decades of research on insect neuropeptide GPCRs: an overview, Frontiers Endocrinol, vol.3, issue.151, pp.1-30, 2012.

S. Terhzaz, N. M. Teets, P. Cabrero, L. Henderson, M. G. Ritchie et al., Insect capa neuropeptides impact desiccation and cold tolerance, P Natl Acad Sci USA, vol.112, issue.9, pp.2882-2889, 2015.

B. Kraus and H. Velthuis, High humidity in the honey bee (Apis mellifera L) brood nest limits reproduction of the parasitic mite Varroa jacobsoni oud, Naturwissenschaften, vol.84, issue.5, pp.217-225, 1997.

S. Andrews, FastQC: a quality control tool for high throughput sequence data, 2010.

C. Cabau, F. Escudie, A. Djari, Y. Guiguen, J. Bobe et al., Compacting and correcting trinity and oases RNA-Seq de novo assemblies, Peer J, vol.5, p.2988, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01506620

M. H. Schulz, D. R. Zerbino, M. Vingron, and E. Birney, Oases: robust de novo RNAseq assembly across the dynamic range of expression levels, Bioinformatics, vol.28, issue.8, pp.1086-92, 2012.

K. Lagesen, P. Hallin, E. A. Rodland, H. H. Staerfeldt, T. Rognes et al., RNAmmer: consistent and rapid annotation of ribosomal RNA genes, Nucleic Acids Res, vol.35, issue.9, pp.3100-3108, 2007.

A. Smit, R. Hubley, P. Green, and . Repeatmasker, , 2013.

P. Jones, D. Binns, H. Y. Chang, M. Fraser, W. Li et al., InterProScan 5: genome-scale protein function classification, Bioinformatics, vol.30, issue.9, pp.1236-1276, 2014.

H. Li and R. Durbin, Fast and accurate short read alignment with burrowswheeler transform, Bioinformatics, vol.25, issue.14, pp.1754-60, 2009.

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan et al., Genome project data processing S. The sequence alignment/ map format and SAMtools, Bioinformatics, vol.25, issue.16, pp.2078-2087, 2009.

A. Mckenna, M. Hanna, E. Banks, A. Sivachenko, K. Cibulskis et al., The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, vol.20, issue.9, pp.1297-303, 2010.

J. Mariette, C. Noirot, I. Nabihoudine, P. Bardou, C. Hoede et al., RNAbrowse: RNA-Seq de novo assembly results browser, PLoS One, vol.9, issue.5, p.96821, 2014.

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. Hocberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J Royal Stat Soc, vol.57, pp.289-300, 1995.

R. Kolde, Pheatmap: pretty Heatmaps, 2015.

H. Wickham, ggplot2: elegant graphics for data analysis, 2009.

R. C. Ghosh, B. V. Ball, M. M. Willcocks, and M. J. Carter, The nucleotide sequence of sacbrood virus of the honey bee: an insect picorna-like virus, J Gen Virol, vol.80, issue.6, pp.1541-1550, 1999.

J. R. Ongus, D. Peters, J. M. Bonmatin, E. Bengsch, J. M. Vlak et al., Complete sequence of a picorna-like virus of the genus Iflavirus replicating in the mite Varroa destructor, J Gen Virol, vol.85, issue.12, pp.3747-55, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00113080

S. Levin, N. Sela, and N. Chejanovsky, Two novel viruses associated with the Apis mellifera pathogenic mite Varroa destructor, Sci Rep, vol.6, p.37710, 2016.

G. Lanzi, J. R. De-miranda, M. B. Boniotti, C. E. Cameron, A. Lavazza et al., Molecular and biological characterization of deformed wing virus of honeybees (Apis mellifera L.), J Virol, vol.80, issue.10, pp.4998-5009, 2006.

N. Leat, B. Ball, V. Govan, and S. Davison, Analysis of the complete genome sequence of black queen-cell virus, a picorna-like virus of honey bees, J Gen Virol, vol.81, issue.8, pp.2111-2120, 2000.

V. A. Govan, N. Leat, M. Allsopp, and S. Davison, Analysis of the complete genome sequence of acute bee paralysis virus shows that it belongs to the novel group of insect-infecting RNA viruses, Virology, vol.277, issue.2, pp.457-63, 2000.

J. R. De-miranda, M. Drebot, S. Tyler, M. Shen, C. E. Cameron et al., Complete nucleotide sequence of Kashmir bee virus and comparison with acute bee paralysis virus, J Gen Virol, vol.85, issue.8, pp.2263-70, 2004.

V. Olivier, P. Blanchard, S. Chaouch, P. Lallemand, F. Schurr et al., Molecular characterisation and phylogenetic analysis of chronic bee paralysis virus, a honey bee virus, Virus Res, vol.132, issue.1-2, pp.59-68, 2008.
URL : https://hal.archives-ouvertes.fr/pasteur-00364263

C. Runckel, M. L. Flenniken, J. C. Engel, J. G. Ruby, D. Ganem et al., Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, Nosema, and Crithidia, PLoS One, vol.6, issue.6, p.20656, 2011.

F. Granberg, M. Vicente-rubiano, C. Rubio-guerri, O. E. Karlsson, D. Kukielka et al., Metagenomic detection of viral pathogens in Spanish honeybees: co-infection by aphid lethal paralysis, Israel acute paralysis and Lake Sinai viruses, PLoS One, vol.8, issue.2, p.57459, 2013.

J. S. Moon, L. L. Domier, N. K. Mccoppin, D. 'arcy, C. J. et al., Nucleotide sequence analysis shows that Rhopalosiphum padi virus is a member of a novel group of insect-infecting RNA viruses, Virology, vol.243, issue.1, pp.54-65, 1998.

J. R. De-miranda, R. S. Cornman, J. D. Evans, E. Semberg, N. Haddad et al., Genome characterization, prevalence and distribution of a maculalike virus from Apis mellifera and Varroa destructor, Viruses, vol.7, issue.7, pp.3586-602, 2015.

E. Maori, S. Lavi, R. Mozes-koch, Y. Gantman, Y. Peretz et al., Isolation and characterization of Israeli acute paralysis virus, a dicistrovirus affecting honeybees in Israel: evidence for diversity due to intra-and inter-species recombination, J Gen Virol, vol.88, issue.12, pp.3428-3466, 2007.

J. R. De-miranda, B. Dainat, B. Locke, G. Cordoni, H. Berthoud et al., Genetic characterization of slow bee paralysis virus of the honeybee (Apis mellifera L.), J Gen Virol, vol.91, issue.10, pp.2524-2554, 2010.

J. Ravoet, D. Smet, L. Wenseleers, T. De-graaf, and D. C. , Genome sequence heterogeneity of Lake Sinai virus found in honey bees and Orf1/RdRP-based polymorphisms in a single host, Virus Res, vol.201, pp.67-72, 2015.

A. Rau and C. Maugis-rabusseau, Transformation and model choice for RNA-seq co-expression analysis
URL : https://hal.archives-ouvertes.fr/hal-01971405

C. Biernacki, G. Celeux, and G. Govaert, Assessing a mixture model for clustering with the integrated completed likelihood, IEEE Trans Pattern Anal Mach Intell, vol.22, pp.719-744, 2000.

A. A. Rahnenfuhrer, J. Lengauer, and T. , Improved scoring of functional groups from gene expression data by decorrelating GO graph structure, Bioinformatics, vol.22, pp.1600-1607, 2006.