P. Buchner, Symbiosis in animals which suck plant juices In Endosymbiosis of Animals with Plant Microorganisms, pp.210-432

A. Douglas, The microbial dimension in insect nutritional ecology, Functional Ecology, vol.395, issue.1, pp.38-47, 2009.
DOI : 10.1111/j.1365-2435.2008.01442.x

P. Baumann, N. Moran, L. Baumann, and M. Dworkin, Bacteriocyte-associated endosymbionts of insects, The Prokaryotes, pp.1-55, 2000.

P. Baumann, BIOLOGY OF BACTERIOCYTE-ASSOCIATED ENDOSYMBIONTS OF PLANT SAP-SUCKING INSECTS, Annual Review of Microbiology, vol.59, issue.1, pp.155-189, 2005.
DOI : 10.1146/annurev.micro.59.030804.121041

H. Ziegler, D. Zimmermann, J. Milburn, D. Zimmermann, and J. Milburn, Nature of Substances in Phloem: Nature of Transported Substances In Transport in Plants I -Phloem Transport, pp.59-100

I. Liadouze, G. Febvay, J. Guillaud, and G. Bonnot, Metabolic fate of energetic amino acids in the aposymbiotic pea aphid Acyrthosiphon pisum (Harris) (Homoptera: Aphididae), Symbiosis, vol.21, pp.115-127, 1996.

G. Febvay, Y. Rahbe, M. Rynkiewicz, J. Guillaud, and G. Bonnot, Fate of dietary sucrose and neosynthesis of amino acids in the pea aphid, Acyrthosiphon pisum, reared on different diets, J Exp Biol, vol.202, pp.2639-2652, 1999.
URL : https://hal.archives-ouvertes.fr/hal-00402190

N. Moran and P. Baumann, Bacterial endosymbionts in animals, Current Opinion in Microbiology, vol.3, issue.3, pp.270-275, 2000.
DOI : 10.1016/S1369-5274(00)00088-6

S. Shigenobu, H. Watanabe, M. Hattori, Y. Sakaki, and H. Ishikawa, Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp, APS. Nature, vol.407, pp.81-86, 2000.

L. Trionnaire, G. Hardie, J. Jaubert-possamai, S. Simon, J. Tagu et al., Shifting from clonal to sexual reproduction in aphids: physiological and developmental aspects, Biology of the Cell, vol.7, issue.8, pp.441-451, 2008.
DOI : 10.1042/BC20070135

A. Dixon and R. Kundu, Resource tracking in aphids: programmed reproductive strategies anticipate seasonal trends in habitat quality, Oecologia, vol.114, issue.1, pp.73-78, 1998.
DOI : 10.1007/s004420050422

T. Miura, C. Braendle, A. Shingleton, G. Sisk, S. Kambhampati et al., A comparison of parthenogenetic and sexual embryogenesis of the pea aphid Acyrthosiphon pisum (Hemiptera: Aphidoidea), J Exp Zool B Mol Dev Evol, vol.295, pp.59-81, 2003.

R. Koga, X. Meng, T. Tsuchida, and T. Fukatsu, Cellular mechanism for selective vertical transmission of an obligate insect symbiont at the bacteriocyte-embryo interface, Proceedings of the National Academy of Sciences, vol.109, issue.20, pp.1230-1237, 2012.
DOI : 10.1073/pnas.1119212109

R. Hinde, The control of the mycetome symbiotes of the aphids Brevicoryne brassicae, Myzus persicae, and Macrosiphum rosae, Journal of Insect Physiology, vol.17, issue.9, p.1791, 1971.
DOI : 10.1016/0022-1910(71)90076-X

R. Blackman, A. Minks, and P. Harrewijn, Reproduction, cytogenetics and development, In Aphids: Their Biology, Natural Enemies and Control, vol.2, issue.1987, pp.163-195

T. Wilkinson, T. Fukatsu, and H. Ishikawa, Transmission of symbiotic bacteria Buchnera to parthenogenetic embryos in the aphid Acyrthosiphon pisum (Hemiptera: Aphidoidea), Arthropod Structure & Development, vol.32, issue.2-3, pp.241-2451471, 2003.
DOI : 10.1016/S1467-8039(03)00036-7

S. Jayaraj, P. Ehrhardt, and H. Schmutterer, The effect of certain antibiotics on reproduction of the black bean aphid, Aphis fabae Scop., Annals of Applied Biology, vol.35, issue.1, pp.13-21, 1967.
DOI : 10.1007/BF00621635

T. Mittler, Dietary amino acid requirements of the aphid Myzus persicae affected by antibiotic uptake, J Nutr, vol.101, pp.1023-1028, 1971.

W. Prosser and A. Douglas, The aposymbiotic aphid: An analysis of chlortetracycline-treated pea aphid, Acyrthosiphon pisum, Journal of Insect Physiology, vol.37, issue.10, pp.713-719, 1991.
DOI : 10.1016/0022-1910(91)90104-8

T. Sasaki, H. Hayashi, and H. Ishikawa, Growth and reproduction of the symbiotic and aposymbiotic pea aphids, Acyrthosiphon pisum maintained on artificial diets, Journal of Insect Physiology, vol.37, issue.10, pp.749-756, 1991.
DOI : 10.1016/0022-1910(91)90109-D

A. Douglas, Requirement of pea aphids (Acyrthosiphon pisum) for their symbiotic bacteria, Entomologia Experimentalis et Applicata, vol.54, issue.2, pp.195-198, 1992.
DOI : 10.1111/j.1570-7458.1992.tb01643.x

I. Consortium, Genome sequence of the pea aphid Acyrthosiphon pisum, PLoS Biol, vol.8, issue.2, p.1000313, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00459970

I. Tamas, L. Klasson, B. Canbäck, A. Näslund, A. Eriksson et al., 50 Million Years of Genomic Stasis in Endosymbiotic Bacteria, Science, vol.296, issue.5577, pp.502376-2379, 2002.
DOI : 10.1126/science.1071278

R. Van-ham, J. Kamerbeek, C. Palacios, C. Rausell, F. Abascal et al., Reductive genome evolution in Buchnera aphidicola, Proceedings of the National Academy of Sciences, vol.100, issue.2, pp.581-586, 2003.
DOI : 10.1073/pnas.0235981100

V. Pérez-brocal, R. Gil, S. Ramos, A. Lamelas, M. Postigo et al., A Small Microbial Genome: The End of a Long Symbiotic Relationship?, Science, vol.314, issue.5797, pp.312-313, 2006.
DOI : 10.1126/science.1130441

A. Lamelas, M. Gosalbes, A. Moya, and A. Latorre, The genome of Buchnera aphidicola from the aphid Cinara tujafilina provides new clues about the evolutionary history of metabolic losses in bacterial endosymbionts, Appl Environ Microbiol, vol.13, pp.4464-4454, 2011.

N. Moran, H. Mclaughlin, and R. Sorek, The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria, Science, vol.323, issue.5912, pp.379-382, 2009.
DOI : 10.1126/science.1167140

A. Wilson, P. Ashton, F. Calevro, H. Charles, S. Colella et al., Genomic insight into the amino acid relations of the pea aphid, Acyrthosiphon pisum, with its symbiotic bacterium Buchnera aphidicola, Insect Molecular Biology, vol.68, pp.249-258, 2010.
DOI : 10.1111/j.1365-2583.2009.00942.x
URL : https://hal.archives-ouvertes.fr/hal-00539196

S. Shigenobu and A. Wilson, Genomic revelations of a mutualism: the pea aphid and its obligate bacterial symbiont, Cellular and Molecular Life Sciences, vol.3, issue.Suppl 2, pp.1297-1309, 2011.
DOI : 10.1007/s00018-011-0645-2

A. Hansen and N. Moran, Aphid genome expression reveals host-symbiont cooperation in the production of amino acids, Proceedings of the National Academy of Sciences, vol.108, issue.7, pp.2849-2854, 2011.
DOI : 10.1073/pnas.1013465108

D. Tagu, S. Dugravot, Y. Outreman, C. Rispe, J. Simon et al., The anatomy of an aphid genome: From sequence to biology, Comptes Rendus Biologies, vol.333, issue.6-7, pp.464-473, 2010.
DOI : 10.1016/j.crvi.2010.03.006
URL : https://hal.archives-ouvertes.fr/hal-00729626

N. Gerardo and A. Wilson, The power of paired genomes, Molecular Ecology, vol.19, issue.10, pp.2038-2040, 2011.
DOI : 10.1111/j.1365-294X.2011.05103.x

R. Gil, B. Sabater-munoz, A. Latorre, F. Silva, and A. Moya, Extreme genome reduction in Buchnera spp.: Toward the minimal genome needed for symbiotic life, Proceedings of the National Academy of Sciences, vol.99, issue.7, pp.4454-4458, 2002.
DOI : 10.1073/pnas.062067299

L. Brinza, J. Viñuelas, L. Cottret, F. Calevro, Y. Rahbé et al., Systemic analysis of the symbiotic function of Buchnera aphidicola, the primary endosymbiont of the pea aphid Acyrthosiphon pisum, Comptes Rendus Biologies, vol.332, issue.11, pp.1034-1049, 2009.
DOI : 10.1016/j.crvi.2009.09.007
URL : https://hal.archives-ouvertes.fr/hal-00539412

N. Moran, H. Dunbar, and J. Wilcox, Regulation of Transcription in a Reduced Bacterial Genome: Nutrient-Provisioning Genes of the Obligate Symbiont Buchnera aphidicola, Journal of Bacteriology, vol.187, issue.12, pp.4229-4237, 2005.
DOI : 10.1128/JB.187.12.4229-4237.2005

N. Reymond, F. Calevro, J. Viñuelas, N. Morin, Y. Rahbé et al., Different Levels of Transcriptional Regulation Due to Trophic Constraints in the Reduced Genome of Buchnera aphidicola APS, Applied and Environmental Microbiology, vol.72, issue.12, pp.7760-7766, 2006.
DOI : 10.1128/AEM.01118-06
URL : https://hal.archives-ouvertes.fr/hal-00391509

A. Wilson, H. Dunbar, G. Davis, W. Hunter, D. Stern et al., A dual-genome microarray for the pea aphid, Acyrthosiphon pisum, and its obligate bacterial symbiont. Buchnera aphidicola, BMC Genomics, vol.7, issue.1, p.50, 2006.
DOI : 10.1186/1471-2164-7-50

J. Viñuelas, F. Calevro, D. Remond, J. Bernillon, Y. Rahbé et al., Conservation of the links between gene transcription and chromosomal organization in the highly reduced genome of Buchnera aphidicola, BMC Genomics, vol.8, issue.1, p.143, 2007.
DOI : 10.1186/1471-2164-8-143

J. Viñuelas, G. Febvay, G. Duport, S. Colella, J. Fayard et al., Multimodal dynamic response of the Buchnera aphidicola pLeu plasmid to variations in leucine demand of its host, the pea aphid Acyrthosiphon pisum, Molecular Microbiology, vol.99, issue.5, pp.1271-1285, 2011.
DOI : 10.1111/j.1365-2958.2011.07760.x

A. Nakabachi, S. Shigenobu, N. Sakazume, T. Shiraki, Y. Hayashizaki et al., Transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, Buchnera, Proceedings of the National Academy of Sciences, vol.102, issue.15, pp.5477-5482, 2005.
DOI : 10.1073/pnas.0409034102

J. Brisson, G. Davis, and D. Stern, Common genome-wide patterns of transcript accumulation underlying the wing polyphenism and polymorphism in the pea aphid (Acyrthosiphon pisum), Evolution & Development, vol.42, issue.4, pp.338-346, 2007.
DOI : 10.1111/j.1525-142X.2007.00170.x

L. Trionnaire, G. Jaubert, S. Sabater-muñoz, B. Benedetto, A. Bonhomme et al., Seasonal photoperiodism regulates the expression of cuticular and signalling protein genes in the pea aphid, Insect Biochemistry and Molecular Biology, vol.37, issue.10, pp.1094-1102, 2007.
DOI : 10.1016/j.ibmb.2007.06.008

L. Trionnaire, G. Francis, F. Jaubert-possamai, S. Bonhomme, J. et al., Transcriptomic and proteomic analyses of seasonal photoperiodism in the pea aphid, BMC Genomics, vol.10, issue.1, p.456, 2009.
DOI : 10.1186/1471-2164-10-456
URL : https://hal.archives-ouvertes.fr/inria-00435791

V. Brault, S. Tanguy, C. Reinbold, L. Trionnaire, G. Arneodo et al., Transcriptomic analysis of intestinal genes following acquisition of pea enation mosaic virus by the pea aphid Acyrthosiphon pisum, Journal of General Virology, vol.91, issue.3, pp.802-808, 2010.
DOI : 10.1099/vir.0.012856-0
URL : https://hal.archives-ouvertes.fr/hal-01205028

B. Hunt, J. Brisson, S. Yi, and M. Goodisman, Functional Conservation of DNA Methylation in the Pea Aphid and the Honeybee, Genome Biology and Evolution, vol.2, pp.719-728, 2010.
DOI : 10.1093/gbe/evq057

A. Gallot, S. Shigenobu, T. Hashiyama, S. Jaubert-possamai, and D. Tagu, Sexual and asexual oogenesis require the expression of unique and shared sets of genes in the insect Acyrthosiphon pisum, BMC Genomics, vol.13, issue.1, p.76, 2012.
DOI : 10.1101/gr.9.9.868
URL : https://hal.archives-ouvertes.fr/hal-01208668

J. Bermingham and T. Wilkinson, Embryo nutrition in parthenogenetic viviparous aphids, Physiological Entomology, vol.32, issue.2, pp.103-109, 2009.
DOI : 10.1111/j.1365-3032.2008.00669.x

A. Douglas, Reproductive failure and the free amino acid pools in pea aphids (Acyrthosiphon pisum) lacking symbiotic bacteria, Journal of Insect Physiology, vol.42, issue.3, pp.247-255, 1996.
DOI : 10.1016/0022-1910(95)00105-0

T. Wilkinson and H. Ishikawa, The assimilation and allocation of nutrients by symbiotic and aposymbiotic pea aphids, Acyrthosiphon pisum, Entomologia Experimentalis et Applicata, vol.91, issue.1, pp.195-201, 1999.
DOI : 10.1046/j.1570-7458.1999.00484.x

T. Wilkinson and H. Ishikawa, Injection of essential amino acids substitutes for bacterial supply in aposymbiotic pea aphids (Acyrthosiphon pisum), Entomologia Experimentalis et Applicata, vol.94, issue.1
DOI : 10.1046/j.1570-7458.2000.00607.x

J. Bermingham, A. Rabatel, F. Calevro, J. Vinuelas, G. Febvay et al., Impact of Host Developmental Age on the Transcriptome of the Symbiotic Bacterium Buchnera aphidicola in the Pea Aphid (Acyrthosiphon pisum), Applied and Environmental Microbiology, vol.75, issue.22, pp.7294-7297, 2009.
DOI : 10.1128/AEM.01472-09
URL : https://hal.archives-ouvertes.fr/hal-00445867

M. Pfaffl, G. Horgan, and L. Dempfle, Relative expression software tool (REST(C)) for group-wise comparison and statistical analysis of relative expression results in real-time PCR, Nucleic Acids Research, vol.30, issue.9, p.36, 2002.
DOI : 10.1093/nar/30.9.e36

S. Shigenobu, R. Bickel, J. Brisson, T. Butts, C. Chang et al., Comprehensive survey of developmental genes in the pea aphid, Acyrthosiphon pisum: frequent lineage-specific duplications and losses of developmental genes, Insect Molecular Biology, vol.234, pp.47-62, 2010.
DOI : 10.1111/j.1365-2583.2009.00944.x

A. Vellozo, A. Véron, P. Baa-puyoulet, J. Huerta-cepas, L. Cottret et al., CycADS: an annotation database system to ease the development and update of BioCyc databases, Database, vol.2011, issue.0, p.8, 2011.
DOI : 10.1093/database/bar008
URL : https://hal.archives-ouvertes.fr/hal-00632965

D. Price, R. Duncan, S. Shigenobu, and A. Wilson, Genome Expansion and Differential Expression of Amino Acid Transporters at the Aphid/Buchnera Symbiotic Interface, Molecular Biology and Evolution, vol.28, issue.11, 2011.
DOI : 10.1093/molbev/msr140

C. Claudel-renard, C. Chevalet, T. Faraut, and D. Kahn, Enzyme-specific profiles for genome annotation: PRIAM, Nucleic Acids Research, vol.31, issue.22, pp.6633-6639, 2003.
DOI : 10.1093/nar/gkg847
URL : https://hal.archives-ouvertes.fr/hal-00427393

J. Huerta-cepas, S. Capella-gutierrez, L. Pryszcz, I. Denisov, D. Kormes et al., PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions, Nucleic Acids Research, vol.39, issue.Database, pp.491-496, 2010.
DOI : 10.1093/nar/gkq1109

A. Bairoch, R. Apweiler, C. Wu, W. Barker, B. Boeckmann et al., The Universal Protein Resource (UniProt), Nucleic Acids Research, vol.33, issue.Database issue, pp.154-159, 2005.
DOI : 10.1093/nar/gki070

J. Colombani, S. Raisin, S. Pantalacci, T. Radimerski, J. Montagne et al., A Nutrient Sensor Mechanism Controls Drosophila Growth, Cell, vol.114, issue.6, pp.739-749, 2003.
DOI : 10.1016/S0092-8674(03)00713-X
URL : https://hal.archives-ouvertes.fr/hal-00322342

G. Attardo, I. Hansen, S. Shiao, and A. Raikhel, Identification of two cationic amino acid transporters required for nutritional signaling during mosquito reproduction, Journal of Experimental Biology, vol.209, issue.16, pp.3071-3078, 2006.
DOI : 10.1242/jeb.02349

R. Duncan, L. Nathanson, and A. Wilson, Novel male-biased expression in paralogs of the aphid slimfast nutrient amino acid transporter expansion, BMC Evolutionary Biology, vol.24, issue.1, p.253, 2011.
DOI : 10.1093/molbev/msm088

E. Bernays and B. Klein, Quantifying the symbiont contribution to essential amino acids in aphids: the importance of tryptophan for Uroleucon ambrosiae, Physiological Entomology, vol.26, issue.4, pp.275-284, 2002.
DOI : 10.1006/mpev.2001.0929

K. Hiruma and L. Riddiford, The molecular mechanisms of cuticular melanization: The ecdysone cascade leading to dopa decarboxylase expression in Manduca sexta, Insect Biochemistry and Molecular Biology, vol.39, issue.4, pp.245-253, 2009.
DOI : 10.1016/j.ibmb.2009.01.008

S. Andersen, Insect cuticular sclerotization: A review, Insect Biochemistry and Molecular Biology, vol.40, issue.3, pp.166-178, 2010.
DOI : 10.1016/j.ibmb.2009.10.007

J. Schneider, A. Buness, W. Huber, J. Volz, P. Kioschis et al., Systematic analysis of T7 RNA polymerase based in vitro linear RNA amplification for use in microarray experiments, BMC Genomics, vol.5, issue.1, p.29, 2004.
DOI : 10.1186/1471-2164-5-29

R. Irizarry, B. Hobbs, C. F. Beazer-barclay, Y. Antonellis, K. Scherf et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data, Biostatistics, vol.4, issue.2, pp.249-264, 2003.
DOI : 10.1093/biostatistics/4.2.249

G. Smyth, Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments, Statistical Applications in Genetics and Molecular Biology, vol.3, issue.1, p.3, 2004.
DOI : 10.2202/1544-6115.1027

S. Dudoit, J. Shaffer, and C. Boldrick, Multiple Hypothesis Testing in Microarray Experiments, Statistical Science, vol.18, issue.1, pp.71-103, 2003.
DOI : 10.1214/ss/1056397487

A. Saeed, V. Sharov, J. White, J. Li, W. Liang et al., TM4: a free, open-source system for microarray data management and analysis, Biotechniques, vol.34, pp.374-378, 2003.

A. Conesa, S. Götz, J. García-gómez, J. Terol, M. Talón et al., Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, vol.21, issue.18, pp.3674-3676, 2005.
DOI : 10.1093/bioinformatics/bti610

N. Blüthgen, K. Brand, B. Cajavec, M. Swat, H. Herzel et al., Biological profiling of gene groups utilizing Gene Ontology, Genome Inform, vol.16, pp.106-115, 2005.

W. Rychlik, OLIGO 7 Primer Analysis Software, Methods Mol Biol, vol.402, pp.35-60, 2007.
DOI : 10.1007/978-1-59745-528-2_2

J. Brisson, A. Ishikawa, and T. Miura, Wing development genes of the pea aphid and differential gene expression between winged and unwinged morphs, Insect Molecular Biology, vol.42, pp.63-73, 2010.
DOI : 10.1111/j.1365-2583.2009.00935.x

M. Pfaffl, A. Tichopad, C. Prgomet, and T. Neuvians, Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper ??? Excel-based tool using pair-wise correlations, Biotechnology Letters, vol.26, issue.6, pp.509-515, 2004.
DOI : 10.1023/B:BILE.0000019559.84305.47

M. Pfaffl, A new mathematical model for relative quantification in real-time RT-PCR, Nucleic Acids Research, vol.29, issue.9, p.45, 2001.
DOI : 10.1093/nar/29.9.e45

J. Henderson, R. Ricker, B. Bidlingmeyer, and C. Woodward, Rapid, accurate, sensitive, and reproducible HPLC analysis of aminoacids. Amino acid analysis using Zorbax Eclipse-AAA columns and the

I. Agilent-technologies, Publication Number 5980, pp.1-10, 1193.

R. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004.
DOI : 10.1093/nar/gkh340
URL : http://doi.org/10.1093/nar/gkh340

M. Gouy, S. Guindon, and O. Gascuel, SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol.27, issue.2, pp.221-224, 2010.
DOI : 10.1093/molbev/msp259
URL : https://hal.archives-ouvertes.fr/lirmm-00705187

O. Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Molecular Biology and Evolution, vol.14, issue.7, pp.685-695, 1997.
DOI : 10.1093/oxfordjournals.molbev.a025808
URL : https://hal.archives-ouvertes.fr/lirmm-00730410

M. Claros and P. Vincens, Computational Method to Predict Mitochondrially Imported Proteins and their Targeting Sequences, European Journal of Biochemistry, vol.30, issue.3, pp.779-786, 1996.
DOI : 10.1016/0014-5793(94)00404-8