R. L. Lora and C. Kim, DNA sequence and global analysis: DNA sequencing: Sequence Production: Donna Muzny 1 , Christie Kovar* 1 , Andy Cree 1 , Joseph Chacko 1 , Mimi N. Chandrabose 1 , Marvin Diep Dao 1 , Huyen H. Dinh 1 , Ramatu Ayiesha Gabisi 1 1 ; Sequence Library Production: Lynne V, Acknowledgments Special thanks to J. Colbourne for insightful discussions on genome project organization and future directions. The members of The International Aphid Genomics Consortium (IAGC) are as follows 1 ; Sequence Production Informatics: Gerald R. Fowler* 1 , Matthew E. Hitchens 1 Ling-Ling Pu 1 , Stephanie N. Bell 1 , Angela Jolivet Johnson 1 , Selina Vattathil 1 , Rex L. Williams Jr. 1 ; Full length ESTs: Shuji Shigenobu 5 AphidBase and bioinformatics resources

T. Miura, *. , J. A. Brisson-linda, and M. , MicroRNA and phenotypic plasticity: Fabrice Legeai 6 Claude Rispe 6 ; Aphid Plant Interactions: Chemoreceptors: Carole Smadja 62 Carole Smadja 62 , Xiao-Li He 63 Renhu Liu 63 , Julio Rozas 64 , Linda M. Field* 63 ; Detoxification enzymes: Stanley Dean Rider Jr. 57 , John Ramsey 33 Georg Jander* 33 ; Salivary glands: Peter D. Ashton 30 Gatehouse 72 ; Virus transmission and transcytosis group: Véronique Brault 75 Circadian rhythms group, Odorant-Binding Proteins: Jing-Jiang Zhou 63 Cuticular proteins: Claude Rispe* 6 , Aviv Dombrovsky 78 Chitinase-like proteins: Atsushi Nakabachi* 4 , Shuji Shigenobu 5 Protease genes

*. Carolan and R. Owain, Yvan Rahbé 31 , Claude Rispe* 6 , Gerald R. Reeck 67 ; AcypiCyc: Augusto Vellozo 31 References 1. Blackman RL, Eastop VF Aphids on the world's crops: an identification and information guide, Hubert Charles* Claude Rispe*, vol.34232336, issue.82

W. Morrison and F. Peairs, Response model concept and economic impact Response model for an introduced pest?the Russian wheat aphid, 1998.

E. Oerke, E. Oerke, H. Dehne, F. Schonbeck, and A. Weber, Estimated crop losses in wheat Crop production and crop protection: estimated losses in major food and cash crops, pp.179-296, 1994.

N. Moran, M. Munson, P. Baumann, and H. Ishikawa, A Molecular Clock in Endosymbiotic Bacteria is Calibrated Using the Insect Hosts, Proceedings of the Royal Society B: Biological Sciences, vol.253, issue.1337, pp.167-171, 1993.
DOI : 10.1098/rspb.1993.0098

A. Gunduz, E. Douglas, and A. , Symbiotic bacteria enable insect to use a nutritionally inadequate diet, Proceedings of the Royal Society B: Biological Sciences, vol.26, issue.2, pp.987-991, 2009.
DOI : 10.1038/35024074

K. Oliver, P. Degnan, G. Burke, and N. Moran, Facultative Symbionts in Aphids and the Horizontal Transfer of Ecologically Important Traits, Annual Review of Entomology, vol.55, issue.1, 2009.
DOI : 10.1146/annurev-ento-112408-085305

C. Von-dohlen, C. Rowe, and O. Heie, A test of morphological hypotheses for tribal and subtribal relationships of Aphidinae (Insecta: Hemiptera: Aphididae) using DNA sequences, Molecular Phylogenetics and Evolution, vol.38, issue.2, pp.316-329, 2006.
DOI : 10.1016/j.ympev.2005.04.035

P. Degnan, T. Leonardo, C. B. Hurwitz, B. Richards, and S. , Dynamics of genome evolution in faculatitve symbionts of aphids, Environ Microbiol -in press, 2009.

P. Degnan, Y. Yu, N. Sisneros, R. Wing, and N. Moran, Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors, Proceedings of the National Academy of Sciences, vol.106, issue.22, pp.9063-9068, 2009.
DOI : 10.1073/pnas.0900194106

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.

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

J. Carolan, C. Fitzroy, P. Ashton, A. Douglas, and T. Wilkinson, The secreted salivary proteome of the pea aphid Acyrthosiphon pisum characterised by mass spectrometry, PROTEOMICS, vol.150, issue.21, pp.2457-2467, 2009.
DOI : 10.1002/pmic.200800692

O. Christiaens, M. Iga, R. Velarde, P. Rougé, and G. Smaggh, Halloween genes and nuclear receptors in ecdysteroid biosynthesis and signaling in the pea aphid, Insect Mol Biol, 2010.

T. Cortés, B. Ortiz-rivas, and D. Martínez-torres, Identification and characterization of circadian clock genes in the pea aphid Acrythosiphon pisum, Insect Mol Biol, 2010.

R. Dale, T. Walsh, C. Tamborindeguy, T. Davies, and J. Amey, Identification of ion channel genes in the Acyrthosiphon pisum genome, Insect Molecular Biology, vol.42, 2010.
DOI : 10.1111/j.1365-2583.2009.00975.x

N. Gerado, B. Altincicek, C. Anselme, H. Atamian, and S. Barribeau, Immunity and defense in the pea aphid, Acrythosiphon pisum Genome Biol, 2010.

D. Gilbert, Aphid and waterflea have a high rate of gene duplications compared to other arthropods, PLoS ONE, 2009.

T. Huang, C. Cook, G. Davis, S. Shigenobu, and R. Chen, Anterior development in the parthenogenetic and viviparous form of the pea aphid, Acyrthosiphon pisum: hunchback and orthodenticle expression, Insect Molecular Biology, vol.121, 2010.
DOI : 10.1111/j.1365-2583.2009.00940.x

J. Huerta-cepas, M. Marcet-houben, M. Pignatelli, A. Moya, and T. Gabaldón, The pea aphid phylome: a complete cataogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosipon pisum genes, Insect Mol Biol, 2010.

H. Huybrechts, J. Bonhomme, S. Minoli, N. Prunier-leterme, and A. Dombrovsky, Neuropeptide and neurohormone precursors in the pea aphid Acyrthosipon pisum, Insect Mol Biol, 2010.

S. Jaubert-possamai, C. Rispe, S. Tanguy, K. Gordon, and T. Walsh, Expansion of the miRNA Pathway in the Hemipteran Insect Acyrthosiphon pisum, Molecular Biology and Evolution, vol.27, issue.5, 2010.
DOI : 10.1093/molbev/msp256

F. Legeai, G. Rizk, T. Walsh, O. Edwards, and K. Gordon, Identification and expression pattern of microRNAs in the insect crop pest Acrythosiphon pisum. (submitted) BMC genomics, 2009.

F. Legeai, S. Shigenobu, J. Gauthier, J. Colbourne, and C. Rispe, AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome, Insect Molecular Biology, vol.21, issue.1, 2010.
DOI : 10.1111/j.1365-2583.2009.00930.x
URL : https://hal.archives-ouvertes.fr/inria-00531562

A. Nakabachi and S. Miyagishima, Expansion of genes encoding a novel type of dynamin in the genome of the pea aphid, Acyrthosiphon pisum, Insect Molecular Biology, vol.254, 2010.
DOI : 10.1111/j.1365-2583.2009.00941.x

A. Nakabachi, S. Shigenobu, and S. Miyagishima, Chitinase-like proteins encoded in the genome of the pea aphid, Acyrthosiphon pisum, Insect Molecular Biology, vol.20, 2010.
DOI : 10.1111/j.1365-2583.2009.00985.x

N. Nikoh, J. Mccutcheon, T. Kudo, S. Miyagishima, and N. Moran, Bacterial Genes in the Aphid Genome: Absence of Functional Gene Transfer from Buchnera to Its Host, PLoS Genetics, vol.21, issue.2, 2010.
DOI : 10.1371/journal.pgen.1000827.s010

M. Ollivier, F. Legeai, and C. Rispe, Comparative analysis of the Acyrthosiphon pisum genome and EST-based gene sets from other aphid species, Insect Mol Biol, 2010.

D. Price, K. Tibbles, S. Shigenobu, A. Smertenko, and C. Russel, Sugar transporters of the major facilitator superfamiliy in aphids; from gene prediction to fucntional characterization, Insect Mol Biol, 2010.

J. Ramsey, S. Macdonald, G. Jander, A. Nakabachi, and G. Thomas, Genomic evidence for complementary purine metabolism in the pea aphid, Acyrthosiphon pisum, and its symbiotic bacterium Buchnera aphidicola, Insect Molecular Biology, vol.250, issue.15, 2010.
DOI : 10.1111/j.1365-2583.2009.00945.x

J. Ramsey, D. Rider, T. Walsh, M. De-vos, and K. Gordon, Comparative analysis of detoxification enzymes in Acyrthosiphon pisum and Myzus persicae, Insect Molecular Biology, vol.29, 2010.
DOI : 10.1111/j.1365-2583.2009.00973.x

S. Rider, D. Srinivasan, and R. Hilgarth, Chromatin remodeling proteins of the pea aphid, Acyrthosiphon pisum, Insect Mol Biol in press, 2010.

S. Shigenobu, R. Bickel, J. Brisson, T. Butts, and C. Chang, 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, 2010.
DOI : 10.1111/j.1365-2583.2009.00944.x

S. Shigenobu, S. Richards, A. Cree, M. Morioka, and T. Fukatsu, A fulllength cDNA resource for the pea aphid, Acyrthosiphon pisum, Insect Mol Biol, 2010.

C. Smadja, P. Shi, R. Butlin, and H. Robertson, Large Gene Family Expansions and Adaptive Evolution for Odorant and Gustatory Receptors in the Pea Aphid, Acyrthosiphon pisum, Molecular Biology and Evolution, vol.26, issue.9, pp.2073-2086, 2009.
DOI : 10.1093/molbev/msp116

D. Srinivasan, B. Fenton, S. Jaubert-possamai, and M. Jaouannet, Analysis of meiosis and cell cycle genes of the facultatively asexual pea aphid, Acyrthosiphon pisum(Hemiptera: Aphididae), Insect Molecular Biology, vol.17, 2010.
DOI : 10.1111/j.1365-2583.2009.00960.x

C. Tamborindeguy, B. Monsion, V. Brault, L. Hunnicutt, and H. Ju, A genomic analysis of transcytosis in the pea aphid, Acyrthosiphon pisum, a mechanism involved in virus transmission, Insect Molecular Biology, vol.176, 2010.
DOI : 10.1111/j.1365-2583.2009.00956.x

T. Walsh, J. Brisson, H. Robertson, K. Gordon, and S. Jaubert-possamai, A functional DNA methylation system in the pea aphid, Acyrthosiphon pisum, Insect Molecular Biology, vol.39, issue.7, 2010.
DOI : 10.1111/j.1365-2583.2009.00974.x

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

J. Zhou, F. Vieira, X. He, C. Smadja, and R. Liu, Comparative analyses of the odorant-binding proteins in Acyrthosiphon pisum, Insect Mol Biol, 2010.

C. Elsik, A. Mackey, J. Reese, N. Milshina, and D. Roos, Creating a honey bee consensus gene set, Genome Biology, vol.8, issue.1, p.13, 2007.
DOI : 10.1186/gb-2007-8-1-r13

J. Huerta-cepas, H. Dopazo, J. Dopazo, and T. Gabaldon, The human phylome, Genome Biol, vol.8, p.109, 2007.

H. Robertson and K. Gordon, Canonical TTAGG-repeat telomeres and telomerase in the honey bee, Apis mellifera, Genome Research, vol.16, issue.11, pp.1345-1351, 2006.
DOI : 10.1101/gr.5085606

H. Fujiwara, M. Osanai, T. Matsumoto, and K. Kojima, Telomere-specific non-LTR retrotransposons and telomere maintenance in the silkworm, Bombyx mori, Chromosome Research, vol.8, issue.5, pp.455-467, 2005.
DOI : 10.1007/s10577-005-0990-9

M. Suzuki, A. Kerr, D. Sousa, D. Bird, and A. , CpG methylation is targeted to transcription units in an invertebrate genome, Genome Research, vol.17, issue.5, pp.625-631, 2007.
DOI : 10.1101/gr.6163007

W. Filipowicz, S. Bhattacharyya, and N. Sonenberg, Mechanisms of posttranscriptional regulation by microRNAs: are the answers in sight, Nat Rev Genet, vol.9, pp.102-114, 2008.

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

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

P. Degnan and N. Moran, Evolutionary genetics of a defensive facultative symbiont of insects: exchange of toxin-encoding bacteriophage, Molecular Ecology, vol.95, issue.3, pp.916-929, 2008.
DOI : 10.1111/j.1365-294X.2007.03616.x

N. Moran, J. Russell, R. Koga, and T. Fukatsu, Evolutionary Relationships of Three New Species of Enterobacteriaceae Living as Symbionts of Aphids and Other Insects, Applied and Environmental Microbiology, vol.71, issue.6, pp.3302-3310, 2005.
DOI : 10.1128/AEM.71.6.3302-3310.2005

A. Nakabachi, S. Shigenobu, N. Sakazume, T. Shiraki, and Y. Hayashizaki, 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

N. Nikoh and A. Nakabachi, Aphids acquired symbiotic genes via lateral gene transfer, BMC Biology, vol.7, issue.1, p.12, 2009.
DOI : 10.1186/1741-7007-7-12
URL : http://doi.org/10.1186/1741-7007-7-12

P. Sunnucks and D. Hales, Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae), Molecular Biology and Evolution, vol.13, issue.3, pp.510-524, 1996.
DOI : 10.1093/oxfordjournals.molbev.a025612

P. Karp, C. Ouzounis, C. Moore-kochlacs, L. Goldovsky, and P. Kaipa, Expansion of the BioCyc collection of pathway/genome databases to 160 genomes, Nucleic Acids Research, vol.33, issue.19, pp.6083-6089, 2005.
DOI : 10.1093/nar/gki892

G. Thomas, J. Zucker, A. Macdonald, A. Sorokin, and I. Goryanin, A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola, BMC Systems Biology, vol.3, issue.1, 2009.
DOI : 10.1186/1752-0509-3-24

T. Sasaki, T. Aoki, H. Hayashi, and H. Ishikawa, Amino acid composition of the honeydew of symbiotic and aposymbiotic pea aphids Acyrthosiphon pisum, Journal of Insect Physiology, vol.36, issue.1, pp.35-40, 1990.
DOI : 10.1016/0022-1910(90)90148-9

A. Lobanov, D. Hatfield, and V. Gladyshev, Selenoproteinless animals: Selenophosphate synthetase SPS1 functions in a pathway unrelated to selenocysteine biosynthesis, Protein Science, vol.17, issue.1, pp.176-182, 2008.
DOI : 10.1110/ps.073261508

C. Chapple and R. Guigo, Relaxation of selective constraints causes independent selenoprotein extinction in insect genomes, PLoS ONE, vol.3, 2008.

A. Clark, M. Eisen, D. Smith, C. Bergman, and B. Oliver, Evolution of genes and genomes on the Drosophila phylogeny, Nature, vol.2, issue.7167, pp.203-218, 2007.
DOI : 10.1038/nature06341

Z. Zou, J. Evans, Z. Lu, P. Zhao, and M. Williams, Comparative genomic analysis of the Tribolium immune system, Genome Biology, vol.8, issue.8, p.177, 2007.
DOI : 10.1186/gb-2007-8-8-r177

S. Mctaggart, C. Conlon, J. Colbourne, M. Blaxter, and T. Little, The components of the Daphnia pulex immune system as revealed by complete genome sequencing BMC Genomics -in press, 2009.

P. Pelosi, J. Zhou, L. Ban, and M. Calvello, Soluble proteins in insect chemical communication, Cellular and Molecular Life Sciences, vol.63, issue.14, pp.1658-1676, 2006.
DOI : 10.1007/s00018-005-5607-0

R. Vogt and L. Riddiford, Pheromone binding and inactivation by moth antennae, Nature, vol.24, issue.5828, pp.161-163, 1981.
DOI : 10.1038/293161a0

J. Laughlin, T. Ha, D. Jones, and D. Smith, Activation of Pheromone-Sensitive Neurons Is Mediated by Conformational Activation of Pheromone-Binding Protein, Cell, vol.133, issue.7, pp.1255-1265, 2008.
DOI : 10.1016/j.cell.2008.04.046

W. Leal, Proteins that make sense The biosynthesis and detection of pheromones and plant volatiles, 2003.

M. Tegoni, V. Campanacci, and C. Cambillau, Structural aspects of sexual attraction and chemical communication in insects, Trends in Biochemical Sciences, vol.29, issue.5, pp.257-264, 2004.
DOI : 10.1016/j.tibs.2004.03.003

R. Vogt, Biochemical diversity of odor detection, pp.391-445, 2003.
DOI : 10.1016/B978-012107151-6/50016-5

A. Sanchez-gracia, F. Vieira, and J. Rozas, Molecular evolution of the major chemosensory gene families in insects, Heredity, vol.17, issue.3, pp.208-216, 2009.
DOI : 10.1111/j.1432-1033.1995.tb20864.x

J. Krieger, O. Klink, C. Mohl, K. Raming, and H. Breer, A candidate olfactory receptor subtype highly conserved across different insect orders, Journal of Comparative Physiology A: Sensory, Neural, and Behavioral Physiology, vol.189, issue.7, pp.519-526, 2003.
DOI : 10.1007/s00359-003-0427-x

H. Robertson and L. Kent, Evolution of the gene lineage encoding the carbon dioxide heterodimeric receptor in insects, J Insect Sci -in press, 2009.

J. Ferrari, H. Godfray, A. Faulconbridge, K. Prior, and S. Via, POPULATION DIFFERENTIATION AND GENETIC VARIATION IN HOST CHOICE AMONG PEA APHIDS FROM EIGHT HOST PLANT GENERA, Evolution, vol.91, issue.8, pp.1574-1584, 2006.
DOI : 10.1554/0014-3820(2000)054[1626:RIBDRO]2.0.CO;2

M. Caillaud and S. Via, Specialized Feeding Behavior Influences Both Ecological Specialization and Assortative Mating in Sympatric Host Races of Pea Aphids, The American Naturalist, vol.156, issue.6, pp.606-621, 2000.
DOI : 10.1086/316991

S. Hogenhout, D. Ammar-el, A. Whitfield, and M. Redinbaugh, Insect Vector Interactions with Persistently Transmitted Viruses, Annual Review of Phytopathology, vol.46, issue.1, pp.327-359, 2008.
DOI : 10.1146/annurev.phyto.022508.092135

G. Chelvanayagam, M. Parker, and P. Board, Fly fishing for GSTs: a unified nomenclature for mammalian and insect glutathione transferases, Chemico-Biological Interactions, vol.133, pp.256-260, 2001.

A. Karley, D. Ashford, L. Minto, J. Pritchard, and A. Douglas, The significance of gut sucrase activity for osmoregulation in the pea aphid, Acyrthosiphon pisum, Journal of Insect Physiology, vol.51, issue.12, pp.1313-1319, 2005.
DOI : 10.1016/j.jinsphys.2005.08.001

C. Rispe, M. Kutsukake, V. Doublet, S. Hudaverdian, and F. Legeai, Large Gene Family Expansion and Variable Selective Pressures for Cathepsin B in Aphids, Molecular Biology and Evolution, vol.25, issue.1, pp.5-17, 2008.
DOI : 10.1093/molbev/msm222
URL : https://hal.archives-ouvertes.fr/inria-00180087

S. Carroll, Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution, Cell, vol.134, issue.1, pp.25-36, 2008.
DOI : 10.1016/j.cell.2008.06.030

T. Corbitt and J. Hardie, Juvenile hormone effects on polymorphism in the pea aphid, A cyrthosiphon pisum, Entomologia Experimentalis et Applicata, vol.15, issue.2, pp.131-136, 1985.
DOI : 10.1111/j.1570-7458.1985.tb03509.x

J. Hardie, Juvenile hormone mimics the photoperiodic apterization of the alate gynopara of aphid, Aphis fabae, Nature, vol.22, issue.5773, pp.602-604, 1980.
DOI : 10.1038/286602a0

X. Zhou, M. Tarver, and M. Scharf, Hexamerin-based regulation of juvenile hormone-dependent gene expression underlies phenotypic plasticity in a social insect, Development, vol.134, issue.3, pp.601-610, 2007.
DOI : 10.1242/dev.02755

M. Ramesh, S. Malik, J. Logsdon, and . Jr, A phylogenomic inventory of meiotic genes; evidence for sex in Giardia and an early eukaryotic origin of meiosis, Curr Biol, vol.15, pp.185-191, 2005.

J. Hardie, The photoperiodic control of wing development in the black bean aphid, Aphis fabae, Journal of Insect Physiology, vol.33, issue.8, pp.543-549, 1987.
DOI : 10.1016/0022-1910(87)90068-0

E. Stafflinger, K. Hansen, F. Hauser, M. Schneider, and G. Cazzamali, Cloning and identification of an oxytocin/vasopressin-like receptor and its ligand from insects, Proceedings of the National Academy of Sciences, vol.105, issue.9, pp.3262-3267, 2008.
DOI : 10.1073/pnas.0710897105

R. Predel, W. Russell, D. Russell, J. Lopez, and J. Esquivel, Comparative peptidomics of four related hemipteran species: Pyrokinins, myosuppressin, corazonin, adipokinetic hormone, sNPF, and periviscerokinins, Peptides, vol.29, issue.2, pp.162-167, 2008.
DOI : 10.1016/j.peptides.2007.08.034

A. Tawfik, S. Tanaka, D. Loof, A. Schoofs, L. Baggerman et al., Identification of the gregarization-associated dark-pigmentotropin in locusts through an albino mutant, Proceedings of the National Academy of Sciences, vol.96, issue.12, pp.7083-7087, 1999.
DOI : 10.1073/pnas.96.12.7083

S. Cyran, A. Buchsbaum, K. Reddy, M. Lin, and N. Glossop, vrille, Pdp1, and dClock Form a Second Feedback Loop in the Drosophila Circadian Clock, Cell, vol.112, issue.3, pp.329-341, 2003.
DOI : 10.1016/S0092-8674(03)00074-6

Q. Yuan, D. Metterville, A. Briscoe, and S. Reppert, Insect Cryptochromes: Gene Duplication and Loss Define Diverse Ways to Construct Insect Circadian Clocks, Molecular Biology and Evolution, vol.24, issue.4, pp.948-955, 2007.
DOI : 10.1093/molbev/msm011

K. Koh, X. Zheng, and A. Sehgal, JETLAG Resets the Drosophila Circadian Clock by Promoting Light-Induced Degradation of TIMELESS, Science, vol.312, issue.5781, pp.1809-1812, 2006.
DOI : 10.1126/science.1124951

A. Wilson, P. Sunnucks, and D. Hales, SHORT PAPER, Genetical Research, vol.69, issue.3, pp.233-236, 1997.
DOI : 10.1017/S0016672397002747

M. Caillaud, M. Boutin, C. Braendle, and J. Simon, A sex-linked locus controls wing polymorphism in males of the pea aphid, Acyrthosiphon pisum (Harris), Heredity, vol.89, issue.5, pp.346-352, 2002.
DOI : 10.1038/sj.hdy.6800146

M. Bennett, I. Leitch, H. Price, and J. Johnston, Comparisons with Caenorhabditis (100 Mb) and Drosophila (175 Mb) Using Flow Cytometry Show Genome Size in Arabidopsis to be 157 Mb and thus 25 % Larger than the Arabidopsis Genome Initiative Estimate of 125 Mb, Annals of Botany, vol.91, issue.5, pp.547-557, 2003.
DOI : 10.1093/aob/mcg057

Y. Kapustin, A. Souvorov, and T. Tatusova, Splign -a hybrid approach to spliced alignments, Research in Computational Molecular Biology, p.741, 2004.

B. Kiryutin and A. Souvorov, New global protein-nucleotide alignment tool, 2005.

A. Souvorov, T. Tatusova, and D. Lipman, Genome annotation with Gnomon -a multi-step combined gene prediction tool, p.125, 2004.

B. Haas, A. Delcher, S. Mount, J. Wortman, R. Smith et al., Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies, Nucleic Acids Research, vol.31, issue.19, pp.5654-5666, 2003.
DOI : 10.1093/nar/gkg770

C. Mungall and D. Emmert, A Chado case study: an ontology-based modular schema for representing genome-associated biological information, Bioinformatics, vol.23, issue.13, pp.337-346, 2007.
DOI : 10.1093/bioinformatics/btm189

P. Zhou, D. Emmert, and P. Zhang, Using Chado to Store Genome Annotation Data, Curr Protoc Bioinformatics Chapter, vol.12, issue.12, p.6, 2006.
DOI : 10.1002/0471250953.bi0906s12

J. Gauthier, F. Legeai, A. Zasadzinski, C. Rispe, and D. Tagu, AphidBase: a database for aphid genomic resources, Bioinformatics, vol.23, issue.6, pp.783-784, 2007.
DOI : 10.1093/bioinformatics/btl682
URL : https://hal.archives-ouvertes.fr/inria-00180141

S. Guindon and O. Gascuel, A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood, Systematic Biology, vol.52, issue.5, pp.696-704, 2003.
DOI : 10.1080/10635150390235520

T. Smith and M. Waterman, Identification of common molecular subsequences, Journal of Molecular Biology, vol.147, issue.1, pp.195-197, 1981.
DOI : 10.1016/0022-2836(81)90087-5

R. Edgar, MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, vol.5, issue.1, p.113, 2004.
DOI : 10.1186/1471-2105-5-113

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. Anisimova and O. Gascuel, Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative, Systematic Biology, vol.55, issue.4, pp.539-552, 2006.
DOI : 10.1080/10635150600755453
URL : https://hal.archives-ouvertes.fr/lirmm-00136658

J. Huerta-cepas, A. Bueno, J. Dopazo, and T. Gabaldon, PhylomeDB: a database for genome-wide collections of gene phylogenies, Nucleic Acids Research, vol.36, issue.Database, pp.491-496, 2008.
DOI : 10.1093/nar/gkm899

T. Gabaldon, Large-scale assignment of orthology: back to phylogenetics?, Genome Biology, vol.9, issue.10, p.235, 2008.
DOI : 10.1186/gb-2008-9-10-235

J. Castresana, Selection of Conserved Blocks from Multiple Alignments for Their Use in Phylogenetic Analysis, Molecular Biology and Evolution, vol.17, issue.4, pp.540-552, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026334

M. Mandrioli, D. Bizzaro, M. Giusti, G. Manicardi, and U. Bianchi, The role of rDNA genes in X chromosome association in the aphid <i>Acyrthosiphon pisum</i>, Genome, vol.42, issue.3, pp.381-386, 1999.
DOI : 10.1139/gen-42-3-381

S. Altschul, T. Madden, A. Schaffer, J. Zhang, and Z. Zhang, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-3402, 1997.
DOI : 10.1093/nar/25.17.3389

H. Quesneville, C. Bergman, O. Andrieu, D. Autard, and D. Nouaud, Combined Evidence Annotation of Transposable Elements in Genome Sequences, PLoS Computational Biology, vol.16, issue.2, pp.166-175, 2005.
DOI : 1367-4803(2000)016[1040:MAPETR]2.0.CO;2
URL : https://hal.archives-ouvertes.fr/hal-00009013

Z. Bao and S. Eddy, Automated De Novo Identification of Repeat Sequence Families in Sequenced Genomes, Genome Research, vol.12, issue.8, pp.1269-1276, 2002.
DOI : 10.1101/gr.88502

R. Edgar and E. Myers, PILER: identification and classification of genomic repeats, Bioinformatics, vol.21, issue.Suppl 1, pp.152-158, 2005.
DOI : 10.1093/bioinformatics/bti1003

K. Katoh, K. Misawa, K. Kuma, and T. Miyata, MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform, Nucleic Acids Research, vol.30, issue.14, pp.3059-3066, 2002.
DOI : 10.1093/nar/gkf436

J. Jurka, V. Kapitonov, A. Pavlicek, P. Klonowski, and O. Kohany, Repbase Update, a database of eukaryotic repetitive elements, Cytogenetic and Genome Research, vol.110, issue.1-4, pp.462-467, 2005.
DOI : 10.1159/000084979

S. Eddy, Profile hidden Markov models, Bioinformatics, vol.14, issue.9, pp.755-763, 1998.
DOI : 10.1093/bioinformatics/14.9.755

J. Jurka, P. Klonowski, V. Dagman, and P. Pelton, Censor???a program for identification and elimination of repetitive elements from DNA sequences, Computers & Chemistry, vol.20, issue.1, pp.119-121, 1996.
DOI : 10.1016/S0097-8485(96)80013-1

G. Benson, Tandem repeats finder: a program to analyze DNA sequences, Nucleic Acids Research, vol.27, issue.2, pp.573-580, 1999.
DOI : 10.1093/nar/27.2.573

R. Kolpakov, G. Bana, and G. Kucherov, mreps: efficient and flexible detection of tandem repeats in DNA, Nucleic Acids Research, vol.31, issue.13, pp.3672-3678, 2003.
DOI : 10.1093/nar/gkg617
URL : https://hal.archives-ouvertes.fr/inria-00099597

X. Huang and A. Madan, CAP3: A DNA Sequence Assembly Program, Genome Research, vol.9, issue.9, pp.868-877, 1999.
DOI : 10.1101/gr.9.9.868

M. Pop, A. Phillippy, A. Delcher, and S. Salzberg, Comparative genome assembly, Briefings in Bioinformatics, vol.5, issue.3, pp.237-248, 2004.
DOI : 10.1093/bib/5.3.237
URL : http://bib.oxfordjournals.org/cgi/content/short/5/3/237

Y. Moriya, M. Itoh, S. Okuda, A. Yoshizawa, and M. Kanehisa, KAAS: an automatic genome annotation and pathway reconstruction server, Nucleic Acids Research, vol.35, issue.Web Server, pp.182-185, 2007.
DOI : 10.1093/nar/gkm321

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

Y. Wang, M. Jorda, P. Jones, R. Maleszka, and X. Ling, Functional CpG Methylation System in a Social Insect, Science, vol.314, issue.5799, pp.645-647, 2006.
DOI : 10.1126/science.1135213

P. Hardin, The Circadian Timekeeping System of Drosophila, Current Biology, vol.15, issue.17, pp.714-722, 2005.
DOI : 10.1016/j.cub.2005.08.019