. Thank-dorith-rotenberg, USA) for giving early access to the unpublished genome assembly of the Thysanoptera species Frankliniella occidentalis (ik5 project). Three reviewers made helpful comments or suggestions

F. Legeai, D. Rispe, . Tagu;-genome-sequencing:-shanlin, J. Liu, M. Zhao et al., Authors' contributions Authors contributing specific working groups are indicated below. Steering committee: F Delmotte

Y. Dna:-k-dufault-thompson, ;. Zhang, N. Zhao, M. Moran;-repetitive-dna:-p-capy, M. Bouallègue et al., , vol.duplications

:. Dna-methylation, D. Brisson;-selenoproteins:-a-ripoll-cladellas, R. Santesmasses, ;. Guigó, D. Barberà et al., odorant, gustatory ligand-binding and extracellular-binding families

I. Bioepar, . Oniris, F. Nantes, I. Bipaa, and A. Ouest,

G. Bioinformatics and . Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, vol.88, p.8003

S. Barcelona, 5 Present address: Institute of Evolutionary Biology (CSIC-UPF), Passeig marítim de la Barceloneta 37-49, p.8003

, INRAE, BF2I, UMR0203, F-69621

C. Génomes, C. Ecologie, U. Paris-sud, U. Ird, . Paris-saclay et al., 18 Department of Cell and Molecular Biology, College of the Environment and Life Sciences, Faculté des Sciences de Tunis, LR01ES05 Biochimie et Biotechnologie, 2092 Tunis, Tunisia. 12 Department Biol, vol.21, p.24

, 25 Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys, vol.23, p.26

, 29 Present affiliation: Bone and Joint Research Center, Chang Gung Memorial Hospital

L. Rheu, ;. France, . Azur, C. Inrae, and I. Sophia-agrobiotech, 34 Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR, vol.5288

D. Pimentel, R. Zuniga, and D. Morrison, Update on the environmental and economic costs associated with alien-invasive species in the United States

, Ecol Econ, vol.52, pp.273-88, 2005.

J. Gurevitch, G. A. Fox, G. M. Wardle, and T. D. Inderjit, Emergent insights from the synthesis of conceptual frameworks for biological invasions, Ecol Lett, vol.14, pp.407-425, 2011.

C. Kueffer, P. Py?ek, and D. M. Richardson, Integrative invasion science: model systems, multi-site studies, focused meta-analysis and invasion syndromes, New Phytol, vol.200, pp.615-648, 2013.

A. Banerjee, E. Duflo, G. Postei-vinay, and T. Watts, Long-run health impacts of income shocks: wine and phylloxera in nineteenth-century France, Rev Econ Stat, vol.92, pp.714-742, 2010.

D. Simberloff, Non-native invasive species and novel ecosystems, vol.7, 1000.

P. Galet and . Phylloxera, Parasites Vigne Tome II, Montpellier: Paysan du Midi, pp.1059-313, 1982.

R. Pouget, Le Phylloxera et les maladies de la vigne, 2015.

Y. Carton, C. Sorensen, J. Smith, and E. Smith, Une coopération exemplaire entre entomologistes français et américains pendant la crise du Phylloxera en France (1868-1895), Ann Société Entomol Fr NS, vol.43, pp.103-128, 2007.

P. Marchal and J. Feytaud, Les données nouvelles sur le phylloxéra. Rev Vitic -Tome XL Ed P Viala, 1913.

N. A. Moran, H. J. Mclaughlin, and R. Sorek, The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria, Science, vol.323, pp.379-82, 2009.

S. Riaz, K. T. Lund, J. Granett, and M. A. Walker, Population diversity of grape phylloxera in California and evidence for sexual reproduction, Am J Enol Vitic, vol.68, pp.218-245, 2017.

J. Granett, M. A. Walker, L. Kocsis, and A. D. Omer, Biology and management of grape phylloxera, Annu Rev Entomol, vol.46, pp.387-412, 2001.

, Genome sequence of the pea aphid Acyrthosiphon pisum, The International Aphid Genomics Consortium, vol.8, 2010.

J. A. Wenger, B. J. Cassone, F. Legeai, J. S. Johnston, R. Bansal et al., Whole genome sequence of the soybean aphid, Aphis glycines Insect Biochem Mol Biol, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01555244

E. Nováková and N. A. Moran, Diversification of genes for carotenoid biosynthesis in aphids following an ancient transfer from a fungus, Mol Biol Evol, vol.29, pp.313-336, 2012.

C. Zhao and P. D. Nabity, Phylloxerids share ancestral carotenoid biosynthesis genes of fungal origin with aphids and adelgids, PLoS One, vol.12, 2017.

N. Nikoh and A. Nakabachi, Aphids acquired symbiotic genes via lateral gene transfer, BMC Biol, vol.7, 2009.

N. Nikoh, J. P. Mccutcheon, T. Kudo, S. Miyagishima, N. A. Moran et al., Bacterial genes in the aphid genome: absence of functional gene transfer from Buchnera to its host, PLoS Genet, vol.6, 2010.

T. Wicker, F. Sabot, A. Hua-van, J. L. Bennetzen, P. Capy et al., A unified classification system for eukaryotic transposable elements, Nat Rev Genet, vol.8, pp.973-82, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00169819

W. Xie, C. Chen, Z. Yang, L. Guo, X. Yang et al., Genome sequencing of the sweetpotato whitefly Bemisia tabaci MED/Q, GigaScience, vol.6, pp.1-7, 2017.

F. Legeai, S. Shigenobu, J. Gauthier, J. Colbourne, C. Rispe et al., AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome, Insect Mol Biol, vol.19, pp.5-12, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02658827

R. Giordano, R. K. Donthu, A. V. Zimin, J. Chavez, I. C. Gabaldon et al., Soybean aphid biotype 1 genome: insights into the invasive biology and adaptive evolution of a major agricultural pest, Insect Biochem Mol Biol, vol.120, 2020.

Y. Li, H. Park, T. E. Smith, and N. A. Moran, Gene family evolution in the pea aphid based on chromosome-level genome assembly, Mol Biol Evol, vol.36, pp.2143-56, 2019.

T. C. Mathers, Y. Chen, G. Kaithakottil, F. Legeai, S. T. Mugford et al., Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species, Genome Biol, vol.18, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01588181

P. Buchner, Endosymbiosis of animals with plant microorganisms, vol.7, 1965.

M. B. Ponsen, A histological description of the alimentary tract and related organs of Phylloxeridae (Homoptera, Aphidoidea), 1997.

S. Vorwerk, D. Martinez-torres, and A. Forneck, Pantoea agglomerans-associated bacteria in grape phylloxera (Daktulosphaira vitifoliae, Fitch), Agric For Entomol, vol.9, pp.57-64, 2007.

A. V. Kellow, M. Sedgley, V. Heeswijck, and R. , Interaction between Vitis vinifera and grape phylloxera: changes in root tissue during nodosity formation

, Ann Bot, vol.93, pp.581-90, 2004.

S. Johnson, I. Hiltpold, and T. Turlings, Behaviour and physiology of root herbivores, vol.45, 2013.

C. Zhao and P. D. Nabity, Plant manipulation through gall formation constrains amino acid transporter evolution in sap-feeding insects, BMC Evol Biol, vol.17, 2017.

A. P. Arp, W. B. Hunter, and K. S. Pelz-stelinski, Annotation of the Asian citrus psyllid genome reveals a reduced innate immune system, Front Physiol, vol.7, 2016.

A. P. Arp, X. Martini, and K. S. Pelz-stelinski, Innate immune system capabilities of the Asian citrus psyllid, Diaphorina citri, J Invertebr Pathol, vol.148, pp.94-101, 2017.

N. Salcedo-porras, A. Guarneri, P. L. Oliveira, and C. Lowenberger, Rhodnius prolixus: identification of missing components of the IMD immune signaling pathway and functional characterization of its role in eliminating bacteria, PLoS One, vol.14, 2019.

G. K. Davis, Cyclical parthenogenesis and viviparity in aphids as evolutionary novelties, J Exp Zoolog B Mol Dev Evol, vol.318, pp.448-59, 2012.

R. D. Mesquita, R. J. Vionette-amaral, C. Lowenberger, R. Rivera-pomar, F. A. Monteiro et al., Genome of Rhodnius prolixus, an insect vector of Chagas disease, reveals unique adaptations to hematophagy and parasite infection, Proc Natl Acad Sci U S A, vol.112, pp.14936-14977, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01323805

C. Smadja, P. Shi, R. K. Butlin, and H. M. Robertson, Large gene family expansions and adaptive evolution for odorant and gustatory receptors in the pea aphid, Acyrthosiphon pisum, Mol Biol Evol, vol.26, pp.2073-86, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01945562

J. Vizueta, J. Rozas, and A. Sánchez-gracia, Comparative genomics reveals thousands of novel chemosensory genes and massive changes in chemoreceptor repertories across chelicerates, Genome Biol Evol, vol.10, pp.1221-1257, 2018.

J. Zhao, Y. Zhang, D. Fan, and J. Feng, Identification and expression profiling of odorant-binding proteins and chemosensory proteins of Daktulosphaira vitifoliae (Hemiptera: Phylloxeridae), J Econ Entomol, vol.110, pp.1813-1833, 2017.

J. S. Ramsey, D. S. Rider, T. K. Walsh, M. D. Vos, K. Gordon et al., Comparative analysis of detoxification enzymes in Acyrthosiphon pisum and Myzus persicae, Insect Mol Biol, vol.19, pp.155-64, 2010.

R. Schama, N. Pedrini, M. P. Juárez, D. R. Nelson, A. Q. Torres et al., Rhodnius prolixus supergene families of enzymes potentially associated with insecticide resistance, Insect Biochem Mol Biol, vol.69, pp.91-104, 2016.

M. Grbi?, T. Van-leeuwen, R. M. Clark, S. Rombauts, P. Rouzé et al., The genome of Tetranychus urticae reveals herbivorous pest adaptations, Nature, vol.479, pp.487-92, 2011.

R. Feyereisen, Arthropod CYPomes illustrate the tempo and mode in P450 evolution, Biochim Biophys Acta BBA -Proteins Proteomics, pp.19-28, 1814.
URL : https://hal.archives-ouvertes.fr/hal-02668726

W. Chen, D. K. Hasegawa, N. Kaur, A. Kliot, P. V. Pinheiro et al., The draft genome of whitefly Bemisia tabaci MEAM1, a global crop pest, provides novel insights into virus transmission, host adaptation, and insecticide resistance, BMC Biol, vol.14, 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.

E. M. Campbell, A. Ball, S. Hoppler, and A. S. Bowman, Invertebrate aquaporins: a review, J Comp Physiol B, vol.178, pp.935-55, 2008.

X. Jing, T. A. White, J. Luan, C. Jiao, Z. Fei et al., Evolutionary conservation of candidate osmoregulation genes in plant phloem sap-feeding insects, Insect Mol Biol, vol.25, pp.251-259, 2016.

K. Katoh and D. M. Standley, MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol Biol Evol, vol.30, pp.772-80, 2013.

S. Capella-gutiérrez and J. M. Silla-martínez, Gabaldón T trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, pp.1972-1973, 2009.

F. Ronquist and J. P. Huelsenbeck, MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinforma Oxf Engl, vol.19, pp.1572-1576, 2003.

F. Abascal, R. Zardoya, and D. Posada, ProtTest: selection of best-fit models of protein evolution, Bioinformatics, vol.21, pp.2104-2109, 2005.

C. J. Doherty and S. A. Kay, Circadian control of global gene expression patterns, Annu Rev Genet, vol.44, pp.419-463, 2010.

M. Barberà, J. M. Collantes-alegre, and D. Martínez-torres, Characterisation, analysis of expression and localisation of circadian clock genes from the perspective of photoperiodism in the aphid Acyrthosiphon pisum, Insect Biochem Mol Biol, vol.83, pp.54-67, 2017.

T. Cortés, B. Ortiz-rivas, and D. Martínez-torres, Identification and characterization of circadian clock genes in the pea aphid Acyrthosiphon pisum, Insect Mol Biol, vol.19, pp.123-162, 2010.

Q. Yuan, D. Metterville, A. D. Briscoe, and S. M. Reppert, Insect cryptochromes: gene duplication and loss define diverse ways to construct insect circadian clocks, Mol Biol Evol, vol.24, pp.948-55, 2007.

M. Barberà and D. Martínez-torres, Identification of the prothoracicotropic hormone (Ptth) coding gene and localization of its site of expression in the pea aphid Acyrthosiphon pisum, Insect Mol Biol, vol.26, pp.654-64, 2017.

O. Keller, F. Odronitz, M. Stanke, M. Kollmar, and S. Waack, Scipio: using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species, BMC Bioinformatics, vol.9, 2008.

G. Slater and E. Birney, Automated generation of heuristics for biological sequence comparison, BMC Bioinformatics, vol.6, p.31, 2005.

E. Birney, M. Clamp, R. Durbin, and G. Genewise, Genome Res, vol.14, pp.988-95, 2004.

E. Lee, G. A. Helt, J. T. Reese, M. C. Munoz-torres, C. P. Childers et al., Web Apollo: a web-based genomic annotation editing platform, Genome Biol, vol.14, 2013.

D. Cao, Y. Liu, W. B. Walker, J. Li, and G. Wang, Molecular characterization of the Aphis gossypii olfactory receptor gene families, PLoS One, vol.9, 2014.

K. Katoh, K. Kuma, H. Toh, and T. Miyata, MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Res, vol.33, pp.511-519, 2005.

S. Guindon, J. Dufayard, V. Lefort, M. Anisimova, W. Hordijk et al., New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst Biol, vol.59, pp.307-328, 2010.
URL : https://hal.archives-ouvertes.fr/lirmm-00511784

V. Lefort, J. Longueville, and O. Gascuel, SMS: smart model selection in PhyML, Mol Biol Evol, vol.34, pp.2422-2426, 2017.
URL : https://hal.archives-ouvertes.fr/lirmm-01794206

M. Anisimova and O. Gascuel, Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative, Syst Biol, vol.55, pp.539-52, 2006.
URL : https://hal.archives-ouvertes.fr/lirmm-00136658

R. D. Finn, P. Coggill, R. Y. Eberhardt, S. R. Eddy, J. Mistry et al., The Pfam protein families database: towards a more sustainable future, Nucleic Acids Res, vol.44, pp.279-85, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01294685

J. Zhou, F. G. Vieira, X. He, C. Smadja, R. Liu et al., Genome annotation and comparative analyses of the odorant-binding proteins and chemosensory proteins in the pea aphid Acyrthosiphon pisum, Insect Mol Biol, vol.19, pp.113-135, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01945559

K. D. Yamada, K. Tomii, and K. Katoh, Application of the MAFFT sequence alignment program to large data-reexamination of the usefulness of chained guide trees, Bioinformatics, vol.32, pp.3246-51, 2016.

A. Stamatakis, RAxML version 8: a tool for phylogenetic analysis and postanalysis of large phylogenies, Bioinformatics, vol.30, pp.1312-1315, 2014.

S. Sawyer, Statistical tests for detecting gene conversion, Mol Biol Evol, vol.6, pp.526-564, 1989.

I. Letunic and P. Bork, Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees, Nucleic Acids Res, vol.44, pp.242-247, 2016.

D. Werck-reichhart and R. Feyereisen, Cytochromes P450: a success story, Genome Biol, vol.1, pp.3003-3004, 2000.
URL : https://hal.archives-ouvertes.fr/hal-02698983

B. Giardine, C. Riemer, R. C. Hardison, R. Burhans, L. Elnitski et al., Galaxy: a platform for interactive large-scale genome analysis, Genome Res, vol.15, pp.1451-1456, 2005.

Y. Du, Q. Zheng, H. Zhai, E. Jiang, and Z. Wang, Selectivity of Phylloxera viticola Fitch (Homoptera: Phylloxeridae) to grape with different resistance and the identification of grape root volatiles, Acta Entomol Sin, vol.52, pp.537-580, 2009.

R. Zhang, B. Wang, G. Grossi, P. Falabella, Y. Liu et al., Molecular basis of alarm pheromone detection in aphids, Curr Biol, vol.27, pp.55-61, 2017.

P. Pelosi, I. Iovinella, A. Felicioli, and F. R. Dani, Soluble proteins of chemical communication: an overview across arthropods, Front Physiol, vol.5, 2014.

W. Xue, J. Fan, Y. Zhang, Q. Xu, Z. Han et al., Identification and expression analysis of candidate odorant-binding protein and chemosensory protein genes by antennal transcriptome of Sitobion avenae, PLoS One, vol.11, 2016.

K. Borden, RING domains: master builders of molecular scaffolds?11Edited by P, E Wright J Mol Biol, vol.295, pp.1103-1115, 2000.

L. K. Mosavi, T. J. Cammett, D. C. Desrosiers, and Z. Peng, The ankyrin repeat as molecular architecture for protein recognition, Protein Sci Publ Protein Soc, vol.13, pp.1435-1483, 2004.

E. Carafoli and J. Krebs, Why calcium? How calcium became the best communicator, J Biol Chem, vol.291, pp.20849-57, 2016.

L. K. Teixeira and S. I. Reed, Ubiquitin ligases and cell cycle control, Annu Rev Biochem, vol.82, pp.387-414, 2013.

C. Zhao, L. N. Escalante, H. Chen, T. R. Benatti, J. Qu et al., A massive expansion of effector genes underlies gall-formation in the wheat pest Mayetiola destructor, Curr Biol, vol.25, pp.613-633, 2015.

M. Pitino and S. A. Hogenhout, Aphid protein effectors promote aphid colonization in a plant species-specific manner, Mol Plant-Microbe Interact, vol.26, pp.130-139, 2012.

D. C. Jeffares, C. J. Penkett, and J. Bähler, Rapidly regulated genes are intron poor, Trends Genet, vol.24, pp.375-383, 2008.

H. Luo and H. Nijveen, Understanding and identifying amino acid repeats, Brief Bioinform, vol.15, pp.582-91, 2014.

A. Craig, R. Ewan, J. Mesmar, V. Gudipati, and A. Sadanandom, E3 ubiquitin ligases and plant innate immunity, J Exp Bot, vol.60, pp.1123-1155, 2009.

M. J. Banfield, Perturbation of host ubiquitin systems by plant pathogen/pest effector proteins, Cell Microbiol, vol.17, pp.18-25, 2015.

J. Stuart, Insect effectors and gene-for-gene interactions with host plants, Curr Opin Insect Sci, vol.9, pp.56-61, 2015.

P. D. Nabity, Insect-induced plant phenotypes: revealing mechanisms through comparative genomics of galling insects and their hosts, Am J Bot, vol.103, pp.979-81, 2016.

T. Will, W. F. Tjallingii, A. Thönnessen, and A. Van-bel, Molecular sabotage of plant defense by aphid saliva, Proc Natl Acad Sci U S A, vol.104, pp.10536-10577, 2007.

M. Hattori, M. Nakamura, S. Komatsu, K. Tsuchihara, Y. Tamura et al., Molecular cloning of a novel calcium-binding protein in the secreted saliva of the green rice leafhopper Nephotettix cincticeps, Insect Biochem Mol Biol, vol.42, pp.1-9, 2012.

C. Zhao, C. Rispe, and P. D. Nabity, Secretory RING finger proteins function as effectors in a grapevine galling insect, BMC Genomics, vol.20, p.923, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02917884

C. J. Lilley, A. Maqbool, D. Wu, H. B. Yusup, L. M. Jones et al., Effector gene birth in plant parasitic nematodes: neofunctionalization of a housekeeping glutathione synthetase gene, PLoS Genet, vol.14, 2018.

H. Boulain, F. Legeai, E. Guy, S. Morlière, N. E. Douglas et al., Fast evolution and lineage-specific gene family expansions of aphid salivary effectors driven by interactions with host-plants, Genome Biol Evol, vol.10, pp.1554-72, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01891942

D. A. Downie, Locating the sources of an invasive pest, grape phylloxera, using a mitochondrial DNA gene genealogy, Mol Ecol, vol.11, pp.2013-2039, 2002.

J. Tello, R. Mammerler, M. ?aji?, and A. Forneck, Major outbreaks in the nineteenth century shaped grape phylloxera contemporary genetic structure in, Europe. Sci Rep, vol.9, pp.1-11, 2019.

J. Planchon, J. Lichtenstein, and . Le-phylloxéra, , p.1873

K. T. Lund, S. Riaz, and M. A. Walker, Population structure, diversity and reproductive mode of the grape phylloxera (Daktulosphaira vitifoliae) across its native range, PLoS One, vol.12, 2017.

P. Hebert, M. Y. Stoeckle, T. S. Zemlak, and C. M. Francis, Identification of birds through DNA barcodes, PLoS Biol, vol.2, 2004.

J. S. Johnston, A. Bernardini, and C. E. Hjelmen, Genome size estimation and quantitative cytogenetics in insects, Insect genomics methods Protoc, pp.15-26, 2019.

E. Bonnivard, C. O. Ravaux, J. Brown, S. C. Higuet, and D. , Survey of genome size in 28 hydrothermal vent species covering 10 families, Genome, vol.52, pp.524-560, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00856109

P. Sunnucks and D. F. Hales, Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae), Mol Biol Evol, vol.13, pp.510-534, 1996.

M. Boetzer and W. Pirovano, SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information, BMC Bioinformatics, vol.15, 2014.

M. Boetzer and W. Pirovano, Toward almost closed genomes with GapFiller

, Genome Biol, vol.13, 2012.

C. Holt and M. Yandell, MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects, BMC Bioinformatics, vol.12, 2011.

O. Keller, M. Kollmar, M. Stanke, and S. Waack, A novel hybrid gene prediction method employing protein multiple sequence alignments, Bioinformatics, vol.27, pp.757-63, 2011.

I. Korf, Gene finding in novel genomes, BMC Bioinformatics, vol.5, p.59, 2004.

C. Rispe, F. Legeai, D. Papura, A. Bretaudeau, S. Hudaverdian et al., De novo transcriptome assembly of the grapevine phylloxera allows identification of genes differentially expressed between leaf-and rootfeeding forms, BMC Genomics, vol.17, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01286528

B. Misof, S. Liu, K. Meusemann, R. S. Peters, A. Donath et al., Phylogenomics resolves the timing and pattern of insect evolution, Science, vol.346, pp.763-770, 2014.

R. Buels, E. Yao, C. M. Diesh, R. D. Hayes, M. Munoz-torres et al., JBrowse: a dynamic web platform for genome visualization and analysis, Genome Biol, vol.17, p.66, 2016.

C. J. Mungall and D. B. Emmert, A Chado case study: an ontology-based modular schema for representing genome-associated biological information, Bioinformatics, vol.23, pp.337-383, 2007.

L. Sanderson, S. P. Ficklin, C. Cheng, J. S. Feltus, F. A. Bett et al., Tripal v1.1: a standards-based toolkit for construction of online genetic and genomic databases, Database, 2013.

A. Bretaudeau, N. Dunn, S. Gladman, B. Grüning, H. Rasche et al., Genome Annotation project: integrating Galaxy and GMOD for genome annotation</p>, F1000Research, vol.7, 2018.

D. R. Laetsch and M. L. Blaxter, BlobTools: interrogation of genome assemblies, F1000Research, vol.6, p.1287, 2017.

M. Bernt, A. Donath, F. Jühling, F. Externbrink, C. Florentz et al., MITOS: improved de novo metazoan mitochondrial genome annotation

, Mol Phylogenet Evol, vol.69, pp.313-322, 2013.

D. Laslett and B. Canbäck, ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences, Bioinformatics, vol.24, pp.172-177, 2008.

H. Quesneville, C. M. Bergman, O. Andrieu, D. Autard, D. Nouaud et al., Combined evidence annotation of transposable elements in genome sequences, PLoS Comput Biol, vol.1, 2005.
URL : https://hal.archives-ouvertes.fr/inserm-00000104

T. Flutre, E. Duprat, C. Feuillet, and H. Quesneville, Considering transposable element diversification in de novo annotation approaches, PLoS One, vol.6, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00956366

J. Huerta-cepas, S. Capella-gutiérrez, L. P. Pryszcz, M. Marcet-houben, and T. Gabaldón, PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome, Nucleic Acids Res, vol.42, pp.897-902, 2014.

G. Landan and D. Graur, Heads or tails: a simple reliability check for multiple sequence alignments, Mol Biol Evol, vol.24, pp.1380-1383, 2007.

R. C. Edgar, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, vol.32, pp.1792-1799, 2004.

T. Lassmann and E. L. Sonnhammer, Kalign -an accurate and fast multiple sequence alignment algorithm, BMC Bioinformatics, vol.6, 2005.

I. M. Wallace, O. O&apos;sullivan, D. G. Higgins, and C. Notredame, M-Coffee: combining multiple sequence alignment methods with T-Coffee, Nucleic Acids Res, vol.34, pp.1692-1701, 2006.

O. Gascuel, BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Mol Biol Evol, vol.14, pp.685-95, 1997.
URL : https://hal.archives-ouvertes.fr/lirmm-00730410

H. Akaike, Information theory and an extension of the maximum likelihood principle, Proc. 2nd Int. Symp. Inf. Theory, 2009.

J. Huerta-cepas, F. Serra, and P. Bork, ETE 3: reconstruction, analysis, and visualization of phylogenomic data, Mol Biol Evol, vol.33, pp.1635-1643, 2016.

M. N. Price, P. S. Dehal, and A. P. Arkin, FastTree 2 -approximately maximumlikelihood trees for large alignments, PLoS One, vol.5, 2010.

S. Q. Le and O. Gascuel, An improved general amino acid replacement matrix, Mol Biol Evol, vol.25, pp.1307-1327, 2008.
URL : https://hal.archives-ouvertes.fr/lirmm-00324106

A. Wehe, M. S. Bansal, J. G. Burleigh, and O. Eulenstein, DupTree: a program for largescale phylogenetic analyses using gene tree parsimony, Bioinformatics, vol.24, pp.1540-1541, 2008.

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

M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler et al., Gene ontology: tool for the unification of biology, Nat Genet, vol.25, pp.25-34, 2000.

F. Al-shahrour, R. Díaz-uriarte, and J. Dopazo, FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes, Bioinformatics, vol.20, pp.578-80, 2004.

F. Supek, M. Bo?njak, N. ?kunca, and T. ?muc, REVIGO summarizes and visualizes long lists of gene ontology terms, PLoS One, vol.6, 2011.

J. Aury, O. Jaillon, L. Duret, B. Noel, C. Jubin et al., Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia, Nature, vol.444, p.171, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00090904

J. Castresana, Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis, Mol Biol Evol, vol.17, pp.540-52, 2000.

Z. Yang, PAML 4: phylogenetic analysis by maximum likelihood, Mol Biol Evol, vol.24, pp.1586-91, 2007.

A. F. Vellozo, A. S. 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, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00632965

A. Conesa, S. Götz, J. M. García-gómez, J. Terol, M. Talón et al., Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, vol.21, pp.3674-3680, 2005.

Y. Moriya, M. Itoh, S. Okuda, A. C. Yoshizawa, and M. Kanehisa, KAAS: an automatic genome annotation and pathway reconstruction server, Nucleic Acids Res, vol.35, pp.182-187, 2007.

C. Claudel-renard, C. Chevalet, T. Faraut, and D. Kahn, Enzyme-specific profiles for genome annotation: PRIAM, Nucleic Acids Res, vol.31, pp.6633-6642, 2003.
URL : https://hal.archives-ouvertes.fr/hal-00427393

R. Caspi, R. Billington, C. A. Fulcher, I. M. Keseler, A. Kothari et al., The MetaCyc database of metabolic pathways and enzymes, Nucleic Acids Res, vol.46, pp.633-642, 2018.

P. D. Karp, M. Latendresse, S. M. Paley, M. Krummenacker, Q. D. Ong et al., Pathway tools version 19.0 update: software for pathway/genome informatics and systems biology, Brief Bioinform, vol.17, pp.877-90, 2016.

P. Baa-puyoulet, N. Parisot, G. Febvay, J. Huerta-cepas, A. F. Vellozo et al., ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods, Database, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01352558

J. L. Steffensen, K. Dufault-thompson, and Y. Zhang, PSAMM: a portable system for the analysis of metabolic models, PLoS Comput Biol, vol.12, 2016.

I. Thiele, N. Vlassis, and R. Fleming, fastGapFill: efficient gap filling in metabolic networks, Bioinformatics, vol.30, pp.2529-2560, 2014.

R. M. Waterhouse, E. V. Kriventseva, S. Meister, Z. Xi, K. S. Alvarez et al., Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes, Science, vol.316, pp.1738-1781, 2007.

J. E. Rebers and L. M. Riddiford, Structure and expression of a Manduca sexta larval cuticle gene homologous to Drosophila cuticle genes, J Mol Biol, vol.203, pp.411-434, 1988.

Z. S. Ioannidou, M. C. Theodoropoulou, N. C. Papandreou, J. H. Willis, and S. J. Hamodrakas, CutProtFam-Pred: detection and classification of putative structural cuticular proteins from sequence alone, based on profile Hidden Markov Models, Insect Biochem Mol Biol, vol.52, pp.51-60, 2014.

A. Gallot, C. Rispe, N. Leterme, J. Gauthier, S. Jaubert-possamai et al., Cuticular proteins and seasonal photoperiodism in aphids, Insect Biochem Mol Biol, vol.40, pp.235-275, 2010.

S. J. Nicholson, M. L. Nickerson, M. Dean, Y. Song, P. R. Hoyt et al., The genome of Diuraphis noxia, a global aphid pest of small grains, BMC Genomics, vol.16, 2015.

F. Sievers, A. Wilm, D. Dineen, T. J. Gibson, K. Karplus et al., Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega, Mol Syst Biol, vol.7, 2011.

A. Dereeper, V. Guignon, G. Blanc, S. Audic, S. Buffet et al., fr: robust phylogenetic analysis for the non-specialist, Nucleic Acids Res, vol.36, pp.465-474, 2008.
URL : https://hal.archives-ouvertes.fr/lirmm-00324099

V. M. Labunskyy, D. L. Hatfield, and V. N. Gladyshev, Selenoproteins: molecular pathways and physiological roles, Physiol Rev, vol.94, pp.739-77, 2014.

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

D. Santesmasses, M. Mariotti, and R. Guigó, Computational identification of the selenocysteine tRNA (tRNASec) in genomes, PLoS Comput Biol, vol.13, 2017.

L. Otero, L. Romanelli-cedrez, A. A. Turanov, V. N. Gladyshev, A. Miranda-vizuete et al., Adjustments, extinction, and remains of selenocysteine incorporation machinery in the nematode lineage, RNA, vol.20, pp.1023-1057, 2014.

M. Mariotti and R. Guigó, Selenoprofiles: profile-based scanning of eukaryotic genome sequences for selenoprotein genes, Bioinformatics, vol.26, pp.2656-63, 2010.

C. A. Villarroel, W. Jonckheere, J. M. Alba, J. J. Glas, W. Dermauw et al., Salivary proteins of spider mites suppress defenses in Nicotiana benthamiana and promote mite reproduction, Plant J, vol.86, pp.119-150, 2016.

C. N. Oates, K. J. Denby, A. A. Myburg, B. Slippers, and S. Naidoo, Insect gallers and their plant hosts: from omics data to systems biology, Int J Mol Sci, vol.2016, pp.1-14

R. Kofler, P. Orozco-terwengel, N. D. Maio, R. V. Pandey, V. Nolte et al., PoPoolation: a toolbox for population genetic analysis of next generation sequencing data from pooled individuals, PLoS One, vol.6, 2011.

L. Raynal, J. Marin, P. Pudlo, M. Ribatet, C. P. Robert et al., ABC random forests for Bayesian parameter inference, Bioinformatics, vol.35, pp.1720-1728, 2019.
URL : https://hal.archives-ouvertes.fr/hal-01337189

C. Rispe, F. Legeai, P. D. Nabity, R. Fernández, A. K. Arora et al., The genome sequence of the grape phylloxera provides insights into the evolution, adaptation and invasion routes of an iconic pest. NCBI accession number PRJNA588186
URL : https://hal.archives-ouvertes.fr/hal-02917617

C. Rispe, F. Legeai, P. D. Nabity, R. Fernández, A. K. Arora et al., The genome sequence of the grape phylloxera provides insights into the evolution, adaptation and invasion routes of an iconic pest. NCBI accession number PRJNA588387
URL : https://hal.archives-ouvertes.fr/hal-02917617

C. Rispe, F. Legeai, P. D. Nabity, R. Fernández, A. K. Arora et al., The genome sequence of the grape phylloxera provides insights into the evolution, adaptation and invasion routes of an iconic pest, Aphidbase repository
URL : https://hal.archives-ouvertes.fr/hal-02917617

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