Genome sequence of the pea aphid Acyrthosiphon pisum

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Publicated to:Plos Biology. 8 (2): e1000313- - 2010-02-01 8(2), DOI: 10.1371/journal.pbio.1000313

Authors: Richards, S; Gibbs, RA; Gerardo, NM; Moran, N; Nakabachi, A; Stern, D; Tagu, D; Wilson, ACC; Muzny, D; Kovar, C; Cree, A; Chacko, J; Chandrabose, MN; Dao, MD; Dinh, HH; Gabisi, RA; Hines, S; Hume, J; Jhangian, SN; Joshi, V; Lewis, LR; Liu, YS; Lopez, J; Morgan, MB; Nguyen, NB; Okwuonu, GO; Ruiz, SJ; Santibanez, J; Wright, RA; Fowler, GR; Hitchens, ME; Lozado, RJ; Moen, C; Steffen, D; Warren, JT; Zhang, JK; Nazareth, LV; Chavez, D; Davis, C; Lee, SL; Patel, BM; Pu, LL; Bell, SN; Johnson, AJ; Vattathil, S; Williams, RL; Shigenobu, S; Dang, PM; Morioka, M; Fukatsu, T; Kudo, T; Miyagishima, SY; Jiang, HY; Worley, KC; Legeai, F; Gauthier, JP; Collin, O; Zhang, L; Chen, HC; Ermolaeva, O; Hlavina, W; Kapustin, Y; Kiryutin, B; Kitts, P; Maglott, D; Murphy, T; Pruitt, K; Sapojnikov, V; Souvorov, A; Thibaud-Nissen, F; Câmara, F; Guigó, R; Stanke, M; Solovyev, V; Kosarev, P; Gilbert, D; Gabaldón, T; Huerta-Cepas, J; Marcet-Houben, M; Pignatelli, M; Moya, A; Rispe, C; Ollivier, M; Quesneville, H; Permal, E; Llorens, C; Futami, R; Hedges, D; Robertson, HM; Alioto, T; Mariotti, M; Nikoh, N; McCutcheon, JP; Burke, G; Kamins, A; Latorre, A; Kudo, T; Moran, NA; Ashton, P; Calevro, F; Charles, H; Colella, S; Douglas, A; Jander, G; Jones, DH; Febvay, G; Kamphuis, LG; Kushlan, PF; Macdonald, S; Ramsey, J; Schwartz, J; Seah, S; Thomas, G; Vellozo, A; Cass, B; Degnan, P; Hurwitz, B; Leonardo, T; Koga, R; Altincicek, B; Anselme, C; Atamian, H; Barribeau, SM; de Vos, M; Duncan, EJ; Evans, J; Ghanim, M; Heddi, A; Kaloshian, I; Vincent-Monegat, C; Parker, BJ; Pérez-Brocal, V; Rahbé, Y; Spragg, CJ; Tamames, J; Tamarit, D; Tamborindeguy, C; Vilcinskas, A; Bickel, RD; Brisson, JA; Butts, T; Chang, CC; Christiaens, O; Davis, GK; Duncan, E; Ferrier, D; Iga, M; Janssen, R; Lu, HL; McGregor, A; Miura, T; Smagghe, G; Smith, J; van der Zee, M; Velarde, R; Wilson, M; Dearden, P; Edwards, OR; Gordon, K; Hilgarth, RS; Rider, SD; Robertson, HM; Srinivasan, D; Walsh, TK; Ishikawa, A; Jaubert-Possamai, S; Fenton, B; Huang, WT; Jones, DH; Rizk, G; Lavenier, D; Nicolas, J; Smadja, C; Robertson, HM; Zhou, JJ; Vieira, FG; He, XL; Liu, RH; Rozas, J; Field, LM; Ashton, PD; Campbell, P; Carolan, JC; Douglas, AE; Fitzroy, CIJ; Reardon, KT; Reeck, GR; Singh, K; Wilkinson, TL; Huybrechts, J; Abdel-latief, M; Robichon, A; Veenstra, JA; Hauser, F; Cazzamali, G; Schneider, M; Williamson, M; Stafflinger, E; Hansen, KK; Grimmelikhuijzen, CJP; Price, DRG; Caillaud, M; van Fleet, E; Ren, QH; Gatehouse, JA; Brault, V; Monsion, B; Diaz, J; Hunnicutt, L; Ju, HJ; Pechuan, X; Aguilar, J; Cortés, T; Ortiz-Rivas, B; Martínez-Torres, D; Dombrovsky, A; Dale, RP; Davies, TGE; Williamson, MS; Jones, A; Sattelle, D; Williamson, S; Wolstenholme, A; Vellozo, A; Cottret, L; Febvay, G; Calevro, F; Sagot, MF; Heckel, DG; Hunter, W

Affiliations

Abteilung Bioinformatik - Author

Advanced Science Institute - Author

ARS, USDA, Natl Peanut Res Lab, Dawson, GA USA - Author

Baylor Coll Med, Human Genome Sequencing Ctr, Houston, TX 77030 USA - Author

Baylor College of Medicine - Author

Boyce Thompson Inst Plant Res, Ithaca, NY USA - Author

Centro de Regulacion Genomica, Barcelona - Author

CIBER Epidemiologia y Salud Publica - Author

CIBEResp, Valencia, Spain - Author

Conselleria Sanidad Generalitat Valenciana, CSISP, Valencia, Spain - Author

Cornell Univ, Dept Entomol, Ithaca, NY 14853 USA - Author

CRG, Bioinformat & Genom Programme, Barcelona, Spain - Author

CSIRO Entomol, CELS, Floreat Pk, Australia - Author

CSIRO Plant Ind, CELS, Floreat Pk, Australia - Author

Ctr Rech Versailles, INRA, Unite Rech Genom Info UR INRA 1164, Versailles, France - Author

Discovery Res Inst, Saitama, Japan - Author

Discovery Research Institute Wako - Author

Emory Univ, O Wayne Rollins Res Ctr, Dept Biol, Atlanta, GA 30322 USA - Author

Emory University - Author

EPI Symbiose, CNRS, IRISA, Rennes, France - Author

Indiana Univ, Dept Biol, Bloomington, IN 47405 USA - Author

Indiana University - Author

INRA Institut National de La Recherche Agronomique - Author

INRA, UMR BiO3P, Domaine De La Motte, Le Rheu, France - Author

Inst Mikrobiol & Genet, Abt Bioinformat, Gottingen, Germany - Author

Institut Cavanilles de Biodiversitat i Biologia Evolutiva - Author

Institut de Recherche en Informatique et Systemes Aleatoires - Author

Institut National des Sciences Appliquees de Lyon - Author

Japan Science and Technology Agency - Author

JST, PRESTO, Saitama 3320012, Japan - Author

Miami Inst Human Genom, Miami, FL USA - Author

Miami Institute for Human Genomics - Author

National Institute of Advanced Industrial Science and Technology - Author

National Institutes of Natural Sciences - Okazaki Institute for Integrative Bioscience - Author

National Library of Medicine - Author

Natl Inst Adv Ind Sci & Technol, Tsukuba, Ibaraki, Japan - Author

Natl Inst Nat Sci, Okazaki Inst Integrat Biosci, Okazaki, Aichi, Japan - Author

NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20892 USA - Author

Open Univ, Div Nat Sci, Chiba, Japan - Author

Princeton Univ, Dept Ecol & Evolutionary Biol, Princeton, NJ 08544 USA - Author

Princeton Univ, Howard Hughes Med Inst, Princeton, NJ 08544 USA - Author

Princeton University - Author

RIKEN, Adv Sci Inst, Wako, Saitama 3510198, Japan - Author

Royal Holloway University of London - Author

Softberry Inc, Mt Kisco, NY 10549 USA - Author

Softberry, Inc. - Author

The Open University of Japan - Author

Unité de Recherche Génomique-Info - Author

Univ Arizona, Ctr Insect Sci, Tucson, AZ 85721 USA - Author

Univ Arizona, Dept Ecol & Evolutionary Biol, Tucson, AZ USA - Author

Univ Giessen, Inst Phytopathol & Appl Zool, Interdisciplinary Res Ctr, Giessen, Germany - Author

Univ Illinois, Dept Entomol, Urbana, IL 61801 USA - Author

Univ London, Dept Comp Sci, Surrey, England - Author

Univ Lyon, CNRS, UMR5558, Lab Biometrie & Biol Evolut, Villeurbanne, France - Author

Univ Lyon, INSA Lyon, INRA, IFR41,UMR203,Biol Fonct Insects & Interact BF2I, Villeurbanne, France - Author

Univ Miami, Dept Biol, Coral Gables, FL 33124 USA - Author

Univ Nice, CNRS 6243, INRA 1301, UMR Interact Biot & Sante Vegetale, Sophia Antipolis, France - Author

Univ Pompeu Fabra, Ctr Regulacio Genom, Barcelona, Spain - Author

Univ Pompeu Fabra, Res Grp Biomed Informat, Barcelona, Spain - Author

Univ Tokyo, Grad Sch Sci, Dept Biol Sci, Tokyo, Japan - Author

Univ Valencia, Inst Cavanilles Biodivers & Biol Evolut, Valencia, Spain - Author

Univ York, Dept Biol, York, N Yorkshire, England - Author

Universitat Pompeu Fabra Barcelona - Author

University of Arizona - Author

University of Illinois at Urbana-Champaign - Author

University of Miami - Author

University of Tokyo - Author

University of Valencia - Author

University of York - Author

USDA ARS National Peanut Research Laboratory - Author

Abstract

Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.

Keywords

AnimalsAphidsApis-melliferaBuchneraCpg methylationDna-sequencesDrosophila circadian clockGene transfer, horizontalGene-expressionGenome, insectPheromone-bindingRepetitive elementsSocial insectSymbiosisSymbiotic bacteriaTandem repeats

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The work has been published in the journal Plos Biology due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2010, it was in position 1/86, thus managing to position itself as a Q1 (Primer Cuartil), in the category Biology.

From a relative perspective, and based on the normalized impact indicator calculated from the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 69.9, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: Dimensions Jun 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-06-29, the following number of citations:

WoS: 557
Europe PMC: 559

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This work has been carried out with international collaboration, specifically with researchers from: Australia; Austria; Belgium; Denmark; France; Germany; Israel; Japan; Netherlands; New Zealand; Sweden; Taiwan; United Kingdom; United States of America.

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