Genome sequence of the pea aphid Acyrthosiphon pisum

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Huerta-Cepas J.Author

June 3, 2024

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Publicated to:Plos Biology. 8 (2): - 2010-01-01 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 Y-S; 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 J; Nazareth LV; Chavez D; Davis C; Lee SL; Patel BM; Pu L-L; Bell SN; Johnson AJ; Vattathil S; Williams Jr RL; Shigenobu S; Dang PM; Morioka M; Fukatsu T; Kudo T; Miyagishima S-Y; Jiang H; Worley KC; Legeai F; Gauthier J-P; Collin O; Zhang L; Chen H-C; 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; Ashton P; Calevro F; Charles H; Colella S; Douglas AE; 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 C-C; Christiaens O; Davis GK; Duncan E; Ferrier D; Iga M; Janssen R; Lu H-L; 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 Jr SD; Srinivasan D; Walsh TK; Ishikawa A; Jaubert-Possamai S; Fenton B; Huang W; Rizk G; Lavenier D; Nicolas J; Smadja C; Zhou J-J; Vieira FG; He X-L; Liu R; Rozas J; Field LM; Campbell P; Carolan JC; 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 Q; Gatehouse JA; Brault V; Monsion B; Diaz J; Hunnicutt L; Ju H-J; 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; Cottret L; Sagot MF; Heckel DG; Hunter W

Affiliations

Advanced Science Institute, Saitama, Japan - Author

Animal and Plant Sciences Department, University of Sheffield, United Kingdom - Author

Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain - Author

Biotechvana, Parc Cientific, Universitat de València, València, Spain - Author

Boyce Thompson Institute for Plant Research, Ithaca, NY, United States - Author

Center de Regulació Genòmica, Universitat Pompeu Fabra, Barcelona, Spain - Author

Center de Regulació Genòmica, Universitat Pompeu Fabra, Barcelona, Spain, Research Group in Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain - Author

Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark - Author

Center for Insect Science, University of Arizona, Tucson, AZ, United States - Author

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

Cooperative Research Centre for National Plant Biosecurity, Canberra, ACT, Australia, Department of Biochemistry, Kansas State University, Manhattan, KS, United States - Author

CSIRO Entomology, Black Mountain Laboratories, Acton, NSW, Australia - Author

CSIRO Entomology, Centre for Environment and Life Sciences (CELS), Floreat Park, WA, Australia - Author

CSIRO Entomology, Centre for Environment and Life Sciences (CELS), Floreat Park, WA, Australia, Cooperative Research Centre for National Plant Biosecurity, Canberra, ACT, Australia - Author

CSIRO Entomology, Centre for Environment and Life Sciences (CELS), Floreat Park, WA, Australia, CSIRO Plant Industry, Centre for Environment and Life Sciences (CELS), Floreat Park, WA, Australia - Author

CSIRO Plant Industry, Centre for Environment and Life Sciences (CELS), Floreat Park, WA, Australia - Author

Departament de Genètica, Universitat de Barcelona, Barcelona, Spain - Author

Department of Biological Chemistry, Rothamsted Research, Harpenden, United Kingdom - Author

Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan - Author

Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom - Author

Department of Biology, Bryn Mawr College, Bryn Mawr, PA, United States - Author

Department of Biology, Emory University, O. Wayne Rollins Research Center, Atlanta, GA, United States - Author

Department of Biology, Indiana University, Bloomington, IN, United States - Author

Department of Biology, Ithaca College, Ithaca, NY, United States - Author

Department of Biology, University of Miami, Coral Gables, FL, United States - Author

Department of Biology, University of York, York, United Kingdom - Author

Department of Biology, Wake Forest University, Winston-Salem, NC, United States - Author

Department of Computer Science, Royal Holloway, University of London, Surrey, United Kingdom - Author

Department of Earth Sciences, Palaeobiology, Uppsala University, Uppsala, Sweden - Author

Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States - Author

Department of Entomology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan - Author

Department of Entomology, Cornell University, Ithaca, NY, United States - Author

Department of Entomology, Texas A and M University, College Station, TX, United States - Author

Department of Entomology, University of Illinois, Urbana-Champaign, IL, United States - Author

Department of Entomology, Volcani Center, Bet Dagan, Israel - Author

Department of Pathobiology, Texas A and M University, College Station, TX, United States - Author

Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States - Author

Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, United States - Author

Department of Virology, Volcani Center, Bet Dagan, Israel - Author

Department of Zoology, University of Oxford, Oxford, United Kingdom - Author

Discovery Research Institute, Saitama, Japan - Author

Division of Natural Sciences, Open University of Japan, Wakaba, Chiba, Japan - Author

ENS Cachan, INRIA, EPI Symbiose, Rennes, France - Author

Freie Universität Berlin, Institut für Angewandte Zoologie, Berlin, Germany - Author

Genomic Sciences Program, North Carolina State University, Raleigh, NC, United States - Author

Graduate Program in Genetics, Genomics and Bioinformatics, Department of Nematology, University of California, Riverside, CA, United States - Author

Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan - Author

Howard Hughes Medical Institute, Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States - Author

Howard Hughes Medical Institute, Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States, PRESTO, JST, 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan, Okazaki Institute for Integrative Bioscience, National Inst - Author

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States - Author

INRA UMR SVQV, Equipe Virologie Vection, Colmar, France - Author

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

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

Institut für Mikrobiologie und Genetik, Abteilung für Bioinformatik, Göttingen, Germany - Author

Institute for Biology, Leiden University, Leiden, Netherlands - Author

Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, València, Spain - Author

Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, València, Spain, Biotechvana, Parc Cientific, Universitat de València, València, Spain - Author

Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, València, Spain, CIBER en Epidemiología y Salud Pública (CIBEResp), Centro Superior de Investigación en Salud Pública (CSISP), Conselleria de Sanidad (Generalitat Valenci - Author

Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, València, Spain, UMR203 Biologie Fonctionnelle Insectes et Interactions (BF2I), INSA-Lyon, Université de Lyon, Villeurbanne, France - Author

Interdisciplinary Research Center, Institute of Phytopathology and Applied Zoology, Justus-Liebig-University of Giessen, Giessen, Germany - Author

J. Craig Venter Institute, Rockville, MD, United States - Author

Lab. Agrozoology, Department Crop Protection, Ghent University, Ghent, Belgium - Author

Max Planck Institute for Chemical Ecology, Jena, Germany - Author

Miami Institute for Human Genomics, 1120 NW 14th Street, Miami, FL, United States - Author

Molecular and Computational Biology, University of Southern California, Los Angeles, CA, United States - Author

MRC Functional Genomics Unit, Department of Phisology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom - Author

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States - Author

National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan - Author

National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, Dunedin, New Zealand - Author

Plant Pathology, SCRI, Invergowrie and The Scottish Crop Research Institute, Dundee, United Kingdom - Author

Research Group of Functional Genomics and Proteomics, Leuven, Belgium - Author

S.; Human Genome Sequencing Center; Baylor College of Medicine; Houston; TX; United States - Author

School of Biological and Biomedical Sciences, Durham University, Durham, United Kingdom - Author

Scottish Oceans Institute, University of St. Andrews, St. Andrews, Fife, United Kingdom - Author

Softberry Inc., Mount Kisco, NY, United States - Author

Syngenta, Jealotts Hill Research Centre, Bracknell, Berkshire, United Kingdom - Author

UCD School of Biology and Environmental Science, University College Dublin, Ireland - Author

UMR Interactions Biotiques et Santé Végétale, INRA 1301, Université de Nice-Sophia Antipolis, Sophia-Antipolis Cedex, France - Author

UMR203 Biologie Fonctionnelle Insectes et Interactions (BF2I), INSA-Lyon, Université de Lyon, Villeurbanne, France - Author

UMR203 Biologie Fonctionnelle Insectes et Interactions (BF2I), INSA-Lyon, Université de Lyon, Villeurbanne, France, UMR Interactions Biotiques et Santé Végétale, INRA 1301, Université de Nice-Sophia Antipolis, Sophia-Antipolis Cedex, France - Author

UMR203 Biologie Fonctionnelle Insectes et Interactions (BF2I), INSA-Lyon, Université de Lyon, Villeurbanne, France, Université de Lyon, CNRS, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France - Author

Unité de Recherches en Génomique-Info (UR INRA 1164), INRA, Centre de Recherche de Versailles, Versailles Cedex, France - Author

United States Department of Agriculture, Agriculture Research Service, U.S. Horticultural Research Lab., Fort Pierce, FL, United States - Author

Université de Bordeaux, CNRS, Talence, France - Author

Université de Lyon, CNRS, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France - Author

Université de Rennes 1, IRISA, EPI Symbiose, Rennes, France - Author

University of Veterinary Medicine Vienna, Institut für Populations-genetik, Veterinärmedizinische Universität Wien, Vienna, Austria - Author

USDA, ARS, National Peanut Research Laboratory, Dawson, GA, United States - Author

USDA-ARS, Bee Research Laboratoy, Beltsville, MD, United States - 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

Acyrthosiphon pisumAphidAphididaeArticleBacteria (microorganisms)BacteriumBiogenic amineBuchnera (proteobacteria)Cell cycleChitinChromatinCircadian rhythmDetoxificationDnaEmbryo developmentEnzyme activationGenomeHexapodaHorizontal gene transferHostHost resistanceImmune systemInsectJuvenile hormoneLife cycleMeiosisMicrornaMitosisMultigene familyNeuropeptideNonhumanPeaPlantPlant insect interactionPlant virusRetinoid x receptorSex determinationSignal transductionSymbiontSymbiosisTelomereTranscription factorVirus transmission

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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: 69.94, 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 Jul 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-07-17, the following number of citations:

Scopus: 851

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

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