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3 de junio de 2024
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Genome sequence of the pea aphid Acyrthosiphon pisum

Publicado en:Plos Biology. 8 (2): - 2010-01-01 8(2), DOI: 10.1371/journal.pbio.1000313

Autores: 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

Afiliaciones

Advanced Science Institute, Saitama, Japan - Autor o Coautor
Animal and Plant Sciences Department, University of Sheffield, United Kingdom - Autor o Coautor
Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Barcelona, Spain - Autor o Coautor
Biotechvana, Parc Cientific, Universitat de València, València, Spain - Autor o Coautor
Boyce Thompson Institute for Plant Research, Ithaca, NY, United States - Autor o Coautor
Center de Regulació Genòmica, Universitat Pompeu Fabra, Barcelona, Spain - Autor o Coautor
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 - Autor o Coautor
Center for Functional and Comparative Insect Genomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark - Autor o Coautor
Center for Insect Science, University of Arizona, Tucson, AZ, United States - Autor o Coautor
CNRS, IRISA, EPI Symbiose, Rennes, France - Autor o Coautor
Cooperative Research Centre for National Plant Biosecurity, Canberra, ACT, Australia, Department of Biochemistry, Kansas State University, Manhattan, KS, United States - Autor o Coautor
CSIRO Entomology, Black Mountain Laboratories, Acton, NSW, Australia - Autor o Coautor
CSIRO Entomology, Centre for Environment and Life Sciences (CELS), Floreat Park, WA, Australia - Autor o Coautor
CSIRO Entomology, Centre for Environment and Life Sciences (CELS), Floreat Park, WA, Australia, Cooperative Research Centre for National Plant Biosecurity, Canberra, ACT, Australia - Autor o Coautor
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 - Autor o Coautor
CSIRO Plant Industry, Centre for Environment and Life Sciences (CELS), Floreat Park, WA, Australia - Autor o Coautor
Departament de Genètica, Universitat de Barcelona, Barcelona, Spain - Autor o Coautor
Department of Biological Chemistry, Rothamsted Research, Harpenden, United Kingdom - Autor o Coautor
Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan - Autor o Coautor
Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom - Autor o Coautor
Department of Biology, Bryn Mawr College, Bryn Mawr, PA, United States - Autor o Coautor
Department of Biology, Emory University, O. Wayne Rollins Research Center, Atlanta, GA, United States - Autor o Coautor
Department of Biology, Indiana University, Bloomington, IN, United States - Autor o Coautor
Department of Biology, Ithaca College, Ithaca, NY, United States - Autor o Coautor
Department of Biology, University of Miami, Coral Gables, FL, United States - Autor o Coautor
Department of Biology, University of York, York, United Kingdom - Autor o Coautor
Department of Biology, Wake Forest University, Winston-Salem, NC, United States - Autor o Coautor
Department of Computer Science, Royal Holloway, University of London, Surrey, United Kingdom - Autor o Coautor
Department of Earth Sciences, Palaeobiology, Uppsala University, Uppsala, Sweden - Autor o Coautor
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, United States - Autor o Coautor
Department of Entomology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan - Autor o Coautor
Department of Entomology, Cornell University, Ithaca, NY, United States - Autor o Coautor
Department of Entomology, Texas A and M University, College Station, TX, United States - Autor o Coautor
Department of Entomology, University of Illinois, Urbana-Champaign, IL, United States - Autor o Coautor
Department of Entomology, Volcani Center, Bet Dagan, Israel - Autor o Coautor
Department of Pathobiology, Texas A and M University, College Station, TX, United States - Autor o Coautor
Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, United States - Autor o Coautor
Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, United States - Autor o Coautor
Department of Virology, Volcani Center, Bet Dagan, Israel - Autor o Coautor
Department of Zoology, University of Oxford, Oxford, United Kingdom - Autor o Coautor
Discovery Research Institute, Saitama, Japan - Autor o Coautor
Division of Natural Sciences, Open University of Japan, Wakaba, Chiba, Japan - Autor o Coautor
ENS Cachan, INRIA, EPI Symbiose, Rennes, France - Autor o Coautor
Freie Universität Berlin, Institut für Angewandte Zoologie, Berlin, Germany - Autor o Coautor
Genomic Sciences Program, North Carolina State University, Raleigh, NC, United States - Autor o Coautor
Graduate Program in Genetics, Genomics and Bioinformatics, Department of Nematology, University of California, Riverside, CA, United States - Autor o Coautor
Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan - Autor o Coautor
Howard Hughes Medical Institute, Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, United States - Autor o Coautor
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 - Autor o Coautor
Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States - Autor o Coautor
INRA UMR SVQV, Equipe Virologie Vection, Colmar, France - Autor o Coautor
INRA, UMR BiO3P, Domaine de La Motte, Le Rheu, France - Autor o Coautor
INRIA, IRISA, EPI Symbiose, Rennes, France - Autor o Coautor
Institut für Mikrobiologie und Genetik, Abteilung für Bioinformatik, Göttingen, Germany - Autor o Coautor
Institute for Biology, Leiden University, Leiden, Netherlands - Autor o Coautor
Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, València, Spain - Autor o Coautor
Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universitat de València, València, Spain, Biotechvana, Parc Cientific, Universitat de València, València, Spain - Autor o Coautor
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 - Autor o Coautor
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 - Autor o Coautor
Interdisciplinary Research Center, Institute of Phytopathology and Applied Zoology, Justus-Liebig-University of Giessen, Giessen, Germany - Autor o Coautor
J. Craig Venter Institute, Rockville, MD, United States - Autor o Coautor
Lab. Agrozoology, Department Crop Protection, Ghent University, Ghent, Belgium - Autor o Coautor
Max Planck Institute for Chemical Ecology, Jena, Germany - Autor o Coautor
Miami Institute for Human Genomics, 1120 NW 14th Street, Miami, FL, United States - Autor o Coautor
Molecular and Computational Biology, University of Southern California, Los Angeles, CA, United States - Autor o Coautor
MRC Functional Genomics Unit, Department of Phisology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom - Autor o Coautor
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States - Autor o Coautor
National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan - Autor o Coautor
National Research Centre for Growth and Development, Department of Biochemistry, University of Otago, Dunedin, New Zealand - Autor o Coautor
Plant Pathology, SCRI, Invergowrie and The Scottish Crop Research Institute, Dundee, United Kingdom - Autor o Coautor
Research Group of Functional Genomics and Proteomics, Leuven, Belgium - Autor o Coautor
S.; Human Genome Sequencing Center; Baylor College of Medicine; Houston; TX; United States - Autor o Coautor
School of Biological and Biomedical Sciences, Durham University, Durham, United Kingdom - Autor o Coautor
Scottish Oceans Institute, University of St. Andrews, St. Andrews, Fife, United Kingdom - Autor o Coautor
Softberry Inc., Mount Kisco, NY, United States - Autor o Coautor
Syngenta, Jealotts Hill Research Centre, Bracknell, Berkshire, United Kingdom - Autor o Coautor
UCD School of Biology and Environmental Science, University College Dublin, Ireland - Autor o Coautor
UMR Interactions Biotiques et Santé Végétale, INRA 1301, Université de Nice-Sophia Antipolis, Sophia-Antipolis Cedex, France - Autor o Coautor
UMR203 Biologie Fonctionnelle Insectes et Interactions (BF2I), INSA-Lyon, Université de Lyon, Villeurbanne, France - Autor o Coautor
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 - Autor o Coautor
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 - Autor o Coautor
Unité de Recherches en Génomique-Info (UR INRA 1164), INRA, Centre de Recherche de Versailles, Versailles Cedex, France - Autor o Coautor
United States Department of Agriculture, Agriculture Research Service, U.S. Horticultural Research Lab., Fort Pierce, FL, United States - Autor o Coautor
Université de Bordeaux, CNRS, Talence, France - Autor o Coautor
Université de Lyon, CNRS, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France - Autor o Coautor
Université de Rennes 1, IRISA, EPI Symbiose, Rennes, France - Autor o Coautor
University of Veterinary Medicine Vienna, Institut für Populations-genetik, Veterinärmedizinische Universität Wien, Vienna, Austria - Autor o Coautor
USDA, ARS, National Peanut Research Laboratory, Dawson, GA, United States - Autor o Coautor
USDA-ARS, Bee Research Laboratoy, Beltsville, MD, United States - Autor o Coautor
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Resumen

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.

Palabras clave

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

Indicios de calidad

Impacto bibliométrico. Análisis de la aportación y canal de difusión

El trabajo ha sido publicado en la revista Plos Biology debido a la progresión y el buen impacto que ha alcanzado en los últimos años, según la agencia WoS (JCR), se ha convertido en una referencia en su campo. En el año de publicación del trabajo, 2010, se encontraba en la posición 1/86, consiguiendo con ello situarse como revista Q1 (Primer Cuartil), en la categoría Biology.

Desde una perspectiva relativa, y atendiendo al indicador del impacto normalizado calculado a partir del Field Citation Ratio (FCR) de la fuente Dimensions, arroja un valor de: 69.87, lo que indica que, de manera comparada con trabajos en la misma disciplina y en el mismo año de publicación, lo ubica como trabajo citado por encima de la media. (fuente consultada: Dimensions Jul 2025)

De manera concreta y atendiendo a las diferentes agencias de indexación, el trabajo ha acumulado, hasta la fecha 2025-07-04, el siguiente número de citas:

  • Scopus: 851

Impacto y visibilidad social

Desde la dimensión de Influencia o adopción social, y tomando como base las métricas asociadas a las menciones e interacciones proporcionadas por agencias especializadas en el cálculo de las denominadas “Métricas Alternativas o Sociales”, podemos destacar a fecha 2025-07-04:

  • El uso, desde el ámbito académico evidenciado por el indicador de la agencia Altmetric referido como agregaciones realizadas por el gestor bibliográfico personal Mendeley, nos da un total de: 907.
  • La utilización de esta aportación en marcadores, bifurcaciones de código, añadidos a listas de favoritos para una lectura recurrente, así como visualizaciones generales, indica que alguien está usando la publicación como base de su trabajo actual. Esto puede ser un indicador destacado de futuras citas más formales y académicas. Tal afirmación es avalada por el resultado del indicador “Capture” que arroja un total de: 928 (PlumX).

Con una intencionalidad más de divulgación y orientada a audiencias más generales podemos observar otras puntuaciones más globales como:

  • El Score total de Altmetric: 45.69.
  • El número de menciones en la red social Facebook: 1 (Altmetric).
  • El número de menciones en la red social X (antes Twitter): 3 (Altmetric).
  • El número de menciones en Wikipedia: 14 (Altmetric).

Es fundamental presentar evidencias que respalden la plena alineación con los principios y directrices institucionales en torno a la Ciencia Abierta y la Conservación y Difusión del Patrimonio Intelectual. Un claro ejemplo de ello es:

  • El trabajo se ha enviado a una revista cuya política editorial permite la publicación en abierto Open Access.

Análisis de liderazgo de los autores institucionales

Este trabajo se ha realizado con colaboración internacional, concretamente con investigadores de: Australia; Austria; Belgium; Denmark; France; Germany; India; Israel; Japan; Netherlands; New Zealand; Sweden; Taiwan; United Kingdom; United States of America.