Genome sequence of the pea aphid Acyrthosiphon pisum

Stephen Richards, Richard A. Gibbs, Nicole M. Gerardo, Nancy Moran, Atsushi Nakabachi, David Stern, Denis Tagu, Alex C.C. Wilson, Donna Muzny, Christie Kovar, Andy Cree, Joseph Chacko, Mimi N. Chandrabose, Marvin Diep Dao, Huyen H. Dinh, Ramatu Ayiesha Gabisi, Sandra Hines, Jennifer Hume, Shalini N. Jhangian, Vandita JoshiLora R. Lewis, Yih Shin Liu, John Lopez, Margaret B. Morgan, Ngoc Bich Nguyen, Geoffrey O. Okwuonu, San Juana Ruiz, Jireh Santibanez, Rita A. Wright, Gerald R. Fowler, Matthew E. Hitchens, Ryan J. Lozado, Charles Moen, David Steffen, James T. Warren, Jingkun Zhang, Lynne V. Nazareth, Dean Chavez, Clay Davis, Sandra L. Lee, Bella Mayurkumar Patel, Ling Ling Pu, Stephanie N. Bell, Angela Jolivet Johnson, Selina Vattathil, Rex L. Williams, Shuji Shigenobu, Phat M. Dang, Mizue Morioka, Takema Fukatsu, Toshiaki Kudo, Shin Ya Miyagishima, Huaiyang Jiang, Kim C. Worley, Fabrice Legeai, Jean Pierre Gauthier, Olivier Collin, Lan Zhang, Hsiu Chuan Chen, Olga Ermolaeva, Wratko Hlavina, Yuri Kapustin, Boris Kiryutin, Paul Kitts, Donna Maglott, Terence Murphy, Kim Pruitt, Victor Sapojnikov, Alexandre Souvorov, Françoise Thibaud-Nissen, Francisco Câmara, Roderic Guigó, Mario Stanke, Victor Solovyev, Peter Kosarev, Don Gilbert, Toni Gabaldón, Jaime Huerta-Cepas, Marina Marcet-Houben, Miguel Pignatelli, Andrés Moya, Claude Rispe, Morgane Ollivier, Hadi Quesneville, Emmanuelle Permal, Carlos Llorens, Ricardo Futami, Dale Hedges, Hugh M. Robertson, Tyler Alioto, Marco Mariotti, Naruo Nikoh, John P. McCutcheon, Gaelen Burke, Alexandra Kamins, Amparo Latorre, Peter Ashton, Federica Calevro, Hubert Charles, Stefano Colella, Angela E. Douglas, Georg Jander, Derek H. Jones, Gérard Febvay, Lars G. Kamphuis, Philip F. Kushlan, Sandy Macdonald, John Ramsey, Julia Schwartz, Stuart Seah, Gavin Thomas, Augusto Vellozo, Bodil Cass, Patrick Degnan, Bonnie Hurwitz, Teresa Leonardo, Ryuichi Koga, Boran Altincicek, Caroline Anselme, Hagop Atamian, Seth M. Barribeau, Martin De Vos, Elizabeth J. Duncan, Jay Evans, Murad Ghanim, Abdelaziz Heddi, Isgouhi Kaloshian, Carole Vincent-Monegat, Ben J. Parker, Vicente Pérez-Brocal, Yvan Rahbé, Chelsea J. Spragg, Javier Tamames, Daniel Tamarit, Cecilia Tamborindeguy, Andreas Vilcinskas, Ryan D. Bickel, Jennifer A. Brisson, Thomas Butts, Chun Che Chang, Olivier Christiaens, Gregory K. Davis, Elizabeth Duncan, David Ferrier, Masatoshi Iga, Ralf Janssen, Hsiao Ling Lu, Alistair McGregor, Toru Miura, Guy Smagghe, James Smith, Maurijn Van Der Zee, Rodrigo Velarde, Megan Wilson, Peter Dearden, Owain R. Edwards, Karl Gordon, Roland S. Hilgarth, Stanley Dean Rider, Dayalan Srinivasan, Thomas K. Walsh, Asano Ishikawa, Stéphanie Jaubert-Possamai, Brian Fenton, Wenting Huang, Guillaume Rizk, Dominique Lavenier, Jacques Nicolas, Carole Smadja, Jing Jiang Zhou, Filipe G. Vieira, Xiao Li He, Renhu Liu, Julio Rozas, Linda M. Field, Peter Campbell, James C. Carolan, Carol I.J. Fitzroy, Karen T. Reardon, Gerald R. Reeck, Karam Singh, Thomas L. Wilkinson, Jurgen Huybrechts, Mohatmed Abdel-Latief, Alain Robichon, Jan A. Veenstra, Frank Hauser, Giuseppe Cazzamali, Martina Schneider, Michael Williamson, Elisabeth Stafflinger, Karina K. Hansen, Cornelis J.P. Grimmelikhuijzen, Daniel R.G. Price, Marina Caillaud, Eric Van Fleet, Qinghu Ren, John A. Gatehouse, Véronique Brault, Baptiste Monsion, Jason Diaz, Laura Hunnicutt, Ho Jong Ju, Ximo Pechuan, José Aguilar, Teresa Cortés, Benjamín Ortiz-Rivas, David Martínez-Torres, Aviv Dombrovsky, Richard P. Dale, T. G.Emyr Davies, Martin S. Williamson, Andrew Jones, David Sattelle, Sally Williamson, Adrian Wolstenholme, Ludovic Cottret, Marie France Sagot, David G. Heckel, Wayne Hunter

Research output: Contribution to journalArticle

670 Scopus citations

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.

Original languageEnglish (US)
Article numbere1000313
JournalPLoS biology
Volume8
Issue number2
DOIs
StatePublished - Feb 2010

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)

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    Richards, S., Gibbs, R. A., Gerardo, N. M., Moran, N., Nakabachi, A., Stern, D., Tagu, D., Wilson, A. C. C., Muzny, D., Kovar, C., Cree, A., Chacko, J., Chandrabose, M. N., Dao, M. D., Dinh, H. H., Gabisi, R. A., Hines, S., Hume, J., Jhangian, S. N., ... Hunter, W. (2010). Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS biology, 8(2), [e1000313]. https://doi.org/10.1371/journal.pbio.1000313