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Genome sequence of the pea aphid Acyrthosiphon pisum

Richards, Stephen; Gibbs, Richard A.; Gerardo, Nicole M.; Moran, Nancy; Nakabachi, Atsushi; Stern, David LU ; Tagu, Denis; Wilson, Alex C C; Muzny, Donna and Kovar, Christie, et al. (2010) In PLoS Biology 8(2). p.1-24
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... (More)

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.

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8
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1 - 24
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Public Library of Science
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1544-9173
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10.1371/journal.pbio.1000313
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English
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3200371b-940b-41f6-ad0b-8060426b23e1
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@article{3200371b-940b-41f6-ad0b-8060426b23e1,
  abstract     = {<p>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.</p>},
  articleno    = {e1000313},
  author       = {Richards, Stephen and Gibbs, Richard A. and Gerardo, Nicole M. and Moran, Nancy and Nakabachi, Atsushi and Stern, David and Tagu, Denis and Wilson, Alex C C and Muzny, Donna and Kovar, Christie and Cree, Andy and Chacko, Joseph and Chandrabose, Mimi N. and Dao, Marvin Diep and Dinh, Huyen H. and Gabisi, Ramatu Ayiesha and Hines, Sandra and Hume, Jennifer and Jhangian, Shalini N. and Joshi, Vandita and Lewis, Lora R. and Liu, Yih Shin and Lopez, John and Morgan, Margaret B. and Nguyen, Ngoc Bich and Okwuonu, Geoffrey O. and Ruiz, San Juana and Santibanez, Jireh and Wright, Rita A. and Fowler, Gerald R. and Hitchens, Matthew E. and Lozado, Ryan J. and Moen, Charles and Steffen, David and Warren, James T. and Zhang, Jingkun and Nazareth, Lynne V. and Chavez, Dean and Davis, Clay and Lee, Sandra L. and Patel, Bella Mayurkumar and Pu, Ling Ling and Bell, Stephanie N. and Johnson, Angela Jolivet and Vattathil, Selina and Williams, Rex L. and Shigenobu, Shuji and Dang, Phat M. and Morioka, Mizue and Fukatsu, Takema and Kudo, Toshiaki and Miyagishima, Shin Ya and Jiang, Huaiyang and Worley, Kim C. and Legeai, Fabrice and Gauthier, Jean Pierre and Collin, Olivier and Zhang, Lan and Chen, Hsiu Chuan and Ermolaeva, Olga and Hlavina, Wratko and Kapustin, Yuri and Kiryutin, Boris and Kitts, Paul and Maglott, Donna and Murphy, Terence and Pruitt, Kim and Sapojnikov, Victor and Souvorov, Alexandre and Thibaud-Nissen, Françoise and Câmara, Francisco and Guigó, Roderic and Stanke, Mario and Solovyev, Victor and Kosarev, Peter and Gilbert, Don and Gabaldón, Toni and Huerta-Cepas, Jaime and Marcet-Houben, Marina and Pignatelli, Miguel and Moya, Andrés and Rispe, Claude and Ollivier, Morgane and Quesneville, Hadi and Permal, Emmanuelle and Llorens, Carlos and Futami, Ricardo and Hedges, Dale and Robertson, Hugh M. and Alioto, Tyler and Mariotti, Marco and Nikoh, Naruo and McCutcheon, John P. and Burke, Gaelen and Kamins, Alexandra and Latorre, Amparo and Ashton, Peter and Calevro, Federica and Charles, Hubert and Colella, Stefano and Douglas, Angela E. and Jander, Georg and Jones, Derek H. and Febvay, Gérard and Kamphuis, Lars G. and Kushlan, Philip F. and Macdonald, Sandy and Ramsey, John and Schwartz, Julia and Seah, Stuart and Thomas, Gavin and Vellozo, Augusto and Cass, Bodil and Degnan, Patrick and Hurwitz, Bonnie and Leonardo, Teresa and Koga, Ryuichi and Altincicek, Boran and Anselme, Caroline and Atamian, Hagop and Barribeau, Seth M. and De Vos, Martin and Duncan, Elizabeth J. and Evans, Jay and Ghanim, Murad and Heddi, Abdelaziz and Kaloshian, Isgouhi and Vincent-Monegat, Carole and Parker, Ben J. and Pérez-Brocal, Vicente and Rahbé, Yvan and Spragg, Chelsea J. and Tamames, Javier and Tamarit, Daniel and Tamborindeguy, Cecilia and Vilcinskas, Andreas and Bickel, Ryan D. and Brisson, Jennifer A. and Butts, Thomas and Chang, Chun Che and Christiaens, Olivier and Davis, Gregory K. and Duncan, Elizabeth and Ferrier, David and Iga, Masatoshi and Janssen, Ralf and Lu, Hsiao Ling and McGregor, Alistair and Miura, Toru and Smagghe, Guy and Smith, James and Van Der Zee, Maurijn and Velarde, Rodrigo and Wilson, Megan and Dearden, Peter and Edwards, Owain R. and Gordon, Karl and Hilgarth, Roland S. and Rider, Stanley Dean and Srinivasan, Dayalan and Walsh, Thomas K. and Ishikawa, Asano and Jaubert-Possamai, Stéphanie and Fenton, Brian and Huang, Wenting and Rizk, Guillaume and Lavenier, Dominique and Nicolas, Jacques and Smadja, Carole and Zhou, Jing Jiang and Vieira, Filipe G. and He, Xiao Li and Liu, Renhu and Rozas, Julio and Field, Linda M. and Campbell, Peter and Carolan, James C. and Fitzroy, Carol I J and Reardon, Karen T. and Reeck, Gerald R. and Singh, Karam and Wilkinson, Thomas L. and Huybrechts, Jurgen and Abdel-Latief, Mohatmed and Robichon, Alain and Veenstra, Jan A. and Hauser, Frank and Cazzamali, Giuseppe and Schneider, Martina and Williamson, Michael and Stafflinger, Elisabeth and Hansen, Karina K. and Grimmelikhuijzen, Cornelis J P and Price, Daniel R G and Caillaud, Marina and Van Fleet, Eric and Ren, Qinghu and Gatehouse, John A. and Brault, Véronique and Monsion, Baptiste and Diaz, Jason and Hunnicutt, Laura and Ju, Ho Jong and Pechuan, Ximo and Aguilar, José and Cortés, Teresa and Ortiz-Rivas, Benjamín and Martínez-Torres, David and Dombrovsky, Aviv and Dale, Richard P. and Davies, T. G Emyr and Williamson, Martin S. and Jones, Andrew and Sattelle, David and Williamson, Sally and Wolstenholme, Adrian and Cottret, Ludovic and Sagot, Marie France and Heckel, David G. and Hunter, Wayne},
  issn         = {1544-9173},
  language     = {eng},
  number       = {2},
  pages        = {1--24},
  publisher    = {Public Library of Science},
  series       = {PLoS Biology},
  title        = {Genome sequence of the pea aphid Acyrthosiphon pisum},
  url          = {http://dx.doi.org/10.1371/journal.pbio.1000313},
  volume       = {8},
  year         = {2010},
}