Genome sequence of the pea aphid Acyrthosiphon pisum

Stephen Richards, Richard A. Gibbs, Nicole M. Gerardo, Nancy Moran, Atsushi Nakabachi, David Stern, Denis Tagu, Alexandra 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

639 Citations (Scopus)

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
Article numbere1000313
JournalPLoS Biology
Volume8
Issue number2
DOIs
StatePublished - Feb 1 2010

Fingerprint

Aphids
Acyrthosiphon pisum
Peas
Genes
Genome
genome
Buchnera
genes
Aphidoidea
Insects
Insect Genome
selenoproteins
genome assembly
plant-insect relations
Selenoproteins
insects
Biological Models
Gene Duplication
Symbiosis
gene duplication

ASJC Scopus subject areas

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

Cite this

Richards, S., Gibbs, R. A., Gerardo, N. M., Moran, N., Nakabachi, A., Stern, D., ... Hunter, W. (2010). Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biology, 8(2), [e1000313]. https://doi.org/10.1371/journal.pbio.1000313

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

In: PLoS Biology, Vol. 8, No. 2, e1000313, 01.02.2010.

Research output: Contribution to journalArticle

Richards, S, Gibbs, RA, Gerardo, NM, Moran, N, Nakabachi, A, Stern, D, Tagu, D, Wilson, A, 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, J, 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, H, 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, 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, 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, Srinivasan, D, Walsh, TK, Ishikawa, A, Jaubert-Possamai, S, Fenton, B, Huang, W, Rizk, G, Lavenier, D, Nicolas, J, Smadja, C, Zhou, JJ, Vieira, FG, He, XL, 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, 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, Cottret, L, Sagot, MF, Heckel, DG & Hunter, W 2010, 'Genome sequence of the pea aphid Acyrthosiphon pisum', PLoS Biology, vol. 8, no. 2, e1000313. https://doi.org/10.1371/journal.pbio.1000313
Richards S, Gibbs RA, Gerardo NM, Moran N, Nakabachi A, Stern D et al. Genome sequence of the pea aphid Acyrthosiphon pisum. PLoS Biology. 2010 Feb 1;8(2). e1000313. https://doi.org/10.1371/journal.pbio.1000313
Richards, Stephen ; Gibbs, Richard A. ; Gerardo, Nicole M. ; Moran, Nancy ; Nakabachi, Atsushi ; Stern, David ; Tagu, Denis ; Wilson, Alexandra ; Muzny, Donna ; Kovar, Christie ; Cree, Andy ; Chacko, Joseph ; Chandrabose, Mimi N. ; Dao, Marvin Diep ; Dinh, Huyen H. ; Gabisi, Ramatu Ayiesha ; Hines, Sandra ; Hume, Jennifer ; Jhangian, Shalini N. ; Joshi, Vandita ; Lewis, Lora R. ; Liu, Yih Shin ; Lopez, John ; Morgan, Margaret B. ; Nguyen, Ngoc Bich ; Okwuonu, Geoffrey O. ; Ruiz, San Juana ; Santibanez, Jireh ; Wright, Rita A. ; Fowler, Gerald R. ; Hitchens, Matthew E. ; Lozado, Ryan J. ; Moen, Charles ; Steffen, David ; Warren, James T. ; Zhang, Jingkun ; Nazareth, Lynne V. ; Chavez, Dean ; Davis, Clay ; Lee, Sandra L. ; Patel, Bella Mayurkumar ; Pu, Ling Ling ; Bell, Stephanie N. ; Johnson, Angela Jolivet ; Vattathil, Selina ; Williams, Rex L. ; Shigenobu, Shuji ; Dang, Phat M. ; Morioka, Mizue ; Fukatsu, Takema ; Kudo, Toshiaki ; Miyagishima, Shin Ya ; Jiang, Huaiyang ; Worley, Kim C. ; Legeai, Fabrice ; Gauthier, Jean Pierre ; Collin, Olivier ; Zhang, Lan ; Chen, Hsiu Chuan ; Ermolaeva, Olga ; Hlavina, Wratko ; Kapustin, Yuri ; Kiryutin, Boris ; Kitts, Paul ; Maglott, Donna ; Murphy, Terence ; Pruitt, Kim ; Sapojnikov, Victor ; Souvorov, Alexandre ; Thibaud-Nissen, Françoise ; Câmara, Francisco ; Guigó, Roderic ; Stanke, Mario ; Solovyev, Victor ; Kosarev, Peter ; Gilbert, Don ; Gabaldón, Toni ; Huerta-Cepas, Jaime ; Marcet-Houben, Marina ; Pignatelli, Miguel ; Moya, Andrés ; Rispe, Claude ; Ollivier, Morgane ; Quesneville, Hadi ; Permal, Emmanuelle ; Llorens, Carlos ; Futami, Ricardo ; Hedges, Dale ; Robertson, Hugh M. ; Alioto, Tyler ; Mariotti, Marco ; Nikoh, Naruo ; McCutcheon, John P. ; Burke, Gaelen ; Kamins, Alexandra ; Latorre, Amparo ; Ashton, Peter ; Calevro, Federica ; Charles, Hubert ; Colella, Stefano ; Douglas, Angela E. ; Jander, Georg ; Jones, Derek H. ; Febvay, Gérard ; Kamphuis, Lars G. ; Kushlan, Philip F. ; Macdonald, Sandy ; Ramsey, John ; Schwartz, Julia ; Seah, Stuart ; Thomas, Gavin ; Vellozo, Augusto ; Cass, Bodil ; Degnan, Patrick ; Hurwitz, Bonnie ; Leonardo, Teresa ; Koga, Ryuichi ; Altincicek, Boran ; Anselme, Caroline ; Atamian, Hagop ; Barribeau, Seth M. ; De Vos, Martin ; Duncan, Elizabeth J. ; Evans, Jay ; Ghanim, Murad ; Heddi, Abdelaziz ; Kaloshian, Isgouhi ; Vincent-Monegat, Carole ; Parker, Ben J. ; Pérez-Brocal, Vicente ; Rahbé, Yvan ; Spragg, Chelsea J. ; Tamames, Javier ; Tamarit, Daniel ; Tamborindeguy, Cecilia ; Vilcinskas, Andreas ; Bickel, Ryan D. ; Brisson, Jennifer A. ; Butts, Thomas ; Chang, Chun Che ; Christiaens, Olivier ; Davis, Gregory K. ; Duncan, Elizabeth ; Ferrier, David ; Iga, Masatoshi ; Janssen, Ralf ; Lu, Hsiao Ling ; McGregor, Alistair ; Miura, Toru ; Smagghe, Guy ; Smith, James ; Van Der Zee, Maurijn ; Velarde, Rodrigo ; Wilson, Megan ; Dearden, Peter ; Edwards, Owain R. ; Gordon, Karl ; Hilgarth, Roland S. ; Rider, Stanley Dean ; Srinivasan, Dayalan ; Walsh, Thomas K. ; Ishikawa, Asano ; Jaubert-Possamai, Stéphanie ; Fenton, Brian ; Huang, Wenting ; Rizk, Guillaume ; Lavenier, Dominique ; Nicolas, Jacques ; Smadja, Carole ; Zhou, Jing Jiang ; Vieira, Filipe G. ; He, Xiao Li ; Liu, Renhu ; Rozas, Julio ; Field, Linda M. ; Campbell, Peter ; Carolan, James C. ; Fitzroy, Carol I J ; Reardon, Karen T. ; Reeck, Gerald R. ; Singh, Karam ; Wilkinson, Thomas L. ; Huybrechts, Jurgen ; Abdel-Latief, Mohatmed ; Robichon, Alain ; Veenstra, Jan A. ; Hauser, Frank ; Cazzamali, Giuseppe ; Schneider, Martina ; Williamson, Michael ; Stafflinger, Elisabeth ; Hansen, Karina K. ; Grimmelikhuijzen, Cornelis J P ; Price, Daniel R G ; Caillaud, Marina ; Van Fleet, Eric ; Ren, Qinghu ; Gatehouse, John A. ; Brault, Véronique ; Monsion, Baptiste ; Diaz, Jason ; Hunnicutt, Laura ; Ju, Ho Jong ; Pechuan, Ximo ; Aguilar, José ; Cortés, Teresa ; Ortiz-Rivas, Benjamín ; Martínez-Torres, David ; Dombrovsky, Aviv ; Dale, Richard P. ; Davies, T. G Emyr ; Williamson, Martin S. ; Jones, Andrew ; Sattelle, David ; Williamson, Sally ; Wolstenholme, Adrian ; Cottret, Ludovic ; Sagot, Marie France ; Heckel, David G. ; Hunter, Wayne. / Genome sequence of the pea aphid Acyrthosiphon pisum. In: PLoS Biology. 2010 ; Vol. 8, No. 2.
@article{11888962b19e40678a79b35c3cb7b1ba,
title = "Genome sequence of the pea aphid Acyrthosiphon pisum",
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.",
author = "Stephen Richards and Gibbs, {Richard A.} and Gerardo, {Nicole M.} and Nancy Moran and Atsushi Nakabachi and David Stern and Denis Tagu and Alexandra Wilson and Donna Muzny and Christie Kovar and Andy Cree and Joseph Chacko and Chandrabose, {Mimi N.} and Dao, {Marvin Diep} and Dinh, {Huyen H.} and Gabisi, {Ramatu Ayiesha} and Sandra Hines and Jennifer Hume and Jhangian, {Shalini N.} and Vandita Joshi and Lewis, {Lora R.} and Liu, {Yih Shin} and John Lopez and Morgan, {Margaret B.} and Nguyen, {Ngoc Bich} and Okwuonu, {Geoffrey O.} and Ruiz, {San Juana} and Jireh Santibanez and Wright, {Rita A.} and Fowler, {Gerald R.} and Hitchens, {Matthew E.} and Lozado, {Ryan J.} and Charles Moen and David Steffen and Warren, {James T.} and Jingkun Zhang and Nazareth, {Lynne V.} and Dean Chavez and Clay Davis and Lee, {Sandra L.} and Patel, {Bella Mayurkumar} and Pu, {Ling Ling} and Bell, {Stephanie N.} and Johnson, {Angela Jolivet} and Selina Vattathil and Williams, {Rex L.} and Shuji Shigenobu and Dang, {Phat M.} and Mizue Morioka and Takema Fukatsu and Toshiaki Kudo and Miyagishima, {Shin Ya} and Huaiyang Jiang and Worley, {Kim C.} and Fabrice Legeai and Gauthier, {Jean Pierre} and Olivier Collin and Lan Zhang and Chen, {Hsiu Chuan} and Olga Ermolaeva and Wratko Hlavina and Yuri Kapustin and Boris Kiryutin and Paul Kitts and Donna Maglott and Terence Murphy and Kim Pruitt and Victor Sapojnikov and Alexandre Souvorov and Fran{\cc}oise Thibaud-Nissen and Francisco C{\^a}mara and Roderic Guig{\'o} and Mario Stanke and Victor Solovyev and Peter Kosarev and Don Gilbert and Toni Gabald{\'o}n and Jaime Huerta-Cepas and Marina Marcet-Houben and Miguel Pignatelli and Andr{\'e}s Moya and Claude Rispe and Morgane Ollivier and Hadi Quesneville and Emmanuelle Permal and Carlos Llorens and Ricardo Futami and Dale Hedges and Robertson, {Hugh M.} and Tyler Alioto and Marco Mariotti and Naruo Nikoh and McCutcheon, {John P.} and Gaelen Burke and Alexandra Kamins and Amparo Latorre and Peter Ashton and Federica Calevro and Hubert Charles and Stefano Colella and Douglas, {Angela E.} and Georg Jander and Jones, {Derek H.} and G{\'e}rard Febvay and Kamphuis, {Lars G.} and Kushlan, {Philip F.} and Sandy Macdonald and John Ramsey and Julia Schwartz and Stuart Seah and Gavin Thomas and Augusto Vellozo and Bodil Cass and Patrick Degnan and Bonnie Hurwitz and Teresa Leonardo and Ryuichi Koga and Boran Altincicek and Caroline Anselme and Hagop Atamian and Barribeau, {Seth M.} and {De Vos}, Martin and Duncan, {Elizabeth J.} and Jay Evans and Murad Ghanim and Abdelaziz Heddi and Isgouhi Kaloshian and Carole Vincent-Monegat and Parker, {Ben J.} and Vicente P{\'e}rez-Brocal and Yvan Rahb{\'e} and Spragg, {Chelsea J.} and Javier Tamames and Daniel Tamarit and Cecilia Tamborindeguy and Andreas Vilcinskas and Bickel, {Ryan D.} and Brisson, {Jennifer A.} and Thomas Butts and Chang, {Chun Che} and Olivier Christiaens and Davis, {Gregory K.} and Elizabeth Duncan and David Ferrier and Masatoshi Iga and Ralf Janssen and Lu, {Hsiao Ling} and Alistair McGregor and Toru Miura and Guy Smagghe and James Smith and {Van Der Zee}, Maurijn and Rodrigo Velarde and Megan Wilson and Peter Dearden and Edwards, {Owain R.} and Karl Gordon and Hilgarth, {Roland S.} and Rider, {Stanley Dean} and Dayalan Srinivasan and Walsh, {Thomas K.} and Asano Ishikawa and St{\'e}phanie Jaubert-Possamai and Brian Fenton and Wenting Huang and Guillaume Rizk and Dominique Lavenier and Jacques Nicolas and Carole Smadja and Zhou, {Jing Jiang} and Vieira, {Filipe G.} and He, {Xiao Li} and Renhu Liu and Julio Rozas and Field, {Linda M.} and Peter Campbell and Carolan, {James C.} and Fitzroy, {Carol I J} and Reardon, {Karen T.} and Reeck, {Gerald R.} and Karam Singh and Wilkinson, {Thomas L.} and Jurgen Huybrechts and Mohatmed Abdel-Latief and Alain Robichon and Veenstra, {Jan A.} and Frank Hauser and Giuseppe Cazzamali and Martina Schneider and Michael Williamson and Elisabeth Stafflinger and Hansen, {Karina K.} and Grimmelikhuijzen, {Cornelis J P} and Price, {Daniel R G} and Marina Caillaud and {Van Fleet}, Eric and Qinghu Ren and Gatehouse, {John A.} and V{\'e}ronique Brault and Baptiste Monsion and Jason Diaz and Laura Hunnicutt and Ju, {Ho Jong} and Ximo Pechuan and Jos{\'e} Aguilar and Teresa Cort{\'e}s and Benjam{\'i}n Ortiz-Rivas and David Mart{\'i}nez-Torres and Aviv Dombrovsky and Dale, {Richard P.} and Davies, {T. G Emyr} and Williamson, {Martin S.} and Andrew Jones and David Sattelle and Sally Williamson and Adrian Wolstenholme and Ludovic Cottret and Sagot, {Marie France} and Heckel, {David G.} and Wayne Hunter",
year = "2010",
month = "2",
day = "1",
doi = "10.1371/journal.pbio.1000313",
language = "English",
volume = "8",
journal = "PLoS Biology",
issn = "1544-9173",
publisher = "Public Library of Science",
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}

TY - JOUR

T1 - Genome sequence of the pea aphid Acyrthosiphon pisum

AU - Richards, Stephen

AU - Gibbs, Richard A.

AU - Gerardo, Nicole M.

AU - Moran, Nancy

AU - Nakabachi, Atsushi

AU - Stern, David

AU - Tagu, Denis

AU - Wilson, Alexandra

AU - Muzny, Donna

AU - Kovar, Christie

AU - Cree, Andy

AU - Chacko, Joseph

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AU - Dao, Marvin Diep

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AU - Gabisi, Ramatu Ayiesha

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AU - Williamson, Michael

AU - Stafflinger, Elisabeth

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AU - Price, Daniel R G

AU - Caillaud, Marina

AU - Van Fleet, Eric

AU - Ren, Qinghu

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AU - Brault, Véronique

AU - Monsion, Baptiste

AU - Diaz, Jason

AU - Hunnicutt, Laura

AU - Ju, Ho Jong

AU - Pechuan, Ximo

AU - Aguilar, José

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AU - Martínez-Torres, David

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AU - Davies, T. G Emyr

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AU - Jones, Andrew

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AU - Sagot, Marie France

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AU - Hunter, Wayne

PY - 2010/2/1

Y1 - 2010/2/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=77649141259&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=77649141259&partnerID=8YFLogxK

U2 - 10.1371/journal.pbio.1000313

DO - 10.1371/journal.pbio.1000313

M3 - Article

C2 - 20186266

AN - SCOPUS:77649141259

VL - 8

JO - PLoS Biology

JF - PLoS Biology

SN - 1544-9173

IS - 2

M1 - e1000313

ER -