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Genome sequence of the pea aphid Acyrthosiphon pisum

Richards S, Gibbs RA, Gerardo NM, Moran N, Nakabachi A, Stern D, Tagu D, Wilson AC, Muzny D, Kovar C, Cree A, Chacko J, Chandrabose MN, 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 Jr, 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 FF, 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, Moran NA, Ashton P, Calevro F, Charles H, Colella S, Douglas A, 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, Gabaldon T, 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 Jr, 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, Ashton PD, Campbell P, Carolan JC, Douglas AE, Fitzroy CI, Reardon KT, Reeck G, 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 CJ, Price DR, 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, Channels I, Dale RP, Davies TG, Williamson MS, Jones A, Sattelle D, Williamson S, Wolstenholme A, Reeck GR, Cottret L, Sagot MF, Heckel DG, Hunter W

PLoS Biology (Impact Factor: 12.69). 01/2009; e1000313.

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.

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