Genome Sequence of the Pea Aphid Acyrthosiphon pisum

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. Citation: The International Aphid Genomics Consortium (2010) Genome Sequence of the Pea Aphid Acyrthosiphon pisum. PLoS Biol 8(2): e1000313. doi:10.1371/ journal.pbio.1000313 Academic Editor: Jonathan A. Eisen, University of California Davis, United States of America Received May 29, 2009; Accepted January 19, 2010; Published February 23, 2010 This is an open-access article distributed under the terms of the Creative Commons Public Domain declaration which stipulates that, once placed in the public domain, this work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. Funding: Work at the Baylor Medical College Human Genome Sequencing Center was funded by grant 5-U54-HG003273 from the National Human Genome Research Institute. AphidBase is supported with funding from the French National Institute for Agricultural Research (INRA) and the French National Institute for Research in Computer Science and Control (INRIA). Pea Aphid Genome Annotation Workshop I was supported by an American Genetic Association Special Event Award and an NRI, US Department of Agriculture Cooperative State Research, Education, and Extension Service 2007-04628 award to ACCW. FgenesH models were donated by Softberry, Inc. This research was additionally supported in part by the Intramural Research Program of the NIH, National Library of Medicine. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Abbreviations: AMP, antimicrobial peptide; CBD, chitin-binding domain; CCEs, carboxyl/choline esterases; CSPs, chemosensory proteins; GPCR, G proteincoupled receptor; GRs, gustatory receptors; GSTs, glutathione S-transferases; JH, juvenile hormone; MFS, major facilitator superfamily; ML, Maximum Likelihood; NJ, Neighbor Joining; OBPs, odorant-binding proteins; Ors, odorant receptors; P450s, P450 monooxygenases; PGRPs, peptidoglycan recognition proteins; RBH, reciprocal best hit; RISC, RNA Induced Silencing Complex; TE, transposable element * E-mail: [email protected] " Membership of the International Aphid Genomics Consortium is provided in the Acknowledgments.