The International Aphid Genomics Consortium has published the 464 Mb draft genome sequence of the pea aphid, Acyrthosiphon pisum, the first whole genome sequence of a basal hemimetabolous insect. This genome provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists that can reproduce both sexually and asexually and have coevolved with an obligate bacterial symbiont, Buchnera aphidicola. The genome analysis revealed extensive gene duplication in over 2000 gene families and loss of evolutionarily conserved genes. Gene family expansions include genes involved in chromatin modification, miRNA synthesis, and sugar transport, while gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome shows that only a limited number of genes have been acquired from bacteria, and the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The genome suggests extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems. The genome sequence reveals that the pea aphid has a low GC content, and gene models were predicted using multiple programs. The genome also shows a high number of U12 introns, which may complicate ab initio gene modeling. The pea aphid genome has a large number of gene duplications, with 2,459 gene families appearing to have undergone aphid lineage-specific duplications. The genome also contains a large number of transposable elements, with 38% of the assembled genome composed of TEs. The pea aphid genome has a full complement of DNA methylation genes, including orthologs for two maintenance DNA methyltransferases, two de novo DNA methyltransferases, and the Dnmt2 found in all sequenced insect genomes. The genome also shows an expansion of the miRNA pathway, with multiple copies of key miRNA-related genes. The pea aphid genome provides insights into the intimate metabolic associations between the insect host and its obligate bacterial symbiont, revealing how the pea aphid's amino acid and purine metabolism might be adapted to support essential amino acid synthesis and nitrogen recycling by Buchnera. The genome also shows that the pea aphid lacks the capacity for de novo synthesis of nine protein-amino acids and the urea cycle, making it incapable of synthesizing a further amino acid, arginine. The genome also reveals that the pea aphid lacks the genetic capacity to utilize selenocysteine, the 21st protein amino acid. The pea aphid genome shows that the immune system is expected to be critical in determining responses to microbial symbionts, but many immuneThe International Aphid Genomics Consortium has published the 464 Mb draft genome sequence of the pea aphid, Acyrthosiphon pisum, the first whole genome sequence of a basal hemimetabolous insect. This genome provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists that can reproduce both sexually and asexually and have coevolved with an obligate bacterial symbiont, Buchnera aphidicola. The genome analysis revealed extensive gene duplication in over 2000 gene families and loss of evolutionarily conserved genes. Gene family expansions include genes involved in chromatin modification, miRNA synthesis, and sugar transport, while gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome shows that only a limited number of genes have been acquired from bacteria, and the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The genome suggests extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems. The genome sequence reveals that the pea aphid has a low GC content, and gene models were predicted using multiple programs. The genome also shows a high number of U12 introns, which may complicate ab initio gene modeling. The pea aphid genome has a large number of gene duplications, with 2,459 gene families appearing to have undergone aphid lineage-specific duplications. The genome also contains a large number of transposable elements, with 38% of the assembled genome composed of TEs. The pea aphid genome has a full complement of DNA methylation genes, including orthologs for two maintenance DNA methyltransferases, two de novo DNA methyltransferases, and the Dnmt2 found in all sequenced insect genomes. The genome also shows an expansion of the miRNA pathway, with multiple copies of key miRNA-related genes. The pea aphid genome provides insights into the intimate metabolic associations between the insect host and its obligate bacterial symbiont, revealing how the pea aphid's amino acid and purine metabolism might be adapted to support essential amino acid synthesis and nitrogen recycling by Buchnera. The genome also shows that the pea aphid lacks the capacity for de novo synthesis of nine protein-amino acids and the urea cycle, making it incapable of synthesizing a further amino acid, arginine. The genome also reveals that the pea aphid lacks the genetic capacity to utilize selenocysteine, the 21st protein amino acid. The pea aphid genome shows that the immune system is expected to be critical in determining responses to microbial symbionts, but many immune