We have established Meloidogyne hapla as a tractable model plant-parasitic nematode amenable to forward and reverse genetics, and we present a complete genome sequence. At 54 Mbp, M. hapla represents not only the smallest nematode genome yet completed, but also the smallest metazoan, and defines a platform to elucidate mechanisms of parasitism by what is the largest uncontrolled group of plant pathogens worldwide. The M. hapla genome encodes significantly fewer genes than does the freeliving nematode Caenorhabditis elegans (most notably through a reduction of odorant receptors and other gene families), yet it has acquired horizontally from other kingdoms numerous genes suspected to be involved in adaptations to parasitism. In some cases, amplification and tandem duplication have occurred with genes suspected of being acquired horizontally and involved in parasitism of plants. Although M. hapla and C. elegans diverged >500 million years ago, many developmental and biochemical pathways, including those for dauer formation and RNAi, are conserved. Although overall genome organization is not conserved, there are areas of microsynteny that may suggest a primary biological function in nematodes for those genes in these areas. This sequence and map represent a wealth of biological information on both the nature of nematode parasitism of plants and its evolution.compaction ͉ dauer ͉ development ͉ horizontal gene transfer ͉ gene N ematodes are an abundant and species-rich animal phylum.They share a common body plan on which various adaptations have evolved, enabling Nematoda to occupy essentially all ecological niches, including being parasites of many other organisms (1). Parasitism of plants appears to have arisen independently in three of the major 12 nematode clades (2) and results in annual losses to world agriculture estimated to exceed $US100 billion (3, 4). The majority of damage is caused by sedentary endoparasitic forms in the order Tylenchida, which includes the root-knot nematodes (Meloidogyne spp., RKN). RKN have a cosmopolitan distribution and a host range that spans most crops, although individual RKN species exhibit a more restricted host range. Mature female RKN release hundreds of eggs onto the surface of the root that hatch in the soil as second-stage larvae (L2) and typically reinfect the same plant. RKN L2 are similar in function to dauer larvae (5), which were first described as an adaptation to parasitism to overcome adverse environmental conditions and facilitate dispersal (6), but have been best studied in the free-living nematode Caenorhabditis elegans (7). These larvae are developmentally arrested, motile, nonfeeding, nonaging, and long-lived. Like C. elegans dauers, RKN L2 are detergent-resistant (5), use the glyoxylate pathway (8), and exhibit intestinal morphology with sparse luminal microvilli and numerous lipid storage vesicles that permit long-term survival in the soil. RKN L2 penetrate the root and migrate intercellularly into the vascular cylinder. Migration is accompanied by extensive ...