The International Rice Genome Sequencing Project (IRGSP) has generated a high-quality, map-based sequence of the rice genome, covering 95% of the 389 Mb genome. The sequence includes almost all euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, with 71% having homologues in Arabidopsis. The rice genome contains a high proportion of transposable elements, and evidence suggests widespread gene transfer from organelles to nuclear chromosomes. The map-based sequence has been useful for identifying genes underlying agronomic traits, and the additional single-nucleotide polymorphisms and simple sequence repeats identified in this study should accelerate improvements in rice production.The International Rice Genome Sequencing Project (IRGSP) has generated a high-quality, map-based sequence of the rice genome, covering 95% of the 389 Mb genome. The sequence includes almost all euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, with 71% having homologues in Arabidopsis. The rice genome contains a high proportion of transposable elements, and evidence suggests widespread gene transfer from organelles to nuclear chromosomes. The map-based sequence has been useful for identifying genes underlying agronomic traits, and the additional single-nucleotide polymorphisms and simple sequence repeats identified in this study should accelerate improvements in rice production.