Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 nontransposable- element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.
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Acknowledgements Work at the RGP was supported by the Ministry of Agriculture, Forestry and Fisheries of Japan. Work at TIGR was supported by grants to C.R.B. from the USDA Cooperative State Research, Education and Extension Service–National Research Initiative, the National Science Foundation and the US Department of Energy. Work at the NCGR was supported by the Chinese Ministry of Science and Technology, the Chinese Academy of Sciences, the Shanghai Municipal Commission of Science and Technology, and the National Natural Science Foundation of China. Work at Genoscope was supported by le Ministère de la Recherche, France. Funding for the work at the AGI and AGCoL was provided by grants to R.A.W. and C.S. from the USDA Cooperative State Research, Education and Extension Service–National Research Initiative, the National Science Foundation, the US Department of Energy and the Rockefeller Foundation. Work at CSHL was supported by grants from the USDA Cooperative State Research, Education and Extension Service–National Research Initiative and from the National Science Foundation. Work at the ASPGC was supported by Academia Sinica, National Science Council, Council of Agriculture, and Institute of Botany, Academia Sinica. The IIRGS acknowledges the Department of Biotechnology, Government of India, for financial assistance and the Indian Council of Agricultural Research, New Delhi, for support. Work at Rice Gene Discovery was supported by BIOTECH and the Princess Sirindhorn’s Plant Germplasm Conservation Initiative Program. Work at PGIR was supported by Rutgers University. The BRIGI was supported by Coordenac¸ão de Aperfeic¸oamento de Pessoal de Nível Superior (CAPES), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Financiadora de Estudos e Projetos - Ministério de Ciência e Tecnologia (FINEP-MCT), Fundac¸ão de Amparo a Pesquisa do Rio Grande do Sul (FAPERGS) and Universidade Federal de Pelotas (UFPel). Work at McGill and York Universities was supported by the National Science and Engineering Research Council of Canada and the Canadian International Development Agency. Funding for H.H. at the National Institute of Agrobiological Sciences was from the Ministry of Agriculture, Forestry, and Fisheries of Japan, and the Program for Promotion of Basic Research Activities for Innovative Biosciences. Funding at Brookhaven National Laboratory was from The Rockefeller Foundation and the Office of Basic Energy Science of the United States Department of Energy. We would like to thank G. Barry and S. Goff for their help in negotiating agreements that permitted the sharing of materials and sequence with the IRGSP. We also acknowledge the work of G. Barry, S. Goff and their colleagues in facilitating the transfer of sequence information and supporting data.