1. Affiliations for participants: National Institute of Agrobiological Sciences/Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
2. The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 20850, USA
3. Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), 500 Caobao Road, Shanghai 200233, China
4. Centre National de Séquençage, INRA-URGV, and CNRS UMR-8030, 2, rue Gaston Crémieux, CP 5706, 91057 EVRY Cedex, France
5. UMR PIA, Cirad-Amis, TA40-03 avenue Agropolis, 34398 Montpellier Cedex 05, France
6. Department of Plant Sciences, BIO5 Institute, The University of Arizona, Tucson, Arizona 85721, USA
7. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11723, USA
8. Institute of Botany, Academia Sinica, 128, Sec. 2, Yen-Chiu-Yuan Rd, Nankang, Taipei 11529, Taiwan
9. National Cheng Kung University, No. 1, Ta-Hsueh Road, Tainan 701, Taiwan
10. National Yang-Ming University, 155, Sec. 2, Li-Nong St, Peitou, Taipei 112, Taiwan
11. Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
12. National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India
13. Waksman Institute, Rutgers University, Piscataway, New Jersey 08854, USA
14. National Institute of Agricultural Science and Technology, RDA, Suwon, 441-707 Republic of Korea
15. Rice Gene Discovery Unit, Kasetsart University, Nakron Pathom 73140, Thailand
16. Centro de Genomica e Fitomelhoramento, UFPel, Pelotas, RS, l 96001-970, Brazil
17. John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
18. Washington University Genome Sequencing Center, 3333 Forest Park Boulevard, St. Louis, Missouri 63108, USA
19. University of Wisconsin, Department of Horticulture, Madison, Wisconsin 53706, USA
20. University of Wisconsin, Department of Plant Pathology, Madison, Wisconsin 53706, USA
21. Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Mishima 411-8540, Japan
22. Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan
23. National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
24. Medical Research Institute, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
25. Japan Biological Information Research Center, Japan Biological Informatics Consortium, Koto-ku, Tokyo 135-0064, Japan
26. Plant Breeding Dept, Cornell University, Ithaca, New York 14850-1901, USA
27. Cold Spring Harbor Laboratory, PO Box 100, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
28. Department of Biology, McGill University, 1205 Dr Penfield Avenue, Montreal, Quebec H3A 1B1, Canada
29. Department of Biology, York University, 4700 Keele Street, Toronto, Ontario M3J 1P3, Canada
30. Biometrics and Bioinformatics Unit, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
31. Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan
32. Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
33. List of participants and affiliations appear at the end of the paper

Correspondence to: Correspondence and requests for materials should be addressed to Takuji Sasaki (Email: tsasaki@nias.affrc.go.jp). The genomic sequence is available under accession numbers AP008207–AP008218 in international databases (DDBJ, GenBank and EMBL).

Abstract

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 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 non-transposable-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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