Nature Abstract DNA Sequence of Rice

"Article: The Map-Based Sequence of the Rice Genome"
International Rice Genome Sequencing Project [*]
Nature, Vol. 436, pp. 793-800 (August 11, 2005).


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 percent of the 389 MBP 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 percent had a putative homolog in Arabidopsis. In a reciprocal analysis, 90 percent of the Arabidopsis proteins had a putative homolog 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 (SNP) and simple sequence repeats identified in our study should accelerate improvements in rice production.
* 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

The Institute for Genomic Research
9712 Medical Center Drive
Rockville, MD 20850; USA

Shanghai Institutes for Biological Sciences
Chinese Academy of Sciences (CAS)
500 Caobao Road
Shanghai 200233; CHINA

Centre National de Séquençage
2, rue Gaston Cr‚mieux, CP 5706
91057 EVRY Cedex; FRANCE

UMR PIA, Cirad-Amis, TA40-03 avenue Agropolis
34398 Montpellier Cedex 05; FRANCE

Department of Plant Sciences
BIO5 Institute
The University of Arizona
Tucson, AZ 85721; USA

Cold Spring Harbor Laboratory
Cold Spring Harbor, NY 11723; USA

Institute of Botany
Academia Sinica, 128, Sec. 2
Yen-Chiu-Yuan Road
Nankang, Taipei 11529; TAIWAN

National Cheng Kung University
No. 1, Ta-Hsueh Road
Tainan 701; TAIWAN

National Yang-Ming University
155, Sec. 2, Li-Nong Street, Peitou
Taipei 112; TAIWAN

Department of Plant Molecular Biology
University of Delhi South Campus
New Delhi 110021; INDIA

National Research Center on Plant Biotechnology
Indian Agricultural Research Institute
New Delhi 110012; INDIA

Waksman Institute
Rutgers University
Piscataway, NJ 08854; USA

National Institute of Agricultural Science and Technology
RDA, Suwon, 441-707; Republic of KOREA

Rice Gene Discovery Unit, Kasetsart University
Nakron Pathom 73140; THAILAND

Centro de Genomica e Fitomelhoramento, UFPel
Pelotas, RS, l 96001-970, BRAZIL

John Innes Center
Norwich Research Park
Colney Norwich NR4 7UH; UK

Washington University Genome Sequencing Center
3333 Forest Park Boulevard
St. Louis, Missouri 63108, USA

Department of Horticulture
University of Wisconsin
Madison, WI 53706; USA

Department of Plant Pathology
University of Wisconsin
Madison, WI 53706; USA

Center for Information Biology and DNA Data Bank of Japan
National Institute of Genetics
Mishima 411-8540; JAPAN

Biological Information Research Center
National Institute of Advanced Industrial Science and Technology
Koto-ku, Tokyo 135-0064; JAPAN

National Institute of Agrobiological Sciences
Tsukuba, Ibaraki 305-8602, JAPAN

Medical Research Institute
Tokyo Medical and Dental University
Bunkyo-ku, Tokyo 113-8510; JAPAN

Japan Biological Information Research Center
Japan Biological Informatics Consortium
Koto-ku, Tokyo 135-0064; JAPAN

Plant Breeding Department
Cornell University
Ithaca, NY 14850-1901; USA

Cold Spring Harbor Laboratory
PO Box 100
1 Bungtown Road
Cold Spring Harbor, NY 11724; USA

Department of Biology
McGill University
1205 Dr. Penfield Avenue
Montreal, Quebec H3A 1B1, CANADA

Department of Biology
York University
4700 Keele Street
Toronto, Ontario M3J 1P3; CANADA

Biometrics and Bioinformatics Unit
International Rice Research Institute
DAPO Box 7777

Graduate School of Natural Sciences
Nagoya City University
Nagoya 467-8501; JAPAN

Biology Department
Brookhaven National Laboratory
Upton, NY 11973; USA

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 ( E-mail:

The genomic sequence is available under accession numbers AP008207 AP008218 in international databases (DDBJ, GenBank, and EMBL).

Received: December 29, 2004; Accepted: May 25, 2005.