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).
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 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.
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* 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
INRA-URGV and CNRS UMR-8030
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
Metro Manila, THE PHILIPPINES
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:
tsasaki@nias.affrc.go.jp).
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.