IC4R003-Genome-2005-16100779

Project Title

• The map-based sequence of the rice genome

The Background of This Project

• Rice (Oryza sativa L.) is the most important food crop in the world and feeds over half of the global population. As the first step in a systematic and complete functional characterization of the rice genome, the International Rice Genome Sequencing Project(IRGSP) has generated and analysed a highly accurate finished sequence of the rice genome that is anchored to the genetic map.The researchers analysis has revealed several salient features of the rice genome.

Plant Culture & Treatment

• The IRGSP sequenced the genome of a single inbred cultivar, Oryza sativa ssp. japonica cv. Nipponbare, and adopted a hierarchical cloneby-clone method using bacterial and P1 artificial chromosome clones(BACs and PACs, respectively).
• The researchers masked the pseudomolecules for repetitive sequences and used the ab initio gene finder FGENESH to identify only non-transposable-element-related genes.

Research Findings

• Providing evidence for a genome size of 389 Mb. This size estimation is ,260 Mb larger than the fully sequenced dicot plant model Arabidopsis thaliana. The researchers generated 370 Mb of finished sequence, representing 95% coverage of the genome and virtually all of the euchromatic regions.Ninety-seven percent of the BAC/PACs and gap sequences (3,360)have been submitted as finished quality in the PLN division of GenBank/DDBJ/EMBL. These and the remaining draft-sequenced clones were used to construct pseudomolecules representing the 12 chromosomes of rice (Fig. 1).

'Figure 1.Maps of the twelve rice chromosomes.'

'Table 2.Size of each chromosome based on sequence data and estimated gaps'

• A total of 37,544 non-transposable-element-related protein-coding sequences were detected, compared with ,28,000–29,000 in Arabidopsis, with a lower gene density of one gene per 9.9 kb in rice. A total of 2,859 genes seem to be unique to rice and the other cereals, some of which might differentiate monocot and dicot lineages.The rice genome is populated by representatives from all known transposon superfamilies, including elements that cannot be easily classified into either class I or II (ref. 40). Previous estimates of the transposon content in the rice genome range from 10 to 25% (refs 21,40). However, the increased availability of transposon query sequences and the use of profile hidden Markov models allow the identification of more divergent elements41 and indicate that the transposon content of the O. sativa ssp. japonica genome is at least 35% (Table 3).

'Table 3.Transposons in the rice genome'

Labs working on this Project

• 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, Maryland 20850, USA.
• Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences (CAS), 500 Caobao Road, Shanghai 200233, China.
• Centre National de Se ´quenc ¸age, INRA-URGV, and CNRS UMR-8030, 2, rue Gaston Cre ´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, Arizona 85721, USA.
• Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11723, USA. 8Institute of Botany, Academia Sinica, 128, Sec. 2, Yen-Chiu-Yuan Rd, 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 St, Peitou, Taipei 112, Taiwan.
• Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
• National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India.
• Waksman Institute, Rutgers University, Piscataway, New Jersey 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 Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK.
• Washington University Genome Sequencing Center, 3333 Forest Park Boulevard, St. Louis, Missouri 63108, USA.
• University of Wisconsin, Department of Horticulture, Madison, Wisconsin 53706, USA.
• University of Wisconsin, Department of Plant Pathology, Madison, Wisconsin 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 Dept, Cornell University, Ithaca, New York 14850-1901, USA.
• Cold Spring Harbor Laboratory, PO Box 100, 1 Bungtown Road, Cold Spring Harbor,New York 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, Philippines.
• Graduate School of Natural Sciences, Nagoya City University, Nagoya 467-8501, Japan.
• Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA.

Corresponding Author

• Takuji Sasaki (tsasaki@nias.affrc.go.jp).