Completion of the rice genome sequence announced
The International Rice Genome Sequencing Project (IRGSP), a consortium of publicly funded laboratories from 10 regions including Japan, the United States of America, the People's Republic of China, Taiwan, France, India, the Republic of Korea, Brazil, Thailand and United Kingdom, has announced the completion of a high quality draft sequence of the rice genome. In a ceremony held at Mita Congress Hall, Tokyo, Japan on December 18, 2002, the Prime Minister of Japan, Mr. Junichiro Koizumi described the sequencing effort as "an epoch making achievement comparable to the completion of the first survey of the entire human genome two years ago". The ceremony was attended by the members of the IRGSP, officials from various government agencies and funding organizations, representatives from major research institutions, scientists and educators.
The sequence data for the entire rice genome is now available in the public domain deposited in public databases such as GenBank, EMBL and DDBJ for free access to all scientists worldwide. This is expected to trigger studies that will lead to further improvement of this crop which provides the staple diet for almost half of the human population. At the same time, it would also provide an important tool in understanding the major cereal crops such as maize, wheat, barley and sorghum, which have been shown to share co-linear gene arrangements with rice.
The IRGSP is comprised of laboratories from 10 regions from Asia, Europe, North and South America, with a common goal of releasing the most accurate sequence of the rice genome. Japan through the Rice Genome Research Program (RGP), a joint collaboration of the National Institute of Agrobiological Sciences (NIAS) and the Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF), is in-charge of sequencing chromosomes 1, 2, 6, 7, 8 and 9 which correspond to almost half of the genome. The US groups comprise of The Institute for Genomic Research, Cold Spring Harbor Laboratory, Clemson University, Washington University, the University of Arizona, Rutgers University and the University of Wisconsin. They are in-charge of sequencing chromosomes 3, 10 and 11. China through the National Center for Gene Research of the Chinese Academy of Sciences is in-charge of chromosome 4. Taiwan is in-charge of chromosome 5 through the Academia Sinica Plant Genome Center. France through Genoscope is in-charge of chromosome 12 and a duplicated region in chromosome 11. Other participating groups include the Korea Rice Genome Research Program (KRGRP), the Indian Initiative for Rice Genome Sequencing (IIRGS), the National Center for Genetic Engineering and Biotechnology (BIOTEC) in Thailand, the Brazilian Rice Genome Initiative (BRIGI) and the John Innes Center in UK. These groups are involved in sequencing specific regions in chromosomes 1, 2, 9 and 11.
A single variety of rice (japonica cultivar Nipponbare) was chosen as the source of DNA for sequencing using the hierarchical shotgun sequencing approach. In this method, rice genomic DNA was first cut into small fragments, consisting of 100,000Ð150,000 nucleotide base pairs (bp), and then cloned using PAC and BAC vectors to construct genomic libraries. These PAC/BAC clones are accurately anchored and ordered to their original position in the rice genome to construct genome-wide physical maps. For sequence analysis, the DNA extracted from ordered PAC/BAC clones was further sheared into smaller fragments and cloned in E.coli cells to construct shotgun clones. The DNA fragments extracted from these clones were then directly subjected to sequencing with automatic DNA sequencers to obtain high-quality shotgun sequence reads. The entire length of the DNA insert in each clone was read with 10- fold average redundancy and the resulting sequences were assembled using a computer program to reconstitute rice DNA fragments as a PAC/BAC clone. The correctly reconstituted rice genome sequences with high level of accuracy (99.99%) were then submitted as phase 2 quality sequence to public databases (DDBJ/GenBank/EMBL) in PAC/BAC units. This policy, as agreed upon by IRGSP, allowed the immediate release of highly accurate genome sequence data to the public domain.
The rice genome sequencing effort was greatly facilitated by contributions from two private companies. In year 2000, Monsanto independently produced a draft sequence of the rice genome and made their BAC clones available to the IRGSP. The Monsanto BAC clone sequence data was combined with the additional data generated by the IRGSP resulting in the production of high quality sequence data and serving in great measure to accelerate the release of sequence information to the public domain. In the early part of year 2002, Syngenta also provided the draft sequence of the rice genome derived by whole genome shotgun sequencing to IRGSP, and this has been very useful in filling the gaps in the sequence-ready physical map by extending the PAC/BAC contigs as well as in filling the sequence gaps in phase 1 and phase 2 sequence.
The high-quality draft sequence corresponds to phase 2 quality in which the sequence has been read at least 10 times and the sequence pieces are ordered and aligned accurately although some gaps still remain. Based on the non-overlapping sequences of the 12 chromosomes, a total of 62,435 genes were predicted within 366 Mb of nucleotide sequence. However this prediction obtained using an automatic prediction program maybe an overestimate and may differ significantly when the sequenced is completely finished (remaining gaps are closed) and the predicted genes are manually curated.
The availability of an accurate high-quality draft sequence will promote ground breaking researches particularly in plant breeding. One of the major goals in crop improvement program is the development of high yielding varieties to cope with an ever increasing population. Although rice has a long history of cultivation dating back to several thousand years, further improvement of this crop by conventional breeding has almost reached its limit. Therefore the genetic blueprint of the rice plant may provide the key in providing a stable food supply to the human race.
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