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The Japanese government's Rice Genome Sequencing Project has been thrown into turmoil by the news that Celera Genomics, the US company set up by geneticist J. Craig Venter, plans to sequence the entire rice genome in just six weeks.

Celera plans to create a commercial database of the rice genome. It would be made available to companies for US$30 million on a five-year contract.

As reported last week in the Japanese biotechnology newsletter Nikkei Biotechnology, Venter plans to sequence the 430-megabase rice genome using the ‘shotgun’ technique. This divides the genome into small, random fragments that are then put together to produce the whole sequence.

Venter confirms that Celera has begun sequencing the rice genome, and says that it is “an important basis for future work on other plant species”. He adds: “We are aware of the sensitivity over the work, given the large economic and political interest involved, but we are proceeding in order to create a database available for others.”

But Venter's initiative has upset researchers involved in the international rice genome project, a ten-year initiative costing US$200 million that plans to complete the sequencing by 2008. The project, led by Japan's Ministry of Agriculture, Forestry and Fisheries (MAFF), had aimed to have sequenced 40 per cent of the genome by 2003.

Takuji Sasaki, leader of MAFF's Rice Genome Research Program, says they will have to speed up their sequencing work. “Although we have been aware of Celera's interest in the rice genome, we are furious at this news,” says Sasaki. He says the current project will adopt a new strategy aimed at creating physical maps of all 12 chromosomes by the end of the year. This will be done by mapping ‘expressed sequence tags’ in rice onto clones of yeast artificial chromosome, focusing on the ‘gene-rich’ portion of the sequence.

But he admits that Japanese researchers will be unable to compete with Celera in terms of the speed of sequencing. The US company, which is partly owned by the laboratory equipment manufacturer Perkin-Elmer, owns nearly 300 high-speed automated DNA sequencers. “We have applied for additional funding to buy DNA sequencers, but will have to wait two years for the budget to come through,” says Sasaki.

Some researchers are sceptical that Celera can complete the sequencing in six weeks. “Six weeks is an exaggeration — a reliable sequence for the rice genome cannot be obtained by such a fast-track method,” says Michio Oishi, director of the Kazusa DNA Research Centre, Japan's first institute dedicated to the sequencing and analysis of DNA.

Oishi predicts that Venter's approach will produce “80 to 90 per cent of the sequence data”, but he notes that the objectives of the two sequencing efforts are very different.

Sasaki says that while the public project aims to provide researchers with complete and reliable sequence data, Venter's effort centres around the aim of “licensing whatever he can achieve”.

But he points out that the sequencing will require mapping data if the isolated genomic sequences are to be reassembled in the correct order. Venter says he has “sufficient information to complete the sequencing work”, although he adds that “Celera would be happy to partner with groups in Japan to help understand the rice genome”.

“Although it would be ideal to collaborate with Celera on this project, there will always be a problem about release of the data,” says Sasaki. Like the Human Genome Project, the rice project has agreed on the immediate release of the sequence data; but others would like the option of seeking patent protection on some of the sequence information.

Slow business: Critics say that Japan has not responded to competition in genome research. Credit: CORBIS/MICHAEL S. YAMASHITA

Oishi, one of a group of leading researchers who released a statement last year urging the government to tackle genome research on a national basis, admits that “Japan has been particularly slow at responding to the intensifying competition in genome research”.

Answering claims that his initiative would damage the 11-nation international rice genome project, whose members include the United States, the European Union, India and China, Venter argues that the public project is still at a very early stage and has made little progress.

“We have the set-up and the technology to proceed with the sequencing work, and although we do not mean to compete with the public initiative, we can't wait until they get their act together,” he says. “Sequencing the genome is just the beginning. We must not forget that post-sequencing work — the analysis of the sequence data — requires far more work.”