US firm's bid to sequence rice genome causes stir in Japan
15 April 1999
[TOKYO] 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 is to sequence the genome as part of an initiative to create a commercial database of the rice genome. It would be made available to private companies for US$30 million for a five-year contract.
As reported initially last week in the Japanese biotechnology newsletter Nikkei Biotechnology, Venter plans to sequence the 430-megabase rice genome using the 'shotgun' technique. This technique divides the genome into small random fragments that are then put together to produce the whole sequence.
Venter's work on plant genomics could go even further - corn and sorghum are possible candidates for future sequencing work, according to the newsletter.
Venter confirms that Celera has begun part of the sequencing of the rice genome, and says that this 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 [with the sequencing effort] 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 been aiming to sequence 40 per cent of the genome by the end of its first five-year term in 2003.
Takuji Sasaki, leader of MAFF's Rice Genome Research Program, says they will have to accelerate the speed of their sequencing work.
"Although we have been aware of Celera's interest in the rice genome, we are infuriated by this news," says Sasaki. He says the current project will now proceed with a new strategy aimed at creating physical maps of all 12 chromosomes by the end of this year. This will be carried out by mapping 'expressed sequence tags' in rice onto clones of yeast artificial chromosome, focusing mainly 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 a slight 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.
He 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 completely different.
Sasaki says that "there is a significant gap between the aims of a commercially orientated project and a research-orientated project". While the public project aims to provide researchers with complete and reliable sequence data, he says that Venter's effort centres around the aim of "licensing whatever he can achieve".
But he points out that the sequencing will require mapping data for the isolated genomic sequences 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".
"Athough 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 genome 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.
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".
Responding to claims that his initiative would damage the international rice genome project, which has 11 partner nations, including 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 cannot 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."
ASAKO SAEGUSA
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Nature © Macmillan Publishers Ltd 1999 Registered No. 785998 England.