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More than half of the world's population depends on rice as a principal source of calories and nutrition. And from a scientific perspective, the genome of this prolific grain offers clues for others, including corn, wheat, and barley. While its cereal cousins dwarf rice's 400-Mb genome, nearly all of the proteins found in these other staples have homologs in rice. As such, rice serves as a model for all cereal agriculture. Unraveling its code may enable scientists to address world hunger in new ways.
In this issue's Hot Papers, Huanming Yang and others at the Beijing Genomics Institute/Center of Genomics and Bioin-formatics produced a draft sequence for the genome of
"I still remember that for the first week, we had more than 10,000 hits to our database, let alone GenBank with the same sequence data," recalls Yang, head of the rice genome project at the Beijing Genomics Institute. "We also received numerous messages expressing excitement over the release of the data." Since then, the Beijing database has had more than 300 million hits, says Yang.
The rice genome, to Yang's surprise, comprised large, duplicated fragments, which he and his colleagues say contribute to protein diversity. Using whole-genome shotgun sequencing, they showed the 466-Mb
...AND AGAINST THE GRAIN
Before its release, Syngenta made a controversial agreement with
"The Syngenta sequence was never made completely public, but they did make it available to international sequencers to speed up the... effort," says Susan McCouch, a rice molecular geneticist at Cornell University in Ithaca, NY. By the end of 2002, the IRGSP released its completed draft sequence, which included Syngenta data. "Syngenta has been very present in moving the public project along," says McCouch.
"It would be hard to identify what percentage was ours and what percentage was theirs," says Rod Wing, director of the Arizona Genomics Institute at the University of Arizona in Tucson and leader of the international effort's US consortium.
ADDING DATA AND DILEMMA
© 2002 AAAS
Functional classification of indica rice genes assigned by homology to A. thaliana genes, according to the Gene Ontology Consortium. Only 36.3% of the 25,426 predicted A. thaliana genes are classified, along with 20.4% of the 53,398 predicted rice genes.
Nonetheless, the publication deal between Syngenta and
"If we have to scan bits at a time, it's not as useful," says Venkatesan Sundaresan, chair of the Plant Biology Section in the Department of Agronomy, University of California, Davis. Shoshi Kikuchi, head of the Laboratory of Gene Expression at the National Institute of Agrobiological Sciences in Tsukuba, Japan, says the data release policy was frustrating, "The limited access to the Syngenta data from our institute blocked the complete mapping of our full-length cDNA clones to the genome sequence at that time." Kikuchi's team eventually published their mapping and annotation of 28,000 cDNAs from
"Partial access is better than no access, but people felt it was a sellout by
"The public effort, which has been going through the sequence very carefully, has sort of been hit by these publications before them," says McCouch. Since then, some countries have dropped their funding, with the United States and Japan picking up much of the financial slack.
THE NEXT HARVEST
In spite of this setback, two new polished sequences for both
According to Wing, the IRGSP's target is to finish the
Efforts are already underway to make sense of the existing data. Leach and her colleagues are investigating mechanisms of disease resistance and defense responses. Sundaresan's group is looking to define roles for genes of unknown function using a random transposon mutagenesis technique.
The Beijing team has begun identifying genes involved in specific metabolic pathways. They've constructed DNA chips, says Yang, containing all the known genes, predicted genes, and necessary controls on a single slide. He adds that the rice chips are available to collaborators worldwide.
In January, both Yang and Kikuchi's groups published descriptions of their databases. The Beijing Genomics Institute's Rice Information System5 (BGI-RIS) presents sequenced, annotated genomes for both
The work is really only just beginning, adds McCouch. "It will be another 10 years before the genomes are completely annotated, and more than that before we understand how the genes are regulated and what they do." Achieving this will involve ongoing concerted international efforts, both private and public, involving multiple institutions. Says McCouch, "Sequencing genomes gives you a huge new perspective of the world, but it's not the end of the game. The fun is just beginning."
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