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on programs suggest that the japonica genome contains between 42,000 and 63,000 genes. The teams analysis doesnt include an average gene length, but they indicate that the sequences most likely to be genes are longer than 500 base pairs.

Like the indica genome, the japonica genome appears to have undergone major duplication events: Approximately 75 percent of the predicted genes in the japonica genome may be duplicates. Much of this duplication may have been accomplished in relatively small episodes, and the most recent duplication event may not be that recent at all, occurring 40 million to 50 million years ago, Goff and the others suggest.

The scientists identified over 40,000 simple-sequence repeats of two, three and four base pairs. As with indica simple-sequence repeats, these could be useful markers for breeding and population genetics studies.

RESEARCH METHODS

Goffs group also used the shotgun method to sequence the japonica genome, eventually assembling the sequenced snippets into 38,357 contigs. Although the researchers used some publicly funded rice genome data as markers to guide the assembly, no public rice genome data was incorporated into their draft.After translating the predicted genes into proteins, the researchers used another software program to sort them into functional categories. The results indicate that the majority of classified japonica genes are involved in cell communications and metabolism. The analysis also identified specialized phosphate transporter genes, critical for plants uptake of this important nutrient from the soil.

ACCURACY

More than 95 percent of publicly available rice gene sequences, and 99 percent of a proprietary collection of over 100,000 rice cDNA sequences, are also contained within the japonica draft genome, Goff said.

As with indica, researchers said their draft is incomplete, but "provide
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Contact: Lisa Onaga
Lonaga@aaas.org
202-326-7088
American Association for the Advancement of Science
4-Apr-2002


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