US Researchers Sequence Japonica Rice Genome

The japonica draft sequence, produced by Stephen A. Goff and colleagues, contains 389 of their estimate of 420 million base pairs for the rice genome. Software prediction programs suggest that the japonica genome contains between 42,000 and 63,000 genes. The team's analysis doesn't 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

Goff's 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.

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 "provides a solid foundation for completing a high-accuracy sequence, enabling gene identification and facilitating physical and genetic mapping."

The rice genome may also aid researchers working on the genomes of other important cereal crops such as maize and wheat. Goff and colleagues were able to match 98 percent of publicly available maize, wheat and barley protein sequences to sequences within the japonica genome. Analysis also confirms that rice shows extensive "synteny" with these cereals--or, conservation of gene order and orientation between comparable chromosomes. The considerable overlap in genomes may make it easier to search for genes of interest, and to identify key regulatory regions across the genomes of these important crops.

Comparing Rice and Arabidopsis

Goff's comparison of the japonica and Arabidopsis genomes revealed similarities in genes related to disease resistance, and in some flowering time genes. Like the indica draft, the japonica draft contains roughly double the number of genes in the Arabidopsis genome, and around 88 percent of Arabidopsis' genes can be found in the rice genome.

Gene Transfer Between Rice, Humans

The japonica team searched for signs of any lateral transfer of genes between the rice and human genomes, a topic of recent interest, with the advent of genetically modified foods. Although rice and humans do share some sequence data, "there was no evidence to indicate that these genes or any genetic material had been laterally transferred to humans or human ancestors," suggesting that gene transfer from genetically modified rice would be unlikely, according to Goff's team.

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-- Rebecca Ham