The Hindu : Rice genome sequencing a revelation

Online edition of India's National Newspaper
Friday, Jun 06, 2003

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National

Rice genome sequencing a revelation

By N. Gopal Raj

THIRUVANANTHAPURAM June 5. The newly ``finished'' sequence of rice Chromosome 10, being published in the coming issue of Science, reveals that it actually carries twice the number of genes than was previously thought.

The result graphically illustrates the substantial benefits to be gained by not being satisfied with draft genome sequences. Rice, which feeds more than half the world, has the distinction of having been the subject of a number of genome sequencing initiatives.

The International Rice Genome Sequencing Project (IRGSP) has gone about the task painstakingly, chopping each of the plant's 12 chromosomes separately into bits and then sequencing each bit. It published a draft sequence for the entire genome last year.

But its principal task has been to prepare a ``finished'' genome sequence. That involves highly accurate sequences carefully aligned to the actual chromosome, giving the correct order of the genes and also their physical position on the chromosome. Getting from the draft to the finished stage is slow and costly, as the process is not automated to any large extent.

But long before IRGSP announced its own draft sequence, two private initiatives published draft versions, using the whole genome shotgun sequencing method. This method, which is much faster, shreds the entire genome at one go into bits and then uses powerful computers to reassemble the sequencing information.

The Beijing Genomics Institute too had used whole genome shotgun sequencing to produce a draft for the indica variety commonly consumed in both China and India. The other initiatives, including IRGSP, have concentrated on the japonica variety.

Scientists have always insisted that achieving a finished genome sequence would be of enormous value. Effective identification and isolation of genes which controlled traits such as drought and saline resistance required a precise, finished map. It would also accelerate global efforts to improve other major food crops, including maize, wheat, barley, sorghum and millet, which have much bigger genomes.

The finished sequence of rice's Chromosome 10 shows that it has 3,471 genes. The draft sequences had suggested that it had only 1,724 genes. Likewise, a comparison with the draft sequence for Chromosome 10 of the indica variety showed that a large proportion of the genes in the latter were interrupted by gaps.

The finished sequence for Chromosome 10, the smallest of rice's chromosomes, shows that genes are concentrated in the longer of its two arms. The short arm was made up of heterochromatin, a stretch of highly compacted DNA with few genes in it.

But even this latest sequence is, strictly speaking, not quite ``finished'' yet. It still has seven gaps, totalling less than four per cent of the chromosome's DNA. Three of these gaps may be closed soon. But the remaining four, which occur in the heterochromatic region, could take time as improvements are needed in the sequencing technology.

The finished sequences for Chromsome 1 and 4 have already been published. The finished sequence for Chromosome 3 is expected by the end of this year. India is involved in sequencing part of Chromosome 11. IRGSP is committed to having the entire finished rice genome sequence ready in 2004.

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