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Two Rice Chromosomes in Nature: Consortium Says Clone-by-Clone Technique Still Important

NEW YORK, Nov. 21-The international nonprofit consortium decoding the rice genome yesterday published the full sequences of chromosomes 1 and 4 of the japonica subspecies of rice. This publication by the International Rice Genome Sequencing Project in the journal Nature comes eight months after Syngenta's publicationof a lower resolution draft of the entire rice genome generated through the whole genome shotgun approach.


A Japanese team lead by the Rice Genome Research Program's Takuji Sasaki analyzed chromosome 1, which they estimated to be about  45.7 megabases long and include roughly 6,756 genes. If this gene frequency is representative of the rest of the genome, the japonica strand of rice is predicted to have a total of 62,500 genes.


The team used the clone-by-clone approach, creating 390 overlapping phage-derived artificial chromosomes (PACs) and bacterial artificial chromosomes (BACs) to obtain the sequence.


This approach, they write, provides an important set of information that the whole genome shotgun approach may miss. Comparing a short segment of their sequence with the indica strain generated through WGS at the Beijing Genomics Institute, the team found only 78 percent similarity, with 65 gaps in the indica sequence. Of 96 genes predicted by their japonica sequence, only 55 were intact in the indica sequence. Thirty-three were partially predicted, and eight were absent altogether.


"This may partly reflect the sequence difference between the two subspecies, although some artefacts in the whole-genome shotgun assembly cannot be ruled out," the authors write.


  Additionally, they say that their approach has uncovered gene families and sets of tandemly repeated genes that may be missed by the WGS approach, which tends to discard repetitive sequences.


The Chinese team, led by Qi Feng of the National Center for Gene Research in Shanghai, published a second paper in the same journal describing chromosome 4 of the same strain of rice. This chromosome, they predict, is roughly 35.6 megabase pairs long and includes 4,658 genes. By this estimate, the entire rice genome would be expected to include about 57,000 genes.


The team also used the clone-by-clone approach, which allowed them to describe subsections of the chromosome that are particularly dense in repetitive sequences. Researchers focused on the phylogenetic relationship between rice strains and between rice and Arabidopsis, finding that the japonica sequence had more than twice as many indels in a 2.3 Mb segment as the indica sequence. These significant differences, the researchers write, indicate that SNPs and indels can be useful for exploring subspecific or varietal differences.

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