Principal Investigator for rice at NIU: Long Mao lmao@niu.edu
Web page and programming author: Rick Johns (rjohns@niu.edu)
We have been looking for large scale repeat structures on rice chromosome 10, duplications on the order of a million bases or so. Such structures have been seen in Arabidopsis, both within individual chromosomes and between chromosomes (Arabidopsis Genome Initiative, Nature 408: 796-815, 2000).
We broke the chromosome up into 10,000 bp segments and used BLASTN to search against the entire chromosome sequence. The results are displayed as a dotplot, with each pixel representing a possible match between 35,000 bp segments of the chromosome. We filtered the BLAST data by plotting only segments that contained BLAST hits with a e-value better than a defined value (1e-40 in the plot below). Also, BLAST hits on sequences repeated more than a defined number of times (5 repeats in the plot below) were not included.
The dotplot below, and the dotplots done with altered minimum BLAST scores and maximum repeats, show a solid diagonal line. This line represents the obvious homology of each segment with itself. No other diagonal lines are easily seen; such lines would indicate the presence of large scale repeats on the chromosome.
When run with the Arabidopsis chromosome sequences, this method was easily able to detect all of the repeat structures that have been described, both within and between chromosomes. Both forward and reverse orientation repeats are seen as diagonal lines away from the main diagonal; the positions of these repeats corresponds well with the published summary chart shown below. Thus our current opinion is that rice chromosome 10 does not contain repeat structures with levels of homology similar to those found in Arabidopsis.
We are contimuing to investigate this question: perhaps there are repeat structures that are smaller or more diverged than in Arabidopsis. We are examining homologies between proteins on chromosome 10, and we are also working with MUMmer, a suffix tree-based method. Results should be forthcoming soon.
Link to more rice chromo 10 dotplots, under different conditions on maximum allowed repeats and minimum BLAST score.
Link to dotplots of Arabidopsis chromosome 1 to other chromosomes, with different conditions.
Taken from the Nature paper mentioned above.