Analysis of intrachromosomal duplications in yeast Saccharomyces cerevisiae: A possible model for their origin

The complete genome of the yeast Saccharomyces cerevisiae was investigated for intrachromosomal duplications at the level of nucleotide sequences. The analysis was performed by looking for long approximate repeats (from 30 to 3,885 bp) present on each of the chromosomes. We show that direct and inve rted repeats exhibit very different characteristics: the two copies of dire ct repeats are more similar and longer than those of inverted repeats. Furt hermore, contrary to the inverted repeats, a large majority of direct repea ts appear to be closely spaced. The distance (delta) between the two copies is generally smaller than 1 kb. Further analysis of these "close direct re peats" shows a negative correlation between delta and the percentage of ide ntity between the two copies, and a positive correlation between delta and repeat length. Moreover, contrary to the other categories of repeats, close direct repeats are mostly located within coding sequences (CDSs). We propo se two hypotheses in order to interpret these observations: first, the dele tion/conversion rate is negatively correlated with delta; second, there exi sts an active duplication mechanism which continuously creates close direct repeats, the other intrachromosomal repeats being the result, by chromosom al rearrangements of these "primary repeats."