Microevolutionary changes in Candida albicans identified by the complex Ca3 fingerprinting probe involve insertions and deletions of the full-length repetitive sequence RPS at specific genomic sites

The 11 kb complex DNA fingerprinting probe Ca3 is effective both in cluster analyses of Candida albicans isolates and in identifying microevolutionary changes in the size of hypervariable genomic fragments. A 2.6 kb EcoRI fra gment of Ca3, the C fragment, retains the capacity to identify these microe volutionary changes, and when the C fragment is cleaved with Sad, the capac ity is retained exclusively by a 1 kb subfragment, C1, which contains a par tial RPS repeat element. The microevolutionary changes identified by Ca3, t herefore, may involve reorganization of RPS elements dispersed throughout t he genome. To test this possibility, hypervariable fragments from several s trains of C. albicans were sequenced and compared. The results demonstrate that the microevolutionary changes identified by Ca3 are due to the inserti on and deletion of full-length tandem RPS elements at specific genomic site s dispersed throughout the C. albicans genome. The RPS elements at these di spersed sites are bordered by the same upstream and downstream sequences. T he frequency of recombination was estimated to be one recombination per 100 0 cell divisions by following RPS reorganization in vitro. The results are inconsistent with unequal recombination between homologous or heterologous chromosomes, but consistent with intrachromosomal recombination. Two altern ative models of intrachromosomal recombination are proposed: unequal sister -chromatid exchange and slipped misalignment at the replication fork.