A NOVEL REPEAT SEQUENCE (CKRS-1) CONTAINING A TANDEMLY REPEATED SUB-ELEMENT (KRE) ACCOUNTS FOR DIFFERENCES BETWEEN CANDIDA-KRUSEI STRAINS FINGERPRINTED WITH THE PROBE CKF1,2

CkF1,2 has been reported as an effective DNA fingerprinting probe of C andida krusei. It is composed of two genomic EcoRI-restriction fragmen ts, F1 and F2, which are approximately 5.4 and 5.2 kb, respectively. S equence analysis of F1 reveals that it is 5261 bp-long, has a GC conte nt of 42.2 mol%, and originates from the intergenic region of the ribo somal RNA cistrons (IGR). F1 comprises 488 bp of the 3' end of a 25s r RNA gene, a non-transcribed spacer region 1 (NTS 1), a 5s gene (121 bp ), and a major portion of the non-transcribed spacer region 2 (NTS2). A 1256 bp-long repeated sequence, CKRS-1, with a GC content of 35 mol% , has been identified in NTS2. CKRS-1 contains eight tandemly repeated sub-elements, kre-0 to kre-7. The first two, kre-0 and kre-1, are 164 bp-long, the next five sub-elements, kre-2 to kre-6, are 165 bp-long, and the last element, kre-7, is 103 bp-long. The eight sub-elements s hare nucleotide-sequence homologies between 66 to 100%, with kre-2, kr e-3 and kre-4 identical, and kre-0 the most divergent. Shorter repeate d sequences were also identified in three regions of F1, which were na med domains ''a'', ''b'' and ''c''. Restriction mapping, cross hybridi zation, and direct comparison of sequences show that F1 and F2 are pol ymophic forms of the IGR and their size difference is due both to the number of kre subelements in CKRS-1 and to a 24-bp deletion in domain ''b''. While F1 contains eight kre sub-elements, F2 contains seven. In C. krusei strain K31, four polymorphic forms of CKRS-1 have been iden tified containing five, six, seven and eight kre sub-elements. CKRS-1 is dispersed on three of the chromosomes of highest molecular weights separated by transverse alternating-field electrophoresis. CKRS-1 does not hybridize significantly to any transcription product. Polymorphis ms in single DNA fingerprints and differences between the DNA fingerpr ints of strains of C. krusei based upon CkF1,2 hybridization patterns therefore appear to be based, at least in part, on the variable number of tandemly repeated kre sub-elements in CKRS-1.