Presence of a Simple Tandem Repeat in the ITS1 Region of the Xylariales Gonzalo Platas, 1 Javier Acero, 3 Joseph A. Borkowski, 2 Vicente Gonza ´ lez, 3 Marı ´a Angeles Portal, 3 Vı ´ctor Rubio, 3 Javier Sa ´ nchez-Ballesteros, 3 Oscar Salazar, 1 Fernando Pela ´ ez 1 1 Centro de Investigacio ´n Ba ´sica, Natural Products Drug Discovery, Merck Sharp & Dohme Research Laboratories, Merck Sharp & Dohme de Espan ˜a, S. A. Josefa Valca ´rcel 38. 28027, Madrid, Spain 2 Bioinformatics Department, Merck Research Laboratories, P.O. Box 2000, Rahway, NJ 07065, USA 3 Departamento de Biotecnologia Microbiana, Centro Nacional de Biotecnologia CNB-CSIC, Campus de Cantoblanco UAM, Crta de Colmenar Km 15,500, 28049-Madrid, Spain Received: 19 October 2000 / Accepted: 21 December 2000 Abstract. A Simple Tandem Repeat sequence of 11 nucleotides has been found in the ITS1 region of the rDNA of members of Order Xylariales. The number of repetitions detected ranged from one to six, and they could be found in pure tandem or interspersed. The same core sequences have also been found in DNA from other organisms, although usually not repeated in tandem. These repetitions could have been generated by slipped strand mispairing. The presence of this sequence increases the normal rate of divergence in the ITS1 of the Xylariales. The phylogenetic implications of the presence of this sequence in the molecular taxonomy of Xylariales are also discussed. The analysis of the ITS1 sequences of a group of Nodu- lisporium sp. isolates has revealed the presence of DNA motifs repeated in tandem [11]. These short tandem repeats (STR) caused an increased rate of mutation in the ITS1 sequence of these fungi. The presence of tandem repetitive sequences in fungi is well documented. The degree of complexity of these repetitions has been reported to be variable [2, 7, 17]. The presence of STR in non-coding fungal DNA has been reported [2, 6], although not in the ITS1 region. The proposed mechanisms of evolution of repetitive sequences include both intra-or inter-strand recombina- tional effects, such as unequal crossing over [14]; or other mechanisms involving failures in the replication of the DNA such as slipped-strand mispairing (SSM) [8] or replication slippage [10]. The SSM is a process in which misalignment inter- mediates are formed during DNA synthesis or recombi- nation, as a result of the slippage of DNA strands in regions containing repeated nucleotides, or repeated se- quences. This phenomenon causes short deletions or insertions and duplications [8]. Short tandem repeats, which arise by chance in DNA sequences, can be expanded by SSM events into long tandem repeats. In addition, mutational changes can cre- ate new motifs that may be propagated by additional SSM events. This would give rise to tandem or inter- spersed repeats of closely related motifs. In this way, as repetitive regions become longer, the probability of non- contiguous SSM would increase by, for example, in- creasing the number of possible nucleation points for slip-outs and the number of repeated units contained in a slip-out [8, 15]. The nuclear rDNA internal transcribed spacer (ITS) sequences are increasingly being used for phylogenetic reconstruction at and below the species level. Although secondary structural elements in this region are known to play an important role in the processing of the pre-RNA, ITS are believed to have few evolutionary constraints and might be expected to evolve at or near the neutral level [3]. Nevertheless the presence of these STR in these sequences could introduce a variability factor that may oppose that affirmation. In a previous work [13], studying the phylogeny of Hypoxylon and related genera based on ribosomal ITS sequences, we observed a remarkable variation on the size of the ITS1 region of these fungi, ranging from 153 Correspondence to: G. Platas CURRENT MICROBIOLOGY Vol. 43 (2001), pp. 43–50 DOI: 10.1007/s002840010258 Current Microbiology An International Journal © Springer-Verlag New York Inc. 2001