Yeast Yeast 2008; 25: 433–448. Published online in Wiley InterScience (www.interscience.wiley.com) DOI: 10.1002/yea.1597 Research Article Chromosome instability and unusual features of some widely used strains of Candida albicans Ausaf Ahmad 1# , M. Anaul Kabir 2# , Anatoliy Kravets 1# , Encarnaci ´ on Andaluz 3 , German Larriba 3 and Elena Rustchenko 1 * 1 Department of Biochemistry and Biophysics, Box 712, University of Rochester Medical Center, Rochester, NY 14642, USA 2 Department of Biotechnology, P. A. College of Engineering, Mangalore, Karnataka 574153, India 3 Departamento de Microbiolog´ ıa, Facultad de Ciencias, Universidad de Extremadura, 06071 Badajoz, Spain *Correspondence to: Elena Rustchenko, Department of Biochemistry and Biophysics, Box 712, University of Rochester Medical Center, Rochester, NY 14642, USA. E-mail: elena bulgac@urmc. rochester.edu # These authors contributed equally. Received: 11 May 2007 Accepted: 9 April 2008 Abstract Electrophoretic karyotyping of the Candida albicans revealed a different migration pattern of ChR in three different stocks of the sequencing strain SC5314. In one stock, the high instability of ChR size prevented the migration of ChR as a compact band; ChR appeared, instead, as a smear. In some stocks, ChR and/or Ch1 ploidy diminished, suggesting mixed populations of disomic and monosomic cells. Similarly, some stocks of widely used derivatives CAI4 and BWP17 contained smearing of ChR. In addition, the most manipulated strain in the lineage of SC5314, the last derivative, BWP17, acquired an increase in the size of Ch7b and revealed an unusual property. BWP17 did not tolerate a well-established procedure of telomere-mediated fragmentation of a chromosome; the remaining intact homologue always duplicated. We suggest that some stocks of SC5314 are unstable and that BWP17 may not be appropriate for general studies. Instead of BWP17 or CAI4, we recommend using for general research CAF4-2, which is a relatively stable Ura - derivative, and which has been successfully used for more than a decade in our laboratory. Copyright  2008 John Wiley & Sons, Ltd. Keywords: C. albicans ; chromosome instability; fragmentation; strain SC5314; CAI4; CAF4-2; BWP17 Introduction Candida albicans is the most prevailing fungal opportunistic pathogen of humans causing super- ficial mucosal infections in healthy individuals, as well as causing infections of blood and vari- ous organs in immunocompromised patients (Odds, 1988). The approximately 14.9 megabase pairs (Mbp) genome of this microbe is organized into eight chromosomes. Although C. albicans is con- sidered to be a natural diploid with 16 chromo- somes, a prominent feature of its karyotype is insta- bility, which increases under various environmental stresses (reviewed by Rustchenko and Sherman, 2002; Rustchenko, 2007a). Extensive in vitro stud- ies demonstrated that in C. albicans, the instability of random chromosomes controls at least catabolic pathways and, thus, causes increased diversity in population with regard to the utilization of different nutrients. Furthermore, specific alterations of spe- cific chromosomes confer survival in specific lethal environments, as, for example, in the best-studied case of the survival on a toxic sugar sorbose due to monosomy of chromosome 5 (Ch5; reviewed by Rustchenko and Sherman, 2002; Rustchenko, 2003a, 2003b; 2007a, 2007b). Recently, the impor- tance of specific alterations has been confirmed in vivo with multiple clinical isolates, in which duplication of an entire left arm of Ch5 conferred resistance to the antifungal fluconazole (Selmecki et al., 2006). Although C. albicans acute ability to sense stresses and mount responses in form of Copyright  2008 John Wiley & Sons, Ltd.