Genome sequence survey and design of microarrays for Candida parapsilosis.
Tristan Rossignol, Mary E. Logue, Geraldine Butler
Department of Biochemistry, Conway Institute, UCD, Belfield, Dublin, Dublin 4, Ireland
Candida parapsilosis is responsible for 15 % of Candida infections and has become one of the most common emerging Candida species. It is of particular concern in neonates and surgical intensive care patients. C. parapsilosis is a particular problem as it tends to grow as biofilms on implanted medical devices conferring resistance to antifungal drugs. We carried out a genome sequence survey of C. parapsilosis CLIB214, covering approximately 0.8X of the haploid genome, and identified more than 3900 open reading frames. This allowed us to design partial genome DNA microarrays for use in expression analysis. For this purpose, 68 base gene-specific oligos have been designed using OligoArray 2.1 software and in house perl scripts. To avoid cross-hybridisation we performed BLASTN analysis against C. parapsilosis contigs and C. albicans ORFs (Haploid set assembly 19) for each oligo. Sequences were redesigned where necessary. We have designed oligos for 3850 open reading frames, which meet criteria for melting temperature, GC content, secondary structure prediction, cross-hybridisation and PHRED score. The oligo set provides us for the first time with a tool to investigate genome wide transcription profiles in C. parapsilosis. We are currently manufacturing in-house arrays, which will be used to study biofilm formation, virulence acquisition, and colony phenotype switching at the genomic level.