Comparative analysis of gene expression in two yeast species and their interspecific hybrid

We compared the genome-wide expression profiles of two yeast species (S. cerevisiae and S. paradoxus) using a two-species microarray that contain species-specific probes and can thus measure the expression levels of the two species simultaneosly. In Addition, we used the array to measure expression levels of the interspecific hybrid of these yeast species, while discriminating between the alleles that correspond to the two parental species. Comparison of the between-species differences and the within-hybrid allele differences allows us to separate cis from trans effects. Also, comparison of the overall expression in the hybrids (both alleles) with their parental species allows us to analyze hybrid over-expression and under-expression. Keywords: comparative transcriptome analysis, hybrid gene expression We analyzed four conditions (rich media, glycerol, heat shock and TSA). For each conditions, we hybridized the pooled sample of both species dyed with cy3/cy5 and a sample of the hybrid dyed with the alternate fluorescent color. Each experiment was done with 2 biological repeats, except for the rich media experiments done with 4 biological repeats.