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Background  Although  Candida albicans  and  Candida dubliniensis  are most closely related, both species behave significantly different with respect to morphogenesis and virulence. In order to gain further insight into the divergent routes for morphogenetic adaptation in both species, we investigated qualitative along with quantitative differences in the transcriptomes of both organisms by cDNA deep sequencing.    Results  Following genome-associated assembly of sequence reads we were able to generate experimentally verified databases containing 6016 and 5972 genes for  C. albicans  and  C. dubliniensis , respectively. About 95% of the transcriptionally active regions (TARs) contain open reading frames while the remaining TARs most likely represent non-coding RNAs. Comparison of our annotations with publically available gene models for  C. albicans  and  C. dubliniensis  confirmed approximately 95% of already predicted genes, but also revealed so far unknown novel TARs in both species. Qualitative cross-species analysis of these databases revealed in addition to 5802 orthologs also 399 and 49 species-specific protein coding genes for  C. albicans  and  C. dubliniensis , respectively. Furthermore, quantitative transcriptional profiling using RNA-Seq revealed significant differences in the expression of orthologs across both species. We defined a core subset of 84 hyphal-specific genes required for both species, as well as a set of 42 genes that seem to be specifically induced during hyphal morphogenesis in  C. albicans .    Conclusions  Species-specific adaptation in  C. albicans  and  C. dubliniensis  is governed by individual genetic repertoires but also by altered regulation of conserved orthologs on the transcriptional level.

Species and condition specific adaptation of the transcriptional landscapes in Candida albicans and Candida dubliniensis