Email updates

Keep up to date with the latest news and content from BMC Genomics and BioMed Central.

Open Access Highly Accessed Research article

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

Christian Grumaz1, Stefan Lorenz2, Philip Stevens2, Elena Lindemann2, Ulrike Schöck3, Julia Retey4, Steffen Rupp2 and Kai Sohn2*

Author Affiliations

1 University of Stuttgart, IGVT, Nobelstr. 12 70569, Stuttgart, Germany

2 Fraunhofer IGB, Nobelstr. 12, 70569, Stuttgart, Germany

3 GATC Biotech, Jakob-Stadler-Platz 7 78467, Konstanz, Germany

4 Genedata, Margarethenstr. 38 4053, Basel, Suisse

For all author emails, please log on.

BMC Genomics 2013, 14:212  doi:10.1186/1471-2164-14-212

Published: 2 April 2013

Abstract

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.

Keywords:
Candida albicans; Candida dubliniensis; Transcriptional landscapes; RNA-Seq; Orthologs