Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq

Vincent M. Bruno; Zhong Wang; Sadie L. Marjani; Ghia M. Euskirchen; Jeffrey Martin; Gavin Sherlock; Michael Snyder

doi:10.1101/gr.109553.110

Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq

¹ Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA;
² DOE Joint Genome Institute (JGI), Walnut Creek, California 94598, USA;
³ Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA;
⁴ Department of Genetics, Stanford University Medical School, Stanford, California 94305-5120, USA

Abstract

Candida albicans is the major invasive fungal pathogen of humans, causing diseases ranging from superficial mucosal infections to disseminated, systemic infections that are often lifethreatening. We have used massively parallel high-throughput sequencing of cDNA (RNA-seq) to generate a high-resolution map of the C. albicans transcriptome under several different environmental conditions. We have quantitatively determined all of the regions that are transcribed under these different conditions, and have identified 602 novel transcriptionally active regions (TARs) and numerous novel introns that are not represented in the current genome annotation. Interestingly, the expression of many of these TARs is regulated in a condition-specific manner. This comprehensive transcriptome analysis significantly enhances the current genome annotation of C. albicans, a necessary framework for a complete understanding of the molecular mechanisms of pathogenesis for this important eukaryotic pathogen.

Footnotes

↵5 Corresponding authors.

E-mail mpsnyder{at}stanford.edu.

E-mail sherlock{at}genome.stanford.edu.

E-mail vmb25{at}email.med.yale.edu.
[Supplemental material is available online at http://www.genome.org. The sequencing data from this study have been submitted to the NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi) under accession no. SRA020929.]
Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.109553.110.