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Series GSE41749 Query DataSets for GSE41749
Status Public on Apr 17, 2013
Title Species- and condition-specific adaptation of the transcriptional landscapes in Candida albicans and Candida dubliniensis
Organisms Candida albicans; Candida dubliniensis
Experiment type Expression profiling by high throughput sequencing
Summary Although Candida albicans and Candida dubliniensis are most closely related, both species significantly behave differently 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. 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. 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.
Overall design We investigated qualitative along with quantitative differences in the transcriptomes of both organisms by cDNA deep sequencing. In a first step, we reevaluated the in silico predicted gene models by collecting experimental data using FLX - technology for sequencing strand-specific and normalized cDNA libraries derived from blastospores and hyphae. In the second step, quantitative RNA-Seq (GAIIX) was applied to C. albicans hyphal cells and C. dubliniensis blastospore and hyphal cells to complement reevaluation of the gene models with FLX data as well as to measure differential gene expression across the species with two biological replicates.
Contributor(s) Grumaz C, Lorenz S, Stevens P, Lindemann E, Schoeck U, Retey J, Rupp S
Citation(s) 23547856
Submission date Oct 22, 2012
Last update date May 15, 2019
Contact name Christian Grumaz
Organization name Fraunhofer IGB
Department MBT
Street address Nobelstr. 12
City Stuttgart
ZIP/Postal code 70569
Country Germany
Platforms (6)
GPL15149 Illumina Genome Analyzer IIx (Candida albicans)
GPL15645 Illumina HiSeq 2000 (Candida albicans)
GPL16201 454 GS FLX Titanium (Candida albicans)
Samples (14)
GSM1023541 C. albicans mix
GSM1023542 C. dubliniensis mix
GSM1023543 C. albicans_YPS-1
BioProject PRJNA178117
SRA SRP016578

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Supplementary file Size Download File type/resource
GSE41749_RAW.tar 196.4 Mb (http)(custom) TAR (of BED, BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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