Abstract
BackgroundThe opportunistic pathogen Candida glabrata is a member of the Saccharomycetaceae yeasts. Like its close relative Saccharomyces cerevisiae, it underwent a whole-genome duplication followed by an extensive loss of genes. Its genome contains a large number of very long tandem repeats, called megasatellites. In order to determine the whole replication program of the C. glabrata genome and its general chromosomal organization, we used deep-sequencing and chromosome conformation capture experiments.ResultsWe identified 253 replication fork origins, genome wide. Centromeres, HML and HMR loci, and most histone genes are replicated early, whereas natural chromosomal breakpoints are located in late-replicating regions. In addition, 275 autonomously replicating sequences (ARS) were identified during ARS-capture experiments, and their relative fitness was determined during growth competition. Analysis of ARSs allowed us to identify a 17-bp consensus, similar to the S. cerevisiae ARS consensus sequence but slightly more constrained. Megasatellites are not in close proximity to replication origins or termini. Using chromosome conformation capture, we also show that early origins tend to cluster whereas non-subtelomeric megasatellites do not cluster in the yeast nucleus.ConclusionsDespite a shorter cell cycle, the C. glabrata replication program shares unexpected striking similarities to S. cerevisiae, in spite of their large evolutionary distance and the presence of highly repetitive large tandem repeats in C. glabrata. No correlation could be found between the replication program and megasatellites, suggesting that their formation and propagation might not be directly caused by replication fork initiation or termination.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-015-0177-6) contains supplementary material, which is available to authorized users.
Highlights
The opportunistic pathogen Candida glabrata is a member of the Saccharomycetaceae yeasts
Identification of chromosomal replication origins and correlations to characterized genetic features It was previously shown that C. glabrata does not respond to a-mating or α-mating pheromones [32]
Fluorescence-activated cell sorting (FACS) analysis showed that approximately 15 % of elutriated cells had already partially replicated their genome because a peak corresponding to G2 DNA content was already visible at T0 (Additional file 1)
Summary
The opportunistic pathogen Candida glabrata is a member of the Saccharomycetaceae yeasts. In order to determine the whole replication program of the C. glabrata genome and its general chromosomal organization, we used deep-sequencing and chromosome conformation capture experiments. Replication properties of the C. glabrata genome were determined using high-throughput sequencing and chromosome conformation capture (3C). A complex dedicated machinery has been set up and propagated throughout evolution. It consists of interdependent cis- and trans-acting factors, respectively replication origins and a protein machinery involved in the catalytic process of replicating DNA. The identification of replication origins in eukaryotes started with the discovery that some autonomous DNA sequences were necessary and sufficient to replicate a plasmid in the model yeast Saccharomyces cerevisiae [1, 2]. Genome-wide catalogs of autonomously replicating sequences (ARS) have been established in S. cerevisiae [3, 4], Lachancea kluyveri [5], Lachancea waltii [6], Kluyveromyces lactis [7], Candida albicans [8], and Pichia pastoris
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