Whole-Genome Sequences and Annotation of the Opportunistic Pathogen Candida albicans Strain SC5314 Grown under Two Different Environmental Conditions

Abstract

The genetic variability of the opportunistic pathogen Candida albicans is an important adaptive mechanism. Here, we present the whole-genome sequences of the C. albicans SC5314 strain under two different growth conditions, providing useful information for comparative genomic studies and further intraspecific analysis.T he fungus Candida albicans is ubiquitously found in the human body and successfully colonizes diverse niches, such as skin and urogenital and gastrointestinal tracts, including internal organs, after tissue invasion and bloodstream dissemination (reviewed in references 1, 2, and 3). Although part of the human microbiota, C. albicans causes severe mucosal and bloodstream opportunistic infections in immunosuppressed hosts, with nearly 400,000 nosocomial cases worldwide with 46 to 75% mortality rates (4).We used the C. albicans strain SC5314, kindly provided to our laboratory by A. Mitchell in the mid-1990s. This strain is considered a reference strain and was isolated in 1984 from a candidemia patient (5). Since then, samples of this strain have been distributed to many laboratories and used in studies worldwide. The genome of one of these samples was previously sequenced by Muzzey and collaborators (6) using nextgeneration sequencing technologies.Our SC5314 (named SC5314-P0) yeast cells were grown on yeast extract-peptonedextrose (YPD) plates (1% wt/vol yeast extract; 2% wt/vol peptone, 2% wt/vol dextrose, and 2% wt/vol agar), and a single colony was used for overnight growth on YPD broth at 28°C and 150 rpm. Total yeast DNA was extracted from samples as described previously (7), and the complete sequencing of mitochondrial and nuclear genomes was carried out by using the Illumina MiSeq 2 ϫ 300-bp method in paired-end mode. The libraries were prepared with a TruSeq DNA v2 Illumina kit according to the manufacturer's technical specifications. FastQC v.0.11.4 software (8) was used to evaluate sequencing quality. Trimming was performed with the CLC Genomics Workbench v.7.5.1 (Qiagen) software with a quality score limit of 0.005 and removal of 45 bp and 20 bp from the 5= and 3= ends, respectively, and reads smaller than 25 bp were discarded. Once the quality filters were approved, reads were mapped to the assembly 22 of the reference strain SC5314 (A22-s07-m01-r18) (available at http://www .candidagenome.org/download/sequence/C_albicans_SC5314/Assembly22/archive/). Duplicated reads were removed after mapping and local realignment were carried out with the Guided Realignment tool (with "force realignment to guidance variants" selected) implemented in CLC Genomics Workbench v.7.5.1 (Qiagen). Genome annotation was performed with Annotate with the GFF file tool available on the same software using the corresponding GFF file (version A22-S05-M04-r02_features_with_ chromosome_sequences.gff). The fraction of the SC5314 genome sequenced was 0.99

Inhibition of the filamentation of Candida albicans by Borojoa patinoi silver nanoparticles

“…When comparing the two species of Candida albicans, we observed that C. albicans SC5314 was more sensitive to both AgNPs than C. albicans ATCC10231, resulting in a higher percentage of inhibition of filamentous forms necessary to initiate an invasive process (80.6% vs 63.0% respectively). Strain ATCC10231 is frequently used for pharmacological purposes, although several studies have shown that this strain produces shorter germ tubes compared to strain SC5314 Thewes, Moran et al [34]; Romo, Pierce et al [29]; Bartelli, Bruno et al [3]. Our results suggest that NPsAg interfered with the cAMP-PKA and MAPK pathways, which are widely employed by fungal pathogens to control the morphological transition Meng, Zhao et al [21].…”

Genome Sequence of a Staphylococcus epidermidis Strain (GTH12) Associated with Candida albicans SC5314 Cultured under Hypoxia at 37°C in Glycerol for 12 Weeks

“…Bloodstream infections caused by Candida albicans are associated with tissue invasion, and staphylococcal infections are believed to be facilitated by these bacterium-hypha associations once S. epidermidis can strongly adhere to C. albicans hyphal and yeast forms ( 1 , 4 – 6 ). In this study, we identified an S. epidermidis strain (GTH12) cocultured with our C. albicans strain SC5314 (generating C. albicans strain SC5314 GTH12), whose genome was previously published ( 7 ). This polymicrobial culture was grown on a YPD plate (1% [wt/vol] yeast extract, 2% [wt/vol] peptone, 2% [wt/vol] dextrose, 2% [wt/vol] agar), and a single colony was used for continuous growth for 12 weeks on YPG broth (1% [wt/vol] yeast extract, 2% [wt/vol] peptone, 2% [wt/vol] glycerol) at 37°C under hypoxic conditions (5 to 15% oxygen level).…”

Stenotrophomonas maltophilia affects the gene expression profiles of the major pathogens Pseudomonas aeruginosa and Staphylococcus aureus in an in vitro multispecies biofilm model

“…Therefore, in this study, we established multispecies biofilms with either two or three species using the above-named model pathogens. In addition, we included Candida albicans , a fungi that is also frequently observed in lung infections ( 30 – 32 ).…”