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Phased Diploid Genome Assemblies for Three Strains of Candida albicans from Oak Trees. G3-GENES GENOMES GENETICS 2019; 9:3547-3554. [PMID: 31540974 PMCID: PMC6829152 DOI: 10.1534/g3.119.400486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Although normally a harmless commensal, Candida albicans, it is also one of the most common causes of bloodstream infections in the U.S. Candida albicans has long been considered an obligate commensal, however, recent studies suggest it can live outside animal hosts. Here, we have generated PacBio sequences and phased genome assemblies for three C. albicans strains from oak trees (NCYC 4144, NCYC 4145, and NCYC 4146). PacBio datasets are high depth (over 400 fold coverage) and more than half of the sequencing data are contained in reads longer than 15 kb. Primary assemblies showed high contiguity with several chromosomes for each strain recovered as single contigs, and greater than half of the alternative haplotype sequence was assembled in haplotigs at least 174 kb long. Using these assemblies we were able to identify structural polymorphisms, including a polymorphic inversion over 100 kb in length. These results show that phased de novo diploid assemblies for C. albicans can enable the study of genomic variation within and among strains of an important fungal pathogen.
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Sellam A, Hogues H, Askew C, Tebbji F, van Het Hoog M, Lavoie H, Kumamoto CA, Whiteway M, Nantel A. Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays. Genome Biol 2010; 11:R71. [PMID: 20618945 PMCID: PMC2926782 DOI: 10.1186/gb-2010-11-7-r71] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 06/07/2010] [Accepted: 07/09/2010] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Compared to other model organisms and despite the clinical relevance of the pathogenic yeast Candida albicans, no comprehensive analysis has been done to provide experimental support of its in silico-based genome annotation. RESULTS We have undertaken a genome-wide experimental annotation to accurately uncover the transcriptional landscape of the pathogenic yeast C. albicans using strand-specific high-density tiling arrays. RNAs were purified from cells growing under conditions relevant to C. albicans pathogenicity, including biofilm, lab-grown yeast and serum-induced hyphae, as well as cells isolated from the mouse caecum. This work provides a genome-wide experimental validation for a large number of predicted ORFs for which transcription had not been detected by other approaches. Additionally, we identified more than 2,000 novel transcriptional segments, including new ORFs and exons, non-coding RNAs (ncRNAs) as well as convincing cases of antisense gene transcription. We also characterized the 5' and 3' UTRs of expressed ORFs, and established that genes with long 5' UTRs are significantly enriched in regulatory functions controlling filamentous growth. Furthermore, we found that genomic regions adjacent to telomeres harbor a cluster of expressed ncRNAs. To validate and confirm new ncRNA candidates, we adapted an iterative strategy combining both genome-wide occupancy of the different subunits of RNA polymerases I, II and III and expression data. This comprehensive approach allowed the identification of different families of ncRNAs. CONCLUSIONS In summary, we provide a comprehensive expression atlas that covers relevant C. albicans pathogenic developmental stages in addition to the discovery of new ORF and non-coding genetic elements.
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Affiliation(s)
- Adnane Sellam
- Biotechnology Research Institute, National Research Council of Canada, 6100 Royalmount, Montréal, Québec, H4P 2R2, Canada.
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Epp E, Walther A, Lépine G, Leon Z, Mullick A, Raymond M, Wendland J, Whiteway M. Forward genetics in Candida albicans that reveals the Arp2/3 complex is required for hyphal formation, but not endocytosis. Mol Microbiol 2010; 75:1182-98. [PMID: 20141603 DOI: 10.1111/j.1365-2958.2009.07038.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Candida albicans is a diploid fungal pathogen lacking a defined complete sexual cycle, and thus has been refractory to standard forward genetic analysis. Instead, transcription profiling and reverse genetic strategies based on Saccharomyces cerevisiae have typically been used to link genes to functions. To overcome restrictions inherent in such indirect approaches, we have investigated a forward genetic mutagenesis strategy based on the UAU1 technology. We screened 4700 random insertion mutants for defects in hyphal development and linked two new genes (ARP2 and VPS52) to hyphal growth. Deleting ARP2 abolished hyphal formation, generated round and swollen yeast phase cells, disrupted cortical actin patches and blocked virulence in mice. The mutants also showed a global lack of induction of hyphae-specific genes upon the yeast-to-hyphae switch. Surprisingly, both arp2 Delta/Delta and arp2 Delta/Delta arp3 Delta/Delta mutants were still able to endocytose FM4-64 and Lucifer Yellow, although as shown by time-lapse movies internalization of FM4-64 was somewhat delayed in mutant cells. Thus the non-essential role of the Arp2/3 complex discovered by forward genetic screening in C. albicans showed that uptake of membrane components from the plasma membrane to vacuolar structures is not dependent on this actin nucleating machinery.
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Affiliation(s)
- Elias Epp
- Biotechnology Research Institute, National Research Council of Canada, Montréal, QC H4P 2R2, Canada
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Kabir MA, Hussain MA. Human fungal pathogen Candida albicans in the postgenomic era: an overview. Expert Rev Anti Infect Ther 2009; 7:121-34. [PMID: 19622061 DOI: 10.1586/14787210.7.1.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Candida albicans is an opportunistic human fungal pathogen and is responsible for candidiasis. Owing to the improvement in healthcare, the number of immunocompromised patients in hospitals has increased worldwide and these individuals are susceptible to infections caused by many pathogenic microbes, among which C. albicans is one of the major players. Currently, the complete genome sequence of this pathogen is available and the size of this was estimated to be of 16 Mb. Annotation of C. albicans genome revealed that there are 6114 open reading frames (ORFs), of which 774 are specific to C. albicans. This poses a challenge as well as an opportunity to the Candida community to understand the functions of the unknown genes, especially those specific to C. albicans. Efforts have been made by the Candida community to systematically delete the ORFs and assign the functions. This will, in turn, help in understanding the biology of C. albicans and its interactions with animals as well as humans, and better drugs can be developed to treat Candida infections. In this article, we review updates on the Candida biology in the context of the availability of the genome sequence, its functional analysis and anti-Candida therapy. Finally, in the light of present trends in Candida research and current challenges, various opportunities are identified and suggestions are made.
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Affiliation(s)
- M Anaul Kabir
- Department of Biotechnology, PA College of Engineering, Kairangala, Mangalore-574153, Karnataka, India.
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Arbour M, Epp E, Hogues H, Sellam A, Lacroix C, Rauceo J, Mitchell A, Whiteway M, Nantel A. Widespread occurrence of chromosomal aneuploidy following the routine production of Candida albicans mutants. FEMS Yeast Res 2009; 9:1070-7. [PMID: 19732157 PMCID: PMC2784216 DOI: 10.1111/j.1567-1364.2009.00563.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
It has come to our attention that approximately 35% of >100 published microarray datasets, where transcript levels were compared between two different strains, exhibit some form of chromosome-specific bias. While some of these arose from the use of strains whose aneuploidies were not known at the time, in a worrisome number of cases the recombinant strains have acquired additional aneuploidies that were not initially present in the parental strain. The aneuploidies often affected a different chromosome than the one harboring the insertion site. The affected strains originated from either CAI-4, RM1000, BWP17 or SN95 and were produced through a variety of strategies. These observations suggest that aneuploidies frequently occur during the production of recombinant strains and have an effect on global transcript profiles outside of the afflicted chromosome(s), thus raising the possibility of unintended phenotypic consequences. Thus, we propose that all Candida albicans mutants and strains should be tested for aneuploidy before being used in further studies. To this end, we describe a new rapid testing method, based on a multiplex quantitative PCR assay, that produces eight bands of distinct sizes from either the left or right arms of each C. albicans chromosome.
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Affiliation(s)
- Mélanie Arbour
- Biotechnology Research Institute, National Research Council of Canada, Montreal, QC, Canada H4P2R2
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Sellam A, Al-Niemi T, McInnerney K, Brumfield S, Nantel A, Suci PA. A Candida albicans early stage biofilm detachment event in rich medium. BMC Microbiol 2009; 9:25. [PMID: 19187560 PMCID: PMC2647545 DOI: 10.1186/1471-2180-9-25] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Accepted: 02/02/2009] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Dispersal from Candida albicans biofilms that colonize catheters is implicated as a primary factor in the link between contaminated catheters and life threatening blood stream infections (BSI). Appropriate in vitro C. albicans biofilm models are needed to probe factors that induce detachment events. RESULTS Using a flow through system to culture C. albicans biofilms we characterized a detachment process which culminates in dissociation of an entire early stage biofilm from a silicone elastomer surface. We analyzed the transcriptome response at time points that bracketed an abrupt transition in which a strong adhesive association with the surface is weakened in the initial stages of the process, and also compared batch and biofilm cultures at relevant time points. K means analysis of the time course array data revealed categories of genes with similar patterns of expression that were associated with adhesion, biofilm formation and glycoprotein biosynthesis. Compared to batch cultures the biofilm showed a pattern of expression of metabolic genes that was similar to the C. albicans response to hypoxia. However, the loss of strong adhesion was not obviously influenced by either the availability of oxygen in the medium or at the silicone elastomer surface. The detachment phenotype of mutant strains in which selected genes were either deleted or overexpressed was characterized. The microarray data indicated that changes associated with the detachment process were complex and, consistent with this assessment, we were unable to demonstrate that transcriptional regulation of any single gene was essential for loss of the strong adhesive association. CONCLUSION The massive dispersal of the early stage biofilm from a biomaterial surface that we observed is not orchestrated at the level of transcriptional regulation in an obvious manner, or is only regulated at this level by a small subpopulation of cells that mediate adhesion to the surface.
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Affiliation(s)
- Adnane Sellam
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, Canada.
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van het Hoog M, Rast TJ, Martchenko M, Grindle S, Dignard D, Hogues H, Cuomo C, Berriman M, Scherer S, Magee BB, Whiteway M, Chibana H, Nantel A, Magee PT. Assembly of the Candida albicans genome into sixteen supercontigs aligned on the eight chromosomes. Genome Biol 2007; 8:R52. [PMID: 17419877 PMCID: PMC1896002 DOI: 10.1186/gb-2007-8-4-r52] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2006] [Revised: 02/28/2007] [Accepted: 04/09/2007] [Indexed: 11/10/2022] Open
Abstract
For Assembly 20 of the Candida albicans genome, the sequence of each of the eight chromosomes was determined, revealing new insights into gene family creation and dispersion, subtelomere organization, and chromosome evolution. Background The 10.9× genomic sequence of Candida albicans, the most important human fungal pathogen, was published in 2004. Assembly 19 consisted of 412 supercontigs, of which 266 were a haploid set, since this fungus is diploid and contains an extensive degree of heterozygosity but lacks a complete sexual cycle. However, sequences of specific chromosomes were not determined. Results Supercontigs from Assembly 19 (183, representing 98.4% of the sequence) were assigned to individual chromosomes purified by pulse-field gel electrophoresis and hybridized to DNA microarrays. Nine Assembly 19 supercontigs were found to contain markers from two different chromosomes. Assembly 21 contains the sequence of each of the eight chromosomes and was determined using a synteny analysis with preliminary versions of the Candida dubliniensis genome assembly, bioinformatics, a sequence tagged site (STS) map of overlapping fosmid clones, and an optical map. The orientation and order of the contigs on each chromosome, repeat regions too large to be covered by a sequence run, such as the ribosomal DNA cluster and the major repeat sequence, and telomere placement were determined using the STS map. Sequence gaps were closed by PCR and sequencing of the products. The overall assembly was compared to an optical map; this identified some misassembled contigs and gave a size estimate for each chromosome. Conclusion Assembly 21 reveals an ancient chromosome fusion, a number of small internal duplications followed by inversions, and a subtelomeric arrangement, including a new gene family, the TLO genes. Correlations of position with relatedness of gene families imply a novel method of dispersion. The sequence of the individual chromosomes of C. albicans raises interesting biological questions about gene family creation and dispersion, subtelomere organization, and chromosome evolution.
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Affiliation(s)
- Marco van het Hoog
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | | | - Mikhail Martchenko
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | | | - Daniel Dignard
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | - Hervé Hogues
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | | | | | | | - BB Magee
- University of Minnesota, Minneapolis, MN, 55455, USA
| | - Malcolm Whiteway
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | - Hiroji Chibana
- Research Center for Pathogenic Fungi and Microbial Toxicoses, Chiba University, Chiba, 260-8673, Japan
| | - André Nantel
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, H4P 2R2, Canada
| | - PT Magee
- University of Minnesota, Minneapolis, MN, 55455, USA
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Man O, Pilpel Y. Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species. Nat Genet 2007; 39:415-21. [PMID: 17277776 DOI: 10.1038/ng1967] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2006] [Accepted: 01/03/2007] [Indexed: 11/08/2022]
Abstract
A major challenge in comparative genomics is to understand how phenotypic differences between species are encoded in their genomes. Phenotypic divergence may result from differential transcription of orthologous genes, yet less is known about the involvement of differential translation regulation in species phenotypic divergence. In order to assess translation effects on divergence, we analyzed approximately 2,800 orthologous genes in nine yeast genomes. For each gene in each species, we predicted translation efficiency, using a measure of the adaptation of its codons to the organism's tRNA pool. Mining this data set, we found hundreds of genes and gene modules with correlated patterns of translational efficiency across the species. One signal encompassed entire modules that are either needed for oxidative respiration or fermentation and are efficiently translated in aerobic or anaerobic species, respectively. In addition, the efficiency of translation of the mRNA splicing machinery strongly correlates with the number of introns in the various genomes. Altogether, we found extensive selection on synonymous codon usage that modulates translation according to gene function and organism phenotype. We conclude that, like factors such as transcription regulation, translation efficiency affects and is affected by the process of species divergence.
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Affiliation(s)
- Orna Man
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot 76100, Israel
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Arnaud MB, Costanzo MC, Skrzypek MS, Shah P, Binkley G, Lane C, Miyasato SR, Sherlock G. Sequence resources at the Candida Genome Database. Nucleic Acids Res 2006; 35:D452-6. [PMID: 17090582 PMCID: PMC1669745 DOI: 10.1093/nar/gkl899] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The Candida Genome Database (CGD, ) contains a curated collection of genomic information and community resources for researchers who are interested in the molecular biology of the opportunistic pathogen Candida albicans. With the recent release of a new assembly of the C.albicans genome, Assembly 20, C.albicans genomics has entered a new era. Although the C.albicans genome assembly continues to undergo refinement, multiple assemblies and gene nomenclatures will remain in widespread use by the research community. CGD has now taken on the responsibility of maintaining the most up-to-date version of the genome sequence by providing the data from this new assembly alongside the data from the previous assemblies, as well as any future corrections and refinements. In this database update, we describe the sequence information available for C.albicans, the sequence information contained in CGD, and the tools for sequence retrieval, analysis and comparison that CGD provides. CGD is freely accessible at and CGD curators may be contacted by email at candida-curator@genome.stanford.edu.
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Affiliation(s)
- Martha B Arnaud
- Department of Genetics, Stanford University Medical School, Stanford, CA 94305-5120, USA.
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Chibana H, Mikami Y. [Structural and functional analyses of MRS (major repeated sequnece) in Candida albicans. Application for genotyping and the eternal way to the complete genome sequence]. NIHON ISHINKIN GAKKAI ZASSHI = JAPANESE JOURNAL OF MEDICAL MYCOLOGY 2006; 47:129-34. [PMID: 16940945 DOI: 10.3314/jjmm.47.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
There are several different types of repeated sequences in the genome of Candida albicans, including the MRS (Major repeated sequence). In 2004, the whole genome sequence of C. albicans was published. Assembly of the sequences to chromosomal length contigs was not achieved, mainly due to interruption of the sequences by MRS. However, MRS including Ca3, 27A and RPS have been playing important roles in a number of epidemiological studies and basic biological investigations into C. albicans chromosome loss events and associated phenotypic changes. Here we summarize structural analyses from subrepeat sequences to the chromosome level, and functional analyses of MRS.
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Affiliation(s)
- Hiroji Chibana
- Research Center for Pathogenic Fungi and Microbial Toxicoses, Chiba University, Japan.
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