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Jodi: /* CGD IS GETTING REMODELLED! */

2026-03-24T20:23:21Z

CGD IS GETTING REMODELLED!

Jodi: /* CGD IS GETTING REMODELLED! */

2026-03-24T20:20:28Z

CGD IS GETTING REMODELLED!

← Older revision		Revision as of 20:20, 24 March 2026
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	# Improved tools that allow for using larger datasets, including the GO Term Finder.		# Improved tools that allow for using larger datasets, including the GO Term Finder.
	# Introduced CGD Swagger UI, offering a convenient way to retrieve data programmatically. This includes an interactive API Playground for testing endpoints and generating Python and R code snippets.		# Introduced CGD Swagger UI, offering a convenient way to retrieve data programmatically. This includes an interactive API Playground for testing endpoints and generating Python and R code snippets.
			# New Synteny Viewer for the species within CGD, available from the Tools menu or on the Homologs page for each locus

	To what do we owe this embarrassment of riches? Our new programmer/developer stepped in just a couple months ago and quickly began building improved tools.		To what do we owe this embarrassment of riches? Our new programmer/developer stepped in just a couple months ago and quickly began building improved tools.

Jodi: /* Newsletter Archives */

2026-03-24T14:35:30Z

Newsletter Archives

← Older revision		Revision as of 14:35, 24 March 2026
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	== CGD Newsletter, Spring 2026 ==		== CGD Newsletter, Spring 2026 ==
			<div class="mw-collapsible mw-collapsed">

	=== About this newsletter ===		=== About this newsletter ===
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	Future studies will have these intriguing questions to tackle.		Future studies will have these intriguing questions to tackle.
			</div>

Jodi: /* Datasets Available in CGD */

2026-03-24T14:31:52Z

Datasets Available in CGD

← Older revision		Revision as of 14:31, 24 March 2026
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	==[http://www.candidagenome.org/jbrowse/index.html?data=cgd_data%2FC_albicans_SC5314&loc=Ca22chr1A_C_albicans_SC5314%3A120520..134789&tracks=DNA%2CTranscribed%20Features%2Csegal_hapA_transposon_hits%2Csegal_hapA_transposon_reads%2ChapA_alb_dub_phyloP_scores%2ChapA_CanLod_phyloP_scores%2ChapA_CTG_phyloP_scores%2ChapA_Sacc_phyloP_scores%2Cbruno_nOxi_hapA_coverage&highlight= <i>C. albicans</i> in JBrowse]==		==[http://www.candidagenome.org/jbrowse/index.html?data=cgd_data%2FC_albicans_SC5314&loc=Ca22chr1A_C_albicans_SC5314%3A120520..134789&tracks=DNA%2CTranscribed%20Features%2Csegal_hapA_transposon_hits%2Csegal_hapA_transposon_reads%2ChapA_alb_dub_phyloP_scores%2ChapA_CanLod_phyloP_scores%2ChapA_CTG_phyloP_scores%2ChapA_Sacc_phyloP_scores%2Cbruno_nOxi_hapA_coverage&highlight= <i>C. albicans</i> in JBrowse]==
			<div class="mw-collapsible mw-collapsed">
	*[https://pubmed.ncbi.nlm.nih.gov/20810668/ Bruno et al., 2010]. Comprehensive annotation of the transcriptome of the human fungal pathogen <i>Candida albicans</i> using RNA-seq. Genome Res. 2010 Oct;20(10):1451-8.		*[https://pubmed.ncbi.nlm.nih.gov/20810668/ Bruno et al., 2010]. Comprehensive annotation of the transcriptome of the human fungal pathogen <i>Candida albicans</i> using RNA-seq. Genome Res. 2010 Oct;20(10):1451-8.
	*[https://pubmed.ncbi.nlm.nih.gov/19465905/ Butler et al., 2009]. Evolution of pathogenicity and sexual reproduction in eight <i>Candida</i> genomes. Nature. 2009 Jun 4;459(7247):657-62.		*[https://pubmed.ncbi.nlm.nih.gov/19465905/ Butler et al., 2009]. Evolution of pathogenicity and sexual reproduction in eight <i>Candida</i> genomes. Nature. 2009 Jun 4;459(7247):657-62.
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	*[https://pubmed.ncbi.nlm.nih.gov/38905306/ Rai, et al., 2024]. Metabolic reprogramming during <i>Candida albicans</i> planktonic-biofilm transition is modulated by the transcription factors <i>Zcf15</i> and <i>Zcf26</i>. PLoS Biol. 2024 Jun 21;22(6):e3002693.		*[https://pubmed.ncbi.nlm.nih.gov/38905306/ Rai, et al., 2024]. Metabolic reprogramming during <i>Candida albicans</i> planktonic-biofilm transition is modulated by the transcription factors <i>Zcf15</i> and <i>Zcf26</i>. PLoS Biol. 2024 Jun 21;22(6):e3002693.
	*[https://pubmed.ncbi.nlm.nih.gov/38921373/ Zhang, et al. 2024]. DNA damage checkpoints govern global gene transcription and exhibit species-specific regulation on <i>HOF1</i> in <i>Candida albicans</i>. J Fungi (Basel). 2024 May 29;10(6):387.		*[https://pubmed.ncbi.nlm.nih.gov/38921373/ Zhang, et al. 2024]. DNA damage checkpoints govern global gene transcription and exhibit species-specific regulation on <i>HOF1</i> in <i>Candida albicans</i>. J Fungi (Basel). 2024 May 29;10(6):387.
			</div>
	==[http://www.candidagenome.org/jbrowse/index.html?data=cgd_data%2FC_parapsilosis_CDC317&loc=Contig005569_C_parapsilosis_CDC317%3A2164961..2179340&tracks=DNA%2CTranscribed%20Features%2Cpara_phyloP_scores%2CCanLod_phyloP_scores%2CCTG_phyloP_scores%2CSacc_phyloP_scores%2Cholland_wt_plnk_1_coverage&highlight= <i>C. parapsilosis</i> in JBrowse]==		==[http://www.candidagenome.org/jbrowse/index.html?data=cgd_data%2FC_parapsilosis_CDC317&loc=Contig005569_C_parapsilosis_CDC317%3A2164961..2179340&tracks=DNA%2CTranscribed%20Features%2Cpara_phyloP_scores%2CCanLod_phyloP_scores%2CCTG_phyloP_scores%2CSacc_phyloP_scores%2Cholland_wt_plnk_1_coverage&highlight= <i>C. parapsilosis</i> in JBrowse]==
			<div class="mw-collapsible mw-collapsed">
	*[https://pubmed.ncbi.nlm.nih.gov/23895281/ Connolly, et al., 2013]. The APSES transcription factor <i>Efg1</i> is a global regulator that controls morphogenesis and biofilm formation in <i>Candida parapsilosis</i>. Mol Microbiol. 2013 Oct;90(1):36-53.		*[https://pubmed.ncbi.nlm.nih.gov/23895281/ Connolly, et al., 2013]. The APSES transcription factor <i>Efg1</i> is a global regulator that controls morphogenesis and biofilm formation in <i>Candida parapsilosis</i>. Mol Microbiol. 2013 Oct;90(1):36-53.
	*[https://pubmed.ncbi.nlm.nih.gov/22192698/ Guida et al., 2011]. Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast <i>Candida parapsilosis</i>. BMC Genomics. 2011 Dec 22:12:628.		*[https://pubmed.ncbi.nlm.nih.gov/22192698/ Guida et al., 2011]. Using RNA-seq to determine the transcriptional landscape and the hypoxic response of the pathogenic yeast <i>Candida parapsilosis</i>. BMC Genomics. 2011 Dec 22:12:628.
			</div>
	==[http://www.candidagenome.org/jbrowse/index.html?data=cgd_data%2FC_dubliniensis_CD36&loc=Chr1_C_dubliniensis_CD36%3A131099..145478&tracks=DNA%2CTranscribed%20Features%2Calb_dub_phyloP_scores%2CCanLod_phyloP_scores%2CCTG_phyloP_scores%2CSacc_phyloP_scores&highlight= <i>C. dubliniensis</i> in JBrowse]==		==[http://www.candidagenome.org/jbrowse/index.html?data=cgd_data%2FC_dubliniensis_CD36&loc=Chr1_C_dubliniensis_CD36%3A131099..145478&tracks=DNA%2CTranscribed%20Features%2Calb_dub_phyloP_scores%2CCanLod_phyloP_scores%2CCTG_phyloP_scores%2CSacc_phyloP_scores&highlight= <i>C. dubliniensis</i> in JBrowse]==
			<div class="mw-collapsible mw-collapsed">
	*[https://pubmed.ncbi.nlm.nih.gov/23547856/ Grumaz et al., 2013]. Species and condition specific adaptation of the transcriptional landscapes in <i>Candida albicans</i> and <i>Candida dubliniensis</i>. BMC Genomics. 2013 Apr 2:14:212.		*[https://pubmed.ncbi.nlm.nih.gov/23547856/ Grumaz et al., 2013]. Species and condition specific adaptation of the transcriptional landscapes in <i>Candida albicans</i> and <i>Candida dubliniensis</i>. BMC Genomics. 2013 Apr 2:14:212.
	*[https://pubmed.ncbi.nlm.nih.gov/33723044/ Singh-Babakh et al., 2021]. Lineage-specific selection and the evolution of virulence in the <i>Candida</i> clade. Proc Natl Acad Sci U S A. 2021 Mar 23;118(12):e2016818118.		*[https://pubmed.ncbi.nlm.nih.gov/33723044/ Singh-Babakh et al., 2021]. Lineage-specific selection and the evolution of virulence in the <i>Candida</i> clade. Proc Natl Acad Sci U S A. 2021 Mar 23;118(12):e2016818118.
			</div>
	==[http://www.candidagenome.org/jbrowse/index.html?data=cgd_data%2FC_glabrata_CBS138&loc=ChrL_C_glabrata_CBS138%3A1176133..1190402&tracks=DNA%2CTranscribed%20Features%2Cglab_phyloP_scores%2CCanNak_phyloP_scores%2CWGD_phyloP_scores%2CSacc_phyloP_scores%2Clinde_ypd_1_coverage&highlight= <i>C. glabrata</i> in JBrowse]==		==[http://www.candidagenome.org/jbrowse/index.html?data=cgd_data%2FC_glabrata_CBS138&loc=ChrL_C_glabrata_CBS138%3A1176133..1190402&tracks=DNA%2CTranscribed%20Features%2Cglab_phyloP_scores%2CCanNak_phyloP_scores%2CWGD_phyloP_scores%2CSacc_phyloP_scores%2Clinde_ypd_1_coverage&highlight= <i>C. glabrata</i> in JBrowse]==
			<div class="mw-collapsible mw-collapsed">
	*[https://pubmed.ncbi.nlm.nih.gov/34591857/ Vu, et al., 2021]. The <i>Candida glabrata Upc2A</i> transcription factor is a global regulator of antifungal drug resistance pathways. PLoS Genet. 2021 Sep 30;17(9):e1009582.		*[https://pubmed.ncbi.nlm.nih.gov/34591857/ Vu, et al., 2021]. The <i>Candida glabrata Upc2A</i> transcription factor is a global regulator of antifungal drug resistance pathways. PLoS Genet. 2021 Sep 30;17(9):e1009582.
	*[https://pubmed.ncbi.nlm.nih.gov/37891489/ Ni, et al., 2023]. The regulatory subunits of CK2 complex mediate DNA damage response and virulence in <i>Candida glabrata</i>. BMC Microbiol. 2023 Oct 28;23(1):317.		*[https://pubmed.ncbi.nlm.nih.gov/37891489/ Ni, et al., 2023]. The regulatory subunits of CK2 complex mediate DNA damage response and virulence in <i>Candida glabrata</i>. BMC Microbiol. 2023 Oct 28;23(1):317.
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	*[https://pubmed.ncbi.nlm.nih.gov/36108742/ Bhakt et al., 2022]. The SET-domain protein <i>CgSet4</i> negatively regulates antifungal drug resistance via the ergosterol biosynthesis transcriptional regulator <i>CgUpc2a</i>. J Biol Chem. 2022 Oct;298(10):102485.		*[https://pubmed.ncbi.nlm.nih.gov/36108742/ Bhakt et al., 2022]. The SET-domain protein <i>CgSet4</i> negatively regulates antifungal drug resistance via the ergosterol biosynthesis transcriptional regulator <i>CgUpc2a</i>. J Biol Chem. 2022 Oct;298(10):102485.
	*[https://pubmed.ncbi.nlm.nih.gov/25586221/ Linde et al., 2015]. Defining the transcriptomic landscape of <i>Candida glabrata</i> by RNA-Seq. Nucleic Acids Res. 2015 Feb 18;43(3):1392-406.		*[https://pubmed.ncbi.nlm.nih.gov/25586221/ Linde et al., 2015]. Defining the transcriptomic landscape of <i>Candida glabrata</i> by RNA-Seq. Nucleic Acids Res. 2015 Feb 18;43(3):1392-406.
			</div>
	==[http://www.candidagenome.org/jbrowse/index.html?data=cgd_data%2FC_auris_B8441&loc=PEKT02000010_C_auris_B8441%3A118601..133000&tracks=DNA%2CTranscribed%20Features%2Cauris_phyloP_scores%2CAurLus_phyloP_scores%2CCTG_phyloP_scores%2CSacc_phyloP_scores&highlight= <i>C. auris</i> in JBrowse]==		==[http://www.candidagenome.org/jbrowse/index.html?data=cgd_data%2FC_auris_B8441&loc=PEKT02000010_C_auris_B8441%3A118601..133000&tracks=DNA%2CTranscribed%20Features%2Cauris_phyloP_scores%2CAurLus_phyloP_scores%2CCTG_phyloP_scores%2CSacc_phyloP_scores&highlight= <i>C. auris</i> in JBrowse]==
			<div class="mw-collapsible mw-collapsed">
	*[https://pubmed.ncbi.nlm.nih.gov/35412372/ Simm, et al., 2022]. Disruption of iron homeostasis and mitochondrial metabolism are promising targets to inhibit <i>Candida auris</i>. Microbiol Spectr 2022 Apr 27;10(2):e0010022.		*[https://pubmed.ncbi.nlm.nih.gov/35412372/ Simm, et al., 2022]. Disruption of iron homeostasis and mitochondrial metabolism are promising targets to inhibit <i>Candida auris</i>. Microbiol Spectr 2022 Apr 27;10(2):e0010022.
	*[https://pubmed.ncbi.nlm.nih.gov/34643421/ Jakab, et al., 2021]. Transcriptional profiling of the <i>Candida auris</i> response to exogenous farnesol exposure mSphere. 2021 Sep-Oct; 6(5): e00710-21.		*[https://pubmed.ncbi.nlm.nih.gov/34643421/ Jakab, et al., 2021]. Transcriptional profiling of the <i>Candida auris</i> response to exogenous farnesol exposure mSphere. 2021 Sep-Oct; 6(5): e00710-21.
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	*[https://pubmed.ncbi.nlm.nih.gov/35652307/ Shivarathri, et al., 2022]. Comparative transcriptomics reveal possible mechanisms of amphotericin B resistance in <i>Candida auris</i>. Antimicrob Agents Chemother. 2022 Jun 21;66(6):e0227621.		*[https://pubmed.ncbi.nlm.nih.gov/35652307/ Shivarathri, et al., 2022]. Comparative transcriptomics reveal possible mechanisms of amphotericin B resistance in <i>Candida auris</i>. Antimicrob Agents Chemother. 2022 Jun 21;66(6):e0227621.
	*[https://pubmed.ncbi.nlm.nih.gov/38466738/ Pelletier, et al., 2024]. <i>Candida auris</i> undergoes adhesin-dependent and -independent cellular aggregation. PLoS Pathog. 2024 Mar 11;20(3):e1012076		*[https://pubmed.ncbi.nlm.nih.gov/38466738/ Pelletier, et al., 2024]. <i>Candida auris</i> undergoes adhesin-dependent and -independent cellular aggregation. PLoS Pathog. 2024 Mar 11;20(3):e1012076
			</div>

	=Newsletter Archives=		=Newsletter Archives=

Jodi: /* Species Comparisons by Topic */

2026-03-24T14:28:57Z

Species Comparisons by Topic

← Older revision		Revision as of 14:28, 24 March 2026
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	==Ploidy==		==Ploidy==
			<div class="mw-collapsible mw-collapsed">
	<B>Notes:</B> <i>Candida albicans</i> and its close relatives are all on a single phylogenetic branch characterized by diploidy, while the two typical haploid species (<i>C. glabrata</i> and <i>C. auris</i>) are on distinct, distantly related branches for which haploidy is the standard form. Note that the two haploid pathogens are more prone to pleiotropic resistance because only a single mutation is needed in the haploid genome to generate stable change.		<B>Notes:</B> <i>Candida albicans</i> and its close relatives are all on a single phylogenetic branch characterized by diploidy, while the two typical haploid species (<i>C. glabrata</i> and <i>C. auris</i>) are on distinct, distantly related branches for which haploidy is the standard form. Note that the two haploid pathogens are more prone to pleiotropic resistance because only a single mutation is needed in the haploid genome to generate stable change.

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	From [https://www.nature.com/articles/s41467-018-07779-6/figures/3 Munoz et al., 2018]		From [https://www.nature.com/articles/s41467-018-07779-6/figures/3 Munoz et al., 2018]
			</div>

	==CUG codon usage==		==CUG codon usage==
			<div class="mw-collapsible mw-collapsed">
	<B>Notes:</B> Yeasts of the <i>Candida</i> clade (as opposed to <i>C. glabrata</i>, also known as <i>Nakaseomyces glabratus</i>, which is on the <i>Saccharomyces</i> clade) have undergone an evolutionary reassignment of the CUG codon from leucine to serine. This is due to a novel serine-tRNA (ser-tRNACAG) that contains a guanosine at position 33, a position that is occupied by a pyrimidine (uridine) in nearly all other tRNAs.		<B>Notes:</B> Yeasts of the <i>Candida</i> clade (as opposed to <i>C. glabrata</i>, also known as <i>Nakaseomyces glabratus</i>, which is on the <i>Saccharomyces</i> clade) have undergone an evolutionary reassignment of the CUG codon from leucine to serine. This is due to a novel serine-tRNA (ser-tRNACAG) that contains a guanosine at position 33, a position that is occupied by a pyrimidine (uridine) in nearly all other tRNAs.

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	From [https://pubmed.ncbi.nlm.nih.gov/19465905/ Butler et al., 2009]		From [https://pubmed.ncbi.nlm.nih.gov/19465905/ Butler et al., 2009]
			</div>
	==Mitochondrial genome==		==Mitochondrial genome==
			<div class="mw-collapsible mw-collapsed">
	<B>Notes:</B> <i>Candida parapsilosis</i> is unusual in having a mitochondrial genome that is linear and capped by telomeric ends. The close relatives of this species, <i>C. orthopsilosis</i> and <i>C. metapsilosis</i> and <i>Candida subhashii</i>, have a mix of circular and linear mitochondrial genomes. The other <i>Candida</i> spp. are exclusively circular.		<B>Notes:</B> <i>Candida parapsilosis</i> is unusual in having a mitochondrial genome that is linear and capped by telomeric ends. The close relatives of this species, <i>C. orthopsilosis</i> and <i>C. metapsilosis</i> and <i>Candida subhashii</i>, have a mix of circular and linear mitochondrial genomes. The other <i>Candida</i> spp. are exclusively circular.

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	From [https://pubmed.ncbi.nlm.nih.gov/16684995/ Kosa et al., 2006]		From [https://pubmed.ncbi.nlm.nih.gov/16684995/ Kosa et al., 2006]
			</div>
	==Filamentous growth==		==Filamentous growth==
			<div class="mw-collapsible mw-collapsed">

	<B>Notes:</B> <i>Candida spp.</i> vary in filamentous growth as a means of infection/invasion. <i>C. albicans</i> and its close relative <i>C. dubliniensis</i> use true hyphae to penetrate tissues, while <i>C. parapsilosis</i> and <i>C. tropicalis</i> can penetrate tissues by means of pseudohyphae (lacking septa). In contrast, <i>C. glabrata</i> almost never forms filaments and infects in the yeast form. <i>C. auris </i> is an outlier in that it infects both by pseudohyphae and in the yeast form.		<B>Notes:</B> <i>Candida spp.</i> vary in filamentous growth as a means of infection/invasion. <i>C. albicans</i> and its close relative <i>C. dubliniensis</i> use true hyphae to penetrate tissues, while <i>C. parapsilosis</i> and <i>C. tropicalis</i> can penetrate tissues by means of pseudohyphae (lacking septa). In contrast, <i>C. glabrata</i> almost never forms filaments and infects in the yeast form. <i>C. auris </i> is an outlier in that it infects both by pseudohyphae and in the yeast form.

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	*<i>C. glabrata</i>		*<i>C. glabrata</i>
	*<i>C. auris</i>		*<i>C. auris</i>
			</div>
	==Biofilms==		==Biofilms==
			<div class="mw-collapsible mw-collapsed">
	<B>Notes:</B> <i>Candida</i> species all form biofilms but not in the same manner. Biofilms all begin as adherence to a surface and then excretion of an extracellular matrix composed mainly of proteins, carbohydrates, and lipids. All species employ extracellular vesicles to facilitate excretion. They differ in the types of cells that inhabit the biofilm environment.		<B>Notes:</B> <i>Candida</i> species all form biofilms but not in the same manner. Biofilms all begin as adherence to a surface and then excretion of an extracellular matrix composed mainly of proteins, carbohydrates, and lipids. All species employ extracellular vesicles to facilitate excretion. They differ in the types of cells that inhabit the biofilm environment.

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	===Biofilms comprising primarily yeast cells===		===Biofilms comprising primarily yeast cells===
	*<i>C. glabrata</i>		*<i>C. glabrata</i>
			</div>
	==Pathogenicity==		==Pathogenicity==
			<div class="mw-collapsible mw-collapsed">
	<B>Notes:</B> <i>Candida</i> species show heterogeneity in pathogenicity, where each species has a unique profile. See descriptions below.		<B>Notes:</B> <i>Candida</i> species show heterogeneity in pathogenicity, where each species has a unique profile. See descriptions below.

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	*As <i>C. auris</i> preferentially colonizes the cooler skin rather than the hotter gut microbiome, new commensalism may be consistent with a recent acquisition of thermotolerance		*As <i>C. auris</i> preferentially colonizes the cooler skin rather than the hotter gut microbiome, new commensalism may be consistent with a recent acquisition of thermotolerance
	*The inclination to colonize skin has made <i>C. auris</i> particularly problematic in hospital settings, where widespread outbreaks have become common		*The inclination to colonize skin has made <i>C. auris</i> particularly problematic in hospital settings, where widespread outbreaks have become common
			</div>
	==Mating/Reproduction==		==Mating/Reproduction==
			<div class="mw-collapsible mw-collapsed">
	<B>Notes:</B> <i>Candida</i> species show heterogeneity in mating/reproduction, as described below. References are by species.		<B>Notes:</B> <i>Candida</i> species show heterogeneity in mating/reproduction, as described below. References are by species.

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	[https://pubmed.ncbi.nlm.nih.gov/30559369/ Muñoz et al., 2018]		[https://pubmed.ncbi.nlm.nih.gov/30559369/ Muñoz et al., 2018]
			</div>
	==Drug resistance==		==Drug resistance==
			<div class="mw-collapsible mw-collapsed">
	<B>Notes:</B> <i>Candida</i> species show distinct drug resistance profiles. While all species can acquire resistance, inherent resistance and/or tolerance is especially concerning for <i>C. auris</i> and <i>C. glabrata</i>, likely due to their haploid genomes.		<B>Notes:</B> <i>Candida</i> species show distinct drug resistance profiles. While all species can acquire resistance, inherent resistance and/or tolerance is especially concerning for <i>C. auris</i> and <i>C. glabrata</i>, likely due to their haploid genomes.

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	===Resistance within biofilms===		===Resistance within biofilms===
	*All species		*All species
			</div>
	==Respiratory metabolism==		==Respiratory metabolism==
			<div class="mw-collapsible mw-collapsed">
	<B>Notes:</B> The Crabtree effect explains why baker’s yeast is also called brewer’s yeast, in that <i>S. cerevisiae</i> preferentially converts sugar to alcohol in lieu of other types of respiration. This is referred to as Crabtree positive. Among the pathogenic yeasts, the only member with this ability is the phylogenetic outlier <i>C. glabrata</i>, which is more closely related to <i>S. cerevisiae</i> than to the other pathogenic yeasts. The other pathogenic yeasts are all Crabtree negative, meaning they do not produce alcohol as a product of respiration. For these non-fermentative yeasts, the ability to utilize many carbon sources (with little preference for glucose) is thought to provide an advantage for pathogenesis in various host niches.		<B>Notes:</B> The Crabtree effect explains why baker’s yeast is also called brewer’s yeast, in that <i>S. cerevisiae</i> preferentially converts sugar to alcohol in lieu of other types of respiration. This is referred to as Crabtree positive. Among the pathogenic yeasts, the only member with this ability is the phylogenetic outlier <i>C. glabrata</i>, which is more closely related to <i>S. cerevisiae</i> than to the other pathogenic yeasts. The other pathogenic yeasts are all Crabtree negative, meaning they do not produce alcohol as a product of respiration. For these non-fermentative yeasts, the ability to utilize many carbon sources (with little preference for glucose) is thought to provide an advantage for pathogenesis in various host niches.

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	===Crabtree positive (fermentative)===		===Crabtree positive (fermentative)===
	*<i>C. glabrata</i>		*<i>C. glabrata</i>
			</div>
	==Virulence Factors==		==Virulence Factors==
			<div class="mw-collapsible mw-collapsed">
	<B>Notes:</B> Pathogenic yeasts vary in use of secreted and membrane-bound virulence factors involved in invasion, damage and translocation.		<B>Notes:</B> Pathogenic yeasts vary in use of secreted and membrane-bound virulence factors involved in invasion, damage and translocation.

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	From [https://pubmed.ncbi.nlm.nih.gov/34506621/ Lim et al., 2021]		From [https://pubmed.ncbi.nlm.nih.gov/34506621/ Lim et al., 2021]
			</div>

	=Datasets Available in CGD=		=Datasets Available in CGD=

Jodi: /* Protocols and Methods */

2026-03-24T14:25:53Z

Protocols and Methods

← Older revision		Revision as of 14:25, 24 March 2026
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	==<i>Candida</i> Identification==		==<i>Candida</i> Identification==
			<div class="mw-collapsible mw-collapsed">
	===Universal primers===		===Universal primers===
	*used to amplify ITS genes for subsequent sequencing to identify species		*used to amplify ITS genes for subsequent sequencing to identify species
Line 883:		Line 884:
	**These are primers ITS86F and ITS4 from the reference [https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0748-9 Park et al.]		**These are primers ITS86F and ITS4 from the reference [https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-019-0748-9 Park et al.]
	**The primers themselves are from older literature, but this combination seems to work best for yeast species		**The primers themselves are from older literature, but this combination seems to work best for yeast species
			</div>
	==<i>Candida albicans</i> Protocols and Methods==		==<i>Candida albicans</i> Protocols and Methods==
			<div class="mw-collapsible mw-collapsed">
	* Basic techniques		* Basic techniques
	**[https://link.springer.com/book/10.1007/978-1-60327-151-6 <i>Candida albicans</i>: Methods and Protocols]		**[https://link.springer.com/book/10.1007/978-1-60327-151-6 <i>Candida albicans</i>: Methods and Protocols]
Line 910:		Line 911:
	** [https://pubmed.ncbi.nlm.nih.gov/23211681/ Junqueira, 2012]. Virulence. 2012 Oct 1;3(6):474-6		** [https://pubmed.ncbi.nlm.nih.gov/23211681/ Junqueira, 2012]. Virulence. 2012 Oct 1;3(6):474-6
	** [https://pubmed.ncbi.nlm.nih.gov/32970818/ Wojda et al., 2020]. Pathog Dis. 2020 Nov 23;78(9):ftaa057		** [https://pubmed.ncbi.nlm.nih.gov/32970818/ Wojda et al., 2020]. Pathog Dis. 2020 Nov 23;78(9):ftaa057
			</div>
	==<i>Candida glabrata</i> (<i>Nakaseomyces glabratus</i>) Protocols and Methods==		==<i>Candida glabrata</i> (<i>Nakaseomyces glabratus</i>) Protocols and Methods==
			<div class="mw-collapsible mw-collapsed">
	* Basic techniques		* Basic techniques
	**[https://link.springer.com/book/10.1007/978-1-0716-2549-1 <i>Candida</i> Species: Methods and Protocols]		**[https://link.springer.com/book/10.1007/978-1-0716-2549-1 <i>Candida</i> Species: Methods and Protocols]
Line 936:		Line 937:
	** [https://pubmed.ncbi.nlm.nih.gov/23211681/ Junqueira, 2012]. Virulence. 2012 Oct 1;3(6):474-6		** [https://pubmed.ncbi.nlm.nih.gov/23211681/ Junqueira, 2012]. Virulence. 2012 Oct 1;3(6):474-6
	** [https://pubmed.ncbi.nlm.nih.gov/32970818/ Wojda et al., 2020]. Pathog Dis. 2020 Nov 23;78(9):ftaa057		** [https://pubmed.ncbi.nlm.nih.gov/32970818/ Wojda et al., 2020]. Pathog Dis. 2020 Nov 23;78(9):ftaa057
			</div>
	==<i>Candida parapsilosis</i> Protocols and Methods==		==<i>Candida parapsilosis</i> Protocols and Methods==
			<div class="mw-collapsible mw-collapsed">
	* Basic techniques		* Basic techniques
	** [https://link.springer.com/book/10.1007/978-1-0716-2549-1 <i>Candida</i> Species: Methods and Protocols]		** [https://link.springer.com/book/10.1007/978-1-0716-2549-1 <i>Candida</i> Species: Methods and Protocols]
Line 959:		Line 960:
	** [https://pubmed.ncbi.nlm.nih.gov/36416551/ Lombardi et al.,2022]. mSphere. 2022 Dec 21;7(6):e0039322		** [https://pubmed.ncbi.nlm.nih.gov/36416551/ Lombardi et al.,2022]. mSphere. 2022 Dec 21;7(6):e0039322
	** [https://pubmed.ncbi.nlm.nih.gov/36008654/ Lombardi and Butler,2022]. Methods Mol Biol. 2022:2542:13-40		** [https://pubmed.ncbi.nlm.nih.gov/36008654/ Lombardi and Butler,2022]. Methods Mol Biol. 2022:2542:13-40
			</div>
	==<i>Candida auris</i> (<i>Candidozyma auris</i>) Protocols and Methods==		==<i>Candida auris</i> (<i>Candidozyma auris</i>) Protocols and Methods==
			<div class="mw-collapsible mw-collapsed">
	* Basic techniques		* Basic techniques
	** [https://link.springer.com/book/10.1007/978-1-0716-2417-3 Candida auris: Methods and Protocols]		** [https://link.springer.com/book/10.1007/978-1-0716-2417-3 Candida auris: Methods and Protocols]
Line 1,001:		Line 1,002:
	** [https://pubmed.ncbi.nlm.nih.gov/29315379/ Chupácová et al., 2018]. Pathog Dis. 2018 Feb 1;76(1)		** [https://pubmed.ncbi.nlm.nih.gov/29315379/ Chupácová et al., 2018]. Pathog Dis. 2018 Feb 1;76(1)
	** [https://pubmed.ncbi.nlm.nih.gov/30386966/ Dekkerová-Chupáčová et al., 2018]. Mycopathologia. 2018 Dec;183(6)		** [https://pubmed.ncbi.nlm.nih.gov/30386966/ Dekkerová-Chupáčová et al., 2018]. Mycopathologia. 2018 Dec;183(6)
			</div>
	==<i>Candida tropicalis</i> Protocols and Methods==		==<i>Candida tropicalis</i> Protocols and Methods==
			<div class="mw-collapsible mw-collapsed">
	* Basic techniques		* Basic techniques
	** [https://link.springer.com/book/10.1007/978-1-0716-2549-1 <i>Candida</i> Species: Methods and Protocols]		** [https://link.springer.com/book/10.1007/978-1-0716-2549-1 <i>Candida</i> Species: Methods and Protocols]
Line 1,023:		Line 1,024:
	** [https://pubmed.ncbi.nlm.nih.gov/23877676/ Forastiero et al., 2013]. Antimicrob Agents Chemother. 2013 Oct;57(10):4769-81		** [https://pubmed.ncbi.nlm.nih.gov/23877676/ Forastiero et al., 2013]. Antimicrob Agents Chemother. 2013 Oct;57(10):4769-81
	** [https://pubmed.ncbi.nlm.nih.gov/32867152/ García-Carnero et al., 2020]. J Fungi (Basel). 2020 Aug 27;6(3):152		** [https://pubmed.ncbi.nlm.nih.gov/32867152/ García-Carnero et al., 2020]. J Fungi (Basel). 2020 Aug 27;6(3):152
			</div>

	=Species Comparisons by Topic=		=Species Comparisons by Topic=

Jodi: /* Candida dubliniensis Strains */

2026-03-24T14:23:59Z

Candida dubliniensis Strains

← Older revision		Revision as of 14:23, 24 March 2026
Line 872:		Line 872:

	<B>References:</B> [https://pubmed.ncbi.nlm.nih.gov/7551019/ Sullivan et al., 1995]. Microbiology (Reading) 1995 Jul:141 ( Pt 7):1507-21.		<B>References:</B> [https://pubmed.ncbi.nlm.nih.gov/7551019/ Sullivan et al., 1995]. Microbiology (Reading) 1995 Jul:141 ( Pt 7):1507-21.
			</div>

	=Protocols and Methods=		=Protocols and Methods=

Jodi: /* Strain Information */

2026-03-24T14:22:48Z

Strain Information

← Older revision		Revision as of 14:22, 24 March 2026
Line 531:		Line 531:

	==<i>Candida albicans</i> Strains==		==<i>Candida albicans</i> Strains==
			<div class="mw-collapsible mw-collapsed">

	===SC5314===		===SC5314===
Line 660:		Line 661:

	<B>References:</B> [https://pubmed.ncbi.nlm.nih.gov/11371541/ Strauss et al. 2001]. J Bacteriol. 2001 Jun;183(12):3761-9.		<B>References:</B> [https://pubmed.ncbi.nlm.nih.gov/11371541/ Strauss et al. 2001]. J Bacteriol. 2001 Jun;183(12):3761-9.
			</div>

	==<i>Candida glabrata</i> (<i>Nakaseomyces glabratus</i>) Strains==		==<i>Candida glabrata</i> (<i>Nakaseomyces glabratus</i>) Strains==
			<div class="mw-collapsible mw-collapsed">
	===B===		===B===
	<B>Genotype:</B> Wild type		<B>Genotype:</B> Wild type
Line 727:		Line 729:

	<B>References:</B> [https://pubmed.ncbi.nlm.nih.gov/16569856/ Tsai et al., 2006]. Antimicrob Agents Chemother. 2006 Apr;50(4):1384-92.		<B>References:</B> [https://pubmed.ncbi.nlm.nih.gov/16569856/ Tsai et al., 2006]. Antimicrob Agents Chemother. 2006 Apr;50(4):1384-92.
			</div>
	==<i>Candida parapsilosis</i> Strains==		==<i>Candida parapsilosis</i> Strains==
			<div class="mw-collapsible mw-collapsed">

	===ATCC 22019===		===ATCC 22019===
Line 777:		Line 780:
	[https://pubmed.ncbi.nlm.nih.gov/15449175/ Nosek et al., 2004]. Mol Genet Genomics 272(2):173-80;		[https://pubmed.ncbi.nlm.nih.gov/15449175/ Nosek et al., 2004]. Mol Genet Genomics 272(2):173-80;
	[https://pubmed.ncbi.nlm.nih.gov/39083682/ Mutalová et al., 2024]. Microbiol Resour Announc. 2024 Jul 31;13(9):e00347-24.		[https://pubmed.ncbi.nlm.nih.gov/39083682/ Mutalová et al., 2024]. Microbiol Resour Announc. 2024 Jul 31;13(9):e00347-24.
			</div>
	==<i>Candida auris</i> (<i>Candidozyma auris</i>) Strains==		==<i>Candida auris</i> (<i>Candidozyma auris</i>) Strains==
			<div class="mw-collapsible mw-collapsed">
	===AR0382 (B11109)===		===AR0382 (B11109)===
	<B>Genotype:</B> Wild type		<B>Genotype:</B> Wild type
Line 823:		Line 826:

	<B>References:</B> [https://pubmed.ncbi.nlm.nih.gov/38722168/ Yang et al., 2024]. Infect Immun. 2024 Jun 11;92(6):e0010324.		<B>References:</B> [https://pubmed.ncbi.nlm.nih.gov/38722168/ Yang et al., 2024]. Infect Immun. 2024 Jun 11;92(6):e0010324.
			</div>
	==<i>Candida tropicalis</i> Strains==		==<i>Candida tropicalis</i> Strains==
			<div class="mw-collapsible mw-collapsed">
	===ATCC 20336 (pK233)===		===ATCC 20336 (pK233)===
	<B>Genotype:</B> Wild type		<B>Genotype:</B> Wild type
Line 860:		Line 863:

	<B>References:</B> [https://pubmed.ncbi.nlm.nih.gov/15849785/ He and Chen, 2005]. Yeast 22(6):481-91.		<B>References:</B> [https://pubmed.ncbi.nlm.nih.gov/15849785/ He and Chen, 2005]. Yeast 22(6):481-91.
			</div>
	==<i>Candida dubliniensis</i> Strains==		==<i>Candida dubliniensis</i> Strains==
			<div class="mw-collapsible mw-collapsed">
	===CD36===		===CD36===
	<B>Genotype:</B> Wild type		<B>Genotype:</B> Wild type

Jodi: /* Current Taxonomy */

2026-03-24T14:21:01Z

Current Taxonomy

← Older revision		Revision as of 14:21, 24 March 2026
Line 513:		Line 513:

	=Current Taxonomy=		=Current Taxonomy=
			<div class="mw-collapsible mw-collapsed">
	The genus <i>Candida</i> was originally formed as a heterogeneous grouping of opportunistic pathogenic budding yeasts that lacked sexual reproduction ([https://pubmed.ncbi.nlm.nih.gov/38895705/ Groenewald et al., 2023]). Further genomic study has revealed evolutionary distances between these species that argues for taxonomic revision within the budding yeast subphylum Saccharomycotina ([https://pubmed.ncbi.nlm.nih.gov/33148650/ Shen et al., 2020], [https://pubmed.ncbi.nlm.nih.gov/39161632/ Liu et al., 2024], [https://pubmed.ncbi.nlm.nih.gov/36632423/ Kidd et al., 2023]). Interestingly, it appears pathogenicity within humans has evolved multiple times in this subphylum ([https://pubmed.ncbi.nlm.nih.gov/35508719/ Rokas, 2022])		The genus <i>Candida</i> was originally formed as a heterogeneous grouping of opportunistic pathogenic budding yeasts that lacked sexual reproduction ([https://pubmed.ncbi.nlm.nih.gov/38895705/ Groenewald et al., 2023]). Further genomic study has revealed evolutionary distances between these species that argues for taxonomic revision within the budding yeast subphylum Saccharomycotina ([https://pubmed.ncbi.nlm.nih.gov/33148650/ Shen et al., 2020], [https://pubmed.ncbi.nlm.nih.gov/39161632/ Liu et al., 2024], [https://pubmed.ncbi.nlm.nih.gov/36632423/ Kidd et al., 2023]). Interestingly, it appears pathogenicity within humans has evolved multiple times in this subphylum ([https://pubmed.ncbi.nlm.nih.gov/35508719/ Rokas, 2022])

Line 525:		Line 525:
	*<i>Nakaseomyces glabratus</i> (syn. <i>Candida glabrata</i> )		*<i>Nakaseomyces glabratus</i> (syn. <i>Candida glabrata</i> )
	*<i>Candidozyma auris</i> (syn. <i>Candida auris</i> )		*<i>Candidozyma auris</i> (syn. <i>Candida auris</i> )
			</div>

	= Strain Information =		= Strain Information =

Jodi: /* Welcome to the CGD Public Wiki */

2026-03-24T14:20:32Z

Welcome to the CGD Public Wiki

← Older revision		Revision as of 14:20, 24 March 2026
Line 2:		Line 2:
	[[File:512px-Candida fungus colony grown on agar media.jpg\|frame\|center]]		[[File:512px-Candida fungus colony grown on agar media.jpg\|frame\|center]]

	~~<div class="mw-collapsible mw-collapsed">~~
	~~This content starts collapsed.~~
	~~</div>~~
	=Seminal Candida Papers =		=Seminal Candida Papers =
	==<i>C. albicans</i>==		==<i>C. albicans</i>==

← Older revision		Revision as of 20:23, 24 March 2026
Line 1,389:		Line 1,389:

	=== CGD IS GETTING REMODELLED! ===		=== CGD IS GETTING REMODELLED! ===

	This is the biggest announcement in many years. You'll soon see a brand-new appearance for CGD that includes:		This is the biggest announcement in many years. You'll soon see a brand-new appearance for CGD that includes:

	# A cleaner interface that makes it easier to find what you need		# A cleaner interface that makes it easier to find what you need
	# An organism selector added to many pages, allowing you to switch quickly between species		# An organism selector added to many pages, allowing you to switch quickly between species
	# Newly searchable tables that allow you to filter the results and/or sort by column		# Newly searchable tables that allow you to filter the results and/or sort by column
	# A brand-new Literature Topic Search tool that allows you to search by topic tag, so you can quickly find all the papers/features related to a given topic or combination of topics.		# A brand-new Literature Topic Search tool that allows you to search by topic tag, so you can quickly find all the papers/features related to a given topic or combination of topics. <br>[[File:Literature Text Search.png\|400px\|thumb\|center]]
			# A brand-new Text Search tool, making it possible to mine CGD data in ways that haven't been possible. <br>[[File:Text Search Tool.png\|400px\|thumb\|center]]
	[[File:Literature Text Search.png\|400px\|thumb\|center]]

	# A brand-new Text Search tool, making it possible to mine CGD data in ways that haven't been possible

	[[File:Text Search Tool.png\|400px\|thumb\|center]]

	# Revisions of outdated pages, including a new "What Is GO?" page that serves as an introduction for trainees		# Revisions of outdated pages, including a new "What Is GO?" page that serves as an introduction for trainees
	# Upgrades to the latest version of JBrowse 2 with the CGD classic style. The visual layout stays nearly identical, but improvements include:		# Upgrades to the latest version of JBrowse 2 with the CGD classic style. The visual layout stays nearly identical, but improvements include:
Line 1,416:		Line 1,408:
	# Introduced CGD Swagger UI, offering a convenient way to retrieve data programmatically. This includes an interactive API Playground for testing endpoints and generating Python and R code snippets.		# Introduced CGD Swagger UI, offering a convenient way to retrieve data programmatically. This includes an interactive API Playground for testing endpoints and generating Python and R code snippets.
	# New Synteny Viewer for the species within CGD, available from the Tools menu or on the Homologs page for each locus		# New Synteny Viewer for the species within CGD, available from the Tools menu or on the Homologs page for each locus

	To what do we owe this embarrassment of riches? Our new programmer/developer stepped in just a couple months ago and quickly began building improved tools.		To what do we owe this embarrassment of riches? Our new programmer/developer stepped in just a couple months ago and quickly began building improved tools.

	That said, we fully expect there will still be bugs and small fixes to make on the new site. Please get in touch whenever you find something that doesn't seem to work correctly. Also, we are open to suggestion for further improvements, so feel free to share your ideas.		That said, we fully expect there will still be bugs and small fixes to make on the new site. Please get in touch whenever you find something that doesn't seem to work correctly. Also, we are open to suggestion for further improvements, so feel free to share your ideas.

	----		----