New and Noteworthy

Candida and Candidiasis 2023 organized by the Microbiology Society will be held in Montreal, Canada on May 13–17, 2023. Abstract submissions are now open until Feb 17, 2023. Registration is now open with early-bird discounts until April 1.

(Posted January 19, 2023)

• C. albicans Genome Snapshot.
• C. glabrata Genome Snapshot.
• C. parapsilosis Genome Snapshot.
• C. dubliniensis Genome Snapshot.
• C. auris Genome Snapshot.
• New papers added to CGD this week.
• View Genome-wide Analysis papers in CGD.

We are pleased to announce the incorporation of a new assembly for the C. glabrata CBS138 genome, which leveraged long-read sequencing to correct previous assembly errors in repetitive regions (Xu et al., 2020). The sub-telomeric regions of all chromosomes were substantially lengthened, resulting in changes of chromosomal coordinates for all genomic features. 31 new protein-coding genes were added. The rDNA region on Chr L was expanded significantly, and a second rDNA region was added to Chr M. 62 genes from the previous assembly were removed, and sequences were corrected for an additional 32 features, ranging from single-base changes to major structural rearrangements. The update adds or corrects the sequences of 45 genes encoding GPI-anchored cell wall proteins (GPI-CWPs), which contain many long tandem repeats.
See this page for a list of added, modified, or removed features.
(Posted August 30, 2022)

Over the 2021 Holiday Break, Stanford blocked CGD's servers from the internet citing security concerns. We are currently in the process of moving CGD to AWS. In the mean time, you may notice that some features are missing and some tools are not fully functional. We are working to restore full functionality as soon as possible.
We apologize for the disruptions this has caused.
(Posted January 3, 2022)

2022 FEBS Advanced Lecture Course on Molecular Mechanisms of Host-pathogen Interactions and Virulence in Human Fungal Pathogens is now scheduled for an in person meeting next May in La Colle sur Loup (France).
Registration is now open at the Meeting website. The registration deadline is February 1st, 2022.
(Posted November 1, 2021)

The Candida and Candidiasis 2021 meeting will take place online on March 21 - 27. Previously accepted presenters have been offered the opportunity to present their work at this meeting. New abstracts can also be submitted at this website. The deadline for new abstract submissions is now extended to Friday, 17 January 2021, 5 pm GMT.
(Posted January 5, 2021)

Read Frank Odds obituary written by Neil Gow, available here.
(Posted August 26, 2020)

From the Microbiology Society:

"Due to the continued spread of SARS-CoV-2, the cause of COVID-19, the Council of the Microbiology Society, as Trustees of the Society, have taken the difficult decision to postpone this year’s Candida and Candidiasis Focused Meeting, due to take place from 19–23 April in Montreal, Canada. We are currently unable to say when this event will take place; however, we have spoken this morning to the Chair of the organising committee and will keep you all updated as we know more."

The entire message is available here. (Posted March 9, 2020)

The conference, organized by the Microbiology Society and taking place on April 19-23, 2020, in Montreal, Canada, is a successor to the highly valued ASM conference series that finished in 2018. The abstract submission deadline is on this Thursday, January 9. Visit the conference website to register, submit your abstract and for more information. (Posted January 6, 2020)

We are pleased to announce the addition of Candida auris B8441 information into CGD. C. auris B8441 was sequenced by the Centers for Disease Control and Prevention (Lockhart et al. 2017). Sequence and annotation were obtained by CGD from GenBank. C. auris is the fifth Candida species for which manually curated data are available in our database, joining C. albicans, C. glabrata, C. parapsilosis, and C. dubliniensis.

The data loading is complete, and:

• C. auris B8441 sequence is now available in all of the CGD tools, including BLAST
• Each C. auris gene now has a Locus Summary page in the database
• Multiple sequence alignments and phylogenetic trees for orthologous groups have been updated to include C. auris orthologs
• C. auris genome and annotation is available in the GBrowse and JBrowse Genome Browsers. In the coming months, we hope to add large-scale datasets to JBrowse, as they become available
• C. auris genes have been assigned predicted function, process, and localization annotations (Gene Ontology terms) based on orthology to other Candida species, and also S. cerevisiae, S. pombe, and A. nidulans
• Protein-coding genes have been assigned predicted annotations based on protein motifs and domains (InterPro), and solved strutures of homologous proteins from PDB have been identified
• Manual curation of the published scientific literature about C. auris genes is ongoing, and experimental data collected from the literature will continue to be added

We look forward to your feedback on the new C. auris species data in CGD. (Posted August 27, 2019)

As you know, the CGD grant is up for renewal this year and we are going to submit an application to the NIH this summer. We have previously asked members of the community to complete a User Survey to help us formulate future directions for CGD and we greatly appreciate the massive response we have received, with all the invaluable suggestions. We are now asking our users for letters of support to accompany the application. It is very important to demonstrate unequivocally how crucial the continued existence of CGD is to Candida research and to the community. We will greatly appreciate if you can email your letter of support to by June 25 and if you also encourage your colleagues and students to do the same. We are counting on your support.
(Posted May 22, 2019)

It was brought to our attention that our CGD Suggestions and Questions form, the one with the reCAPTCHA box, was not working properly. There may have been messages that were inadvertently lost. If you recently tried to contact CGD and never received a response, it is most likely because we have not seen your message. We sincerely apologize for this. The problem is now fixed and we also implemented measures to alert us to this kind of issues in the future.
(Posted February 4, 2019)

Candida glabrata Multi Locus Sequence Typing (MLST) database at PubMLST.org is accepting submissions again. As of August 2018, the C. glabrata MLST database hosted at pubmlst.org has re-opened its submission pipeline. They welcome submissions of new alleles and sequence types as well as isolate data from ongoing or published studies. Also the submission of genome data is possible to place them into the phylogenetic context of the current MLST scheme.

Please visit pubmlst.org/cglabrata for more information.
(Posted August 27, 2018)

The sequence and annotation of C. lusitaniae strain CBS 6936, described in Durrens et al. (2017), has been made available at CGD. We provide downloads for sequences, chromosomal features, gff files and protein domain predictions. In addition, C. lusitaniae CBS 6936 is included among the datasets searchable by our multi-species BLAST tool. The sequence and annotation were obtained by CGD from NCBI.
(Posted February 27, 2018)

CGD has added tracks in JBrowse showing the evolutionary conservation of genomic features for C. albicans SC5314, C. glabrata CBS138, C. dubliniensis CD36, and C. parapsilosis CDC317. Conservation is shown in four optional quantitative tracks, representing increasing levels of evolutionary diversity. In general, the top level (derived from an alignment of 3 closely related species) will show the highest levels of conservation, and include intergenic regions, while the lowest level (derived from an alignment of 12 distantly-related budding yeasts) will show the least conservation, and include only the most highly-conserved genes and features. Conservation scores were produced with the phyloP program (Siepel et al, 2005), based on whole-genome alignments produced by the program TBA (Blanchette et al, 2004).

Conservation scores and their underlying alignments and phylogenetic models are available for download in the CGD downloads directory. Please see our JBrowse Help Page for more information about JBrowse at CGD.
(Posted December 20, 2017)

CGD has implemented JBrowse, the fast, intuitive, and customizable genome browser developed by the Generic Model Organism Database project (GMOD). JBrowse allows users to quickly view large-scale sequence data in a genomic context, at multiple zoom-levels of resolution, from base pairs in individual sequence reads to read-density summaries across large genomic regions. Initially, we have loaded the following datasets:

• Gene expression in C. albicans in a variety of experimental conditions from Bruno et al, 2010
• Gene expression in C. glabrata in a variety of experimental conditions from Linde, Duggan et al, 2015
• High-throughput genomic sequence of C. albicans SC5314 from Muzzey et al, 2013, that was the basis of Assembly 22

We will be adding additional high-throughput datasets in the coming months.

JBrowse can be launched from any CGD feature's Locus Summary Page by clicking on the JBrowse logo about halfway down the page:

The JBrowse window will be centered upon that feature.

Alternately, mouse-over "JBrowse" on the top menu bar of any CGD page, then select and click your organism of interest in the drop-down menu. The browser window will be centered on an arbitrary location of the genome.

Please see our JBrowse Help Page for more details.
(Posted September 29, 2016)

We have corrected the haplotype assignments on chromosome 3 of C. albicans SC5314, based on comparisons of haplotype data (Legrand et al, 2008; Berman and Forche, 2016) with sequence data (Muzzey et al, 2013) for both the wild-type diploid strain and the strain RBY10-10, which is homozygous for chromosome 3A. This analysis supported the exchange of approximately 845 kbp between chromosome 3A and chromosome 3B of Assembly 22 at CGD, including the entire left arm of the chromosome, and a portion of the right arm extending from CEN3 to within the coding sequence of the gene C3_04040W (orf19.2804). This results in sequence and gene model boundary changes for most chromosome 3 features. (Posted June 22, 2016)

We now provide links on CGD Homology Pages and CGD Multi-Genome BLAST results pages to gene annotations from EnsemblFungi for the seven Candida-related strains for which we provide sequence and gene model downloads, but do not actively curate: C. albicans WO-1, C. guilliermondii ATCC 6260, C. lusitaniae ATCC 42720, C. orthopsilosis Co 90-125, C. tropicalis MYA-3404, D. hansenii CBS767 and L. elongisporus NRLL YB-4239. These replace the links to annotations formerly provided by the Broad Institute Fungal Genome Initiative, which are no longer supported. (Posted June 6, 2016)

We have released a major sequence update for C. albicans SC5314 (Assembly 22, version s06-m01-r01). Based on reanalysis by CGD of all available sequence data, the update affects more than 300 features, correcting many ORF translation errors and resolving many sequence ambiguities. The specific sequence changes can be viewed on our Chromosome History pages. (Posted February 2, 2016)

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