The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data
Open accessAbstract
The Candida Genome Database (CGD, http://www.candidagenome.org/) is a freely available online resource that provides gene, protein and sequence information for multiple Candida species, along with web-based tools for accessing, analyzing and exploring these data. The mission of CGD is to facilitate and accelerate research into Candida pathogenesis and biology, by curating the scientific literature in real time, and connecting literature-derived annotations to the latest version of the genomic sequence and its annotations. Here, we report the incorporation into CGD of Assembly 22, the first chromosome-level, phased diploid assembly of the C. albicans genome, coupled with improvements that we have made to the assembly using additional available sequence data. We also report the creation of systematic identifiers for C. albicans genes and sequence features using a system similar to that adopted by the yeast community over two decades ago. Finally, we describe the incorporation of JBrowse into CGD, which allows online browsing of mapped high throughput sequencing data, and its implementation for several RNA-Seq data sets, as well as the whole genome sequencing data that was used in the construction of Assembly 22.
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C. glabrata harbors five PIR paralogs (PIR1-PIR5), all annotated as orthologs of Neurospora crassa NCU04033-a protein shown to function as a cell wall stabilizer with significant functional redundancy among family members.
“C. glabrata harbors five PIR paralogs (PIR1–PIR5) [47], all annotated as orthologs of Neurospora crassa NCU04033—a protein shown to function as a cell wall stabilizer with significant functional redundancy among family members [48].”
From Calcineurin‐Dependent Stress Adaptation Enables Caspofungin Heteroresistance Leading to Stable Resistance in <i>Candida Glabrata</i> (2026) · cites this paper as [47]
Citation [47] is attached to the claim that C. glabrata has five PIR paralogs (PIR1–PIR5); the orthology and cell-wall claims are attached to [48]. The Introduction mentions C. glabrata, but neither it nor the passages returned for searches on PIR1–PIR5 and PIR paralogs addresses the number of PIR genes. (LLM, conf=0.73)
Experimental — accuracy not yet measuredSkin microbial communities can restrict bacterial pathogens through metabolic competition and immune modulation.
“Since skin microbial communities can restrict bacterial pathogens through metabolic competition and immune modulation [69–72]”
From Host–Candida auris interactions in the skin (2026) · cites this paper as [71]
The Introduction discusses Candida as a fungal pathogen, while the other matching passages are references. Searches for skin microbial communities, bacterial pathogens, metabolic competition, and immune modulation found no passage in our copy addressing the claimed protective effect. (LLM, conf=0.76)
Experimental — accuracy not yet measuredFewer than 1% of C. auris open reading frames have been functionally characterized.
“Although fewer than 1% of C. auris open reading frames have been functionally characterized [71]”
From Host–Candida auris interactions in the skin (2026) · cites this paper as [71]
The Introduction’s “Systematic ORF nomenclature” section discusses identifiers for C. albicans ORFs, and “Incorporation of JBrowse” describes datasets for C. albicans, C. glabrata, and C. parapsilosis; neither gives a functional-characterization rate for C. auris. Searches for C. auris, fewer than 1%, and functionally characterized ORFs found no passage addressing the claim. The indexed passages have no page numbers. (LLM, conf=0.76)
Experimental — accuracy not yet measured
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- Authors
- Skrzypek, M. S., Binkley, J., Binkley, G., Miyasato, S. R., Simison, M., & Sherlock, G.
- Affiliations
- Stanford Medicine (US)
- Corresponding author
- Sherlock, Gavin
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-10-13
- Volume
- 45
- Issue
- D1
- Pages
- D592-D596
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC5210628
- OpenAlex
- W2530772399
- Cited by
- 455
- References
- 45
- Citations by year
- 2026: 35 · 2025: 61 · 2024: 68 · 2023: 44 · 2022: 45 · 2021: 69 · 2020: 38 · 2019: 45 · 2018: 39 · 2017: 10 · 2016: 1
- FWCI
- 16.64
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- National Institute of Dental and Craniofacial Research (R01DE015873)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Yeasts and Rust Fungi Studies
- Keywords
- Candida albicans, genome assembly, JBrowse, RNA-seq, genome annotation, fungal genomics
- MeSH terms
- Candida, Fungal Proteins, Software, Open Reading Frames, Genome, Fungal, Computational Biology, Genomics, Databases, Nucleic Acid, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing, Web Browser
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