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Cited by 458Fungal and yeast genetics researchGenomics and Phylogenetic StudiesYeasts and Rust Fungi Studies

The DOI matches its Crossref record; 45 of the 45 references it cites were found in a registry or an index.

The Candida Genome Database (CGD): incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data

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Skrzypek, Marek S., Binkley, Jonathan, Binkley, Gail, Miyasato, Stuart R., Simison, Matt, Sherlock, Gavin·2017·Nucleic Acids Research
DOI 10.1093/nar/gkw924PMC PMC5210628
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Abstract

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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Figure 1. JBrowse Visualization of RNA-Seq data at CGD. JBrowse display of the region around the C. albicans serum-inducible gene HWP1, showing aligned RNA-Seq reads from serum-treated cells (37). The red and blue bars in the top track of the main display window show genes annotated at CGD: red for genes encoded on the ‘W’ strand (+), blue for genes on the ‘C’ strand (–). HWP1 is the second gene from the left. Clicking on a bar brings up an information window for that gene, and includes a link to its CGD Locus Summary Page. The green bar graph below the gene track shows the density of aligned RNA-Seq reads along to the chromosome, plotted on a log scale. The bottom track shows all the aligned RNA-Seq reads along the chromosome: each short bar in the bottom track represents a unique read. In this example the sequence reads are strand-specific: pink bars indicate reads transcribed from the ‘W’ strand, and light-blue bars indicate reads transcribed from the ‘C’ strand. Clicking on a bar brings up information about the read, including the sequence and quality score for each base. Menus and controls at the top of the browser provide navigation, zoom and search functionalities, and allow users to load their own data.
Figure 1. JBrowse Visualization of RNA-Seq data at CGD. JBrowse display of the region around the C. albicans serum-inducible gene HWP1, showing aligned RNA-Seq reads from serum-treated cells (37). The red and blue bars in the top track of the main display window show genes annotated at CGD: red for genes encoded on the ‘W’ strand (+), blue for genes on the ‘C’ strand (–). HWP1 is the second gene from the left. Clicking on a bar brings up an information window for that gene, and includes a link to its CGD Locus Summary Page. The green bar graph below the gene track shows the density of aligned RNA-Seq reads along to the chromosome, plotted on a log scale. The bottom track shows all the aligned RNA-Seq reads along the chromosome: each short bar in the bottom track represents a unique read. In this example the sequence reads are strand-specific: pink bars indicate reads transcribed from the ‘W’ strand, and light-blue bars indicate reads transcribed from the ‘C’ strand. Clicking on a bar brings up information about the read, including the sequence and quality score for each base. Menus and controls at the top of the browser provide navigation, zoom and search functionalities, and allow users to load their own data.CC BY-NC · PubMed Central

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Metadata

Authors
Skrzypek, M. S., Binkley, J., Binkley, G., Miyasato, S. R., Simison, M., & Sherlock, G.
Affiliations
Stanford Medicine (US)
Corresponding author
Sherlock, Gavin
ORCID
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
DOI
10.1093/nar/gkw924
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
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 › Immunology and Microbiology › Microbiology › 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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