Comparative genome analysis and gene finding in Candida species using CGOB

Sarah L Maguire, Seán S ÓhÉigeartaigh, Kevin P Byrne, Markus S Schröder, Peadar O'Gaora, Kenneth H Wolfe, Geraldine Butler

Research output: Contribution to journalArticle

67 Citations (Scopus)

Abstract

The Candida Gene Order Browser (CGOB) was developed as a tool to visualize and analyze synteny relationships in multiple Candida species, and to provide an accurate, manually curated set of orthologous Candida genes for evolutionary analyses. Here, we describe major improvements to CGOB. The underlying structure of the database has been changed significantly. Genomic features are now based directly on genome annotations rather than on protein sequences, which allows non-protein features such as centromere locations in Candida albicans and tRNA genes in all species to be included. The data set has been expanded to 13 species, including genomes of pathogens (C. albicans, C. parapsilosis, C. tropicalis, and C. orthopsilosis), and those of xylose-degrading species with important biotechnological applications (C. tenuis, Scheffersomyces stipitis, and Spathaspora passalidarum). Updated annotations of C. parapsilosis, C. dubliniensis, and Debaryomyces hansenii have been incorporated. We discovered more than 1,500 previously unannotated genes among the 13 genomes, ranging in size from 29 to 3,850 amino acids. Poorly conserved and rapidly evolving genes were also identified. Re-analysis of the mating type loci of the xylose degraders suggests that C. tenuis is heterothallic, whereas both Spa. passalidarum and S. stipitis are homothallic. As well as hosting the browser, the CGOB website (http://cgob.ucd.ie) gives direct access to all the underlying genome annotations, sequences, and curated orthology data.

Original languageEnglish
Pages (from-to)1281-91
Number of pages11
JournalMolecular Biology and Evolution
Volume30
Issue number6
DOIs
Publication statusPublished - Jun 2013
Externally publishedYes

Keywords

  • Amino Acid Sequence
  • Candida
  • Databases, Genetic
  • Genes, Fungal
  • Genome, Fungal
  • Genomics
  • Models, Theoretical
  • Molecular Sequence Annotation
  • Molecular Sequence Data
  • Phylogeny
  • Sequence Alignment
  • Software
  • User-Computer Interface
  • Journal Article
  • Research Support, Non-U.S. Gov't

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  • Cite this

    Maguire, S. L., ÓhÉigeartaigh, S. S., Byrne, K. P., Schröder, M. S., O'Gaora, P., Wolfe, K. H., & Butler, G. (2013). Comparative genome analysis and gene finding in Candida species using CGOB. Molecular Biology and Evolution, 30(6), 1281-91. https://doi.org/10.1093/molbev/mst042