Comparative genome analysis and gene finding in Candida species using CGOB

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 underly...

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Bibliographic Details
Published in:Molecular biology and evolution 2013-06, Vol.30 (6), p.1281-1291
Main Authors: Maguire, Sarah L, ÓhÉigeartaigh, Seán S, Byrne, Kevin P, Schröder, Markus S, O'Gaora, Peadar, Wolfe, Kenneth H, Butler, Geraldine
Format: Article
Language:English
Subjects:
Amino Acid Sequence
Candida - classification
Candida - genetics
Candida albicans
Comparative analysis
Databases, Genetic
Debaryomyces hansenii
Evolutionary biology
Fast Tracks
Fungi
Genes, Fungal
Genome, Fungal
Genomes
Genomics - methods
Models, Theoretical
Molecular Sequence Annotation
Molecular Sequence Data
Pathogens
Phylogeny
RNA-protein interactions
Sequence Alignment
Software
User-Computer Interface
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Summary: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.
ISSN:0737-4038
1537-1719
DOI:10.1093/molbev/mst042