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Open Access Research article

Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser

David A Fitzpatrick12*, Peadar O'Gaora3, Kevin P Byrne4 and Geraldine Butler1*

Author affiliations

1 UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland

2 Department of Biology, The National University of Ireland, Maynooth, County Kildare, Ireland

3 UCD School of Medicine and Medical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland

4 Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin 2, Ireland

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Citation and License

BMC Genomics 2010, 11:290  doi:10.1186/1471-2164-11-290

Published: 10 May 2010

Abstract

Background

Candida species are the most common cause of opportunistic fungal infection worldwide. Recent sequencing efforts have provided a wealth of Candida genomic data. We have developed the Candida Gene Order Browser (CGOB), an online tool that aids comparative syntenic analyses of Candida species. CGOB incorporates all available Candida clade genome sequences including two Candida albicans isolates (SC5314 and WO-1) and 8 closely related species (Candida dubliniensis, Candida tropicalis, Candida parapsilosis, Lodderomyces elongisporus, Debaryomyces hansenii, Pichia stipitis, Candida guilliermondii and Candida lusitaniae). Saccharomyces cerevisiae is also included as a reference genome.

Results

CGOB assignments of homology were manually curated based on sequence similarity and synteny. In total CGOB includes 65617 genes arranged into 13625 homology columns. We have also generated improved Candida gene sets by merging/removing partial genes in each genome. Interrogation of CGOB revealed that the majority of tandemly duplicated genes are under strong purifying selection in all Candida species. We identified clusters of adjacent genes involved in the same metabolic pathways (such as catabolism of biotin, galactose and N-acetyl glucosamine) and we showed that some clusters are species or lineage-specific. We also identified one example of intron gain in C. albicans.

Conclusions

Our analysis provides an important resource that is now available for the Candida community. CGOB is available at http://cgob.ucd.ie webcite.