Fitzpatrick, David A. and O'Gaora, Peadar and Byrne, Kevin P. and Butler, Geraldine
Analysis of gene evolution and metabolic
pathways using the Candida Gene Order Browser.
BMC Genomics, 11 (290).
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
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.
||Analysis; gene evolution; metabolic
pathways; Candida; Gene Order Browser;
||Science & Engineering > Biology
||29 Sep 2010 16:02
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