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

Hdl Handle:
http://hdl.handle.net/10147/119160
Title:
Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser
Authors:
Fitzpatrick, David A; O'Gaora, Peadar; Byrne, Kevin P; Butler, Geraldine
Citation:
BMC Genomics. 2010 May 10;11(1):290
Issue Date:
10-May-2010
URI:
http://hdl.handle.net/10147/119160
Abstract:
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.
Item Type:
Journal Article

Full metadata record

DC FieldValue Language
dc.contributor.authorFitzpatrick, David A-
dc.contributor.authorO'Gaora, Peadar-
dc.contributor.authorByrne, Kevin P-
dc.contributor.authorButler, Geraldine-
dc.date.accessioned2011-01-11T12:48:18Z-
dc.date.available2011-01-11T12:48:18Z-
dc.date.issued2010-05-10-
dc.identifierhttp://dx.doi.org/10.1186/1471-2164-11-290-
dc.identifier.citationBMC Genomics. 2010 May 10;11(1):290-
dc.identifier.urihttp://hdl.handle.net/10147/119160-
dc.description.abstractAbstract 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.-
dc.titleAnalysis of gene evolution and metabolic pathways using the Candida Gene Order Browser-
dc.typeJournal Article-
dc.language.rfc3066en-
dc.rights.holderFitzpatrick et al.; licensee BioMed Central Ltd.-
dc.description.statusPeer Reviewed-
dc.date.updated2010-12-16T01:04:18Z-
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