[Beg-evodevo] Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser
Note how in this paper synteny information is used to confirm the existence of functional gene clusters. Klaas *Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser* David A Fitzpatrick email, Peadar O'Gaora email, Kevin P Byrne email and Geraldine Butler BMC Genomics 2010, 11:290doi:10.1186/1471-2164-11-290 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. 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. Our analysis provides an important resource that is now available for the Candida community. CGOB is available at http://cgob.ucd.ie. http://www.biomedcentral.com/1471-2164/11/290/abstract
Klaas Vandepoele wrote:
Note how in this paper synteny information is used to confirm the existence of functional gene clusters.
Klaas
*Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser* David A Fitzpatrick email, Peadar O'Gaora email, Kevin P Byrne email and Geraldine Butler
BMC Genomics 2010, 11:290doi:10.1186/1471-2164-11-290
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. 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. Our analysis provides an important resource that is now available for the Candida community. CGOB is available at http://cgob.ucd.ie.
http://www.biomedcentral.com/1471-2164/11/290/abstract
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-- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Associate Department Director, VIB Department of Plant Systems Biology Group Leader Bioinformatics and Systems Biology Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer@psb.vib-ugent.be http://bioinformatics.psb.ugent.be/
participants (2)
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Klaas Vandepoele -
Yves Van de Peer