Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser
David A Fitzpatrick1, Peadar O'Gaora, Kevin P Byrne
1UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland. david.fitzpatrick@nuim.ie
BMC Genomics
|May 13, 2010
Summary
The Candida Gene Order Browser (CGOB) facilitates comparative genomic analysis of Candida species. This tool reveals conserved gene clusters and evolutionary insights, aiding fungal infection research.
Area of Science:
- Mycology
- Genomics
- Bioinformatics
Background:
- Candida species are leading causes of opportunistic fungal infections globally.
- Extensive genomic data is available for Candida.
- Comparative genomic analysis is crucial for understanding fungal evolution and pathogenesis.
Purpose of the Study:
- To develop an online tool, the Candida Gene Order Browser (CGOB), for comparative syntenic analysis of Candida species.
- To integrate available genomic data for multiple Candida species and a reference genome.
Main Methods:
- Developed the Candida Gene Order Browser (CGOB) incorporating genome sequences from Candida clade species and Saccharomyces cerevisiae.
- Manually curated homology assignments based on sequence similarity and synteny.
- Generated improved gene sets by merging/removing partial genes.
Main Results:
- CGOB contains 65,617 genes organized into 13,625 homology columns.
- Identified that most tandemly duplicated genes are under strong purifying selection across Candida species.
- Discovered species or lineage-specific gene clusters involved in metabolic pathways and one instance of intron gain in Candida albicans.
Conclusions:
- The Candida Gene Order Browser (CGOB) serves as a valuable resource for the Candida research community.
- CGOB enables deeper insights into Candida genome evolution and organization.
- The tool is publicly accessible at http://cgob.ucd.ie.
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