Abstract
BackgroundCandida 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.ResultsCGOB 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.ConclusionsOur analysis provides an important resource that is now available for the Candida community. CGOB is available at http://cgob.ucd.ie.
Highlights
Candida species are the most common cause of opportunistic fungal infection worldwide
Candida Gene Order Browser (CGOB) structure and Candida genome editing Version 1 of CGOB includes ten Candida genomes obtained from a variety of sequencing centers (Table 1), together with the genome from S. cerevisiae
CGOB's visual display consists of horizontal tracks representing chromosomal segments and pillars (Figure 2)
Summary
Candida species are the most common cause of opportunistic fungal infection worldwide. Candida species account for approximately 10% of all bloodstream infections [1] and worldwide are the most common cause of opportunistic fungal infection [2] Due to their increasing clinical importance, recent sequencing projects have determined the complete sequence of ten Candida genomes, including common pathogenic species and species rarely, if ever, associated with disease [3,4,5,6,7]. Debaryomyces hansenii and Pichia stipitis are close relatives of Candida species [8] Some species, such as C. lusitaniae, were assigned two names, one (Candida lusitaniae) referring to the asexual (anamorph) form, and one (Clavispora lusitaniae) to the sexual (teleomorph) form. We refer to the above as Candida species that belong to the CTG clade [5,8,10]
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