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Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis

Riccombeni, A; Vidanes, G; Proux-Wéra, E; Wolfe, KH; Butler, G; (2012) Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis. PLoS One , 7 (4) , Article e35750. 10.1371/journal.pone.0035750. Green open access

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Abstract

Candida orthopsilosis is closely related to the fungal pathogen Candida parapsilosis. However, whereas C. parapsilosis is a major cause of disease in immunosuppressed individuals and in premature neonates, C. orthopsilosis is more rarely associated with infection. We sequenced the C. orthopsilosis genome to facilitate the identification of genes associated with virulence. Here, we report the de novo assembly and annotation of the genome of a Type 2 isolate of C. orthopsilosis. The sequence was obtained by combining data from next generation sequencing (454 Life Sciences and Illumina) with paired-end Sanger reads from a fosmid library. The final assembly contains 12.6 Mb on 8 chromosomes. The genome was annotated using an automated pipeline based on comparative analysis of genomes of Candida species, together with manual identification of introns. We identified 5700 protein-coding genes in C. orthopsilosis, of which 5570 have an ortholog in C. parapsilosis. The time of divergence between C. orthopsilosis and C. parapsilosis is estimated to be twice as great as that between Candida albicans and Candida dubliniensis. There has been an expansion of the Hyr/Iff family of cell wall genes and the JEN family of monocarboxylic transporters in C. parapsilosis relative to C. orthopsilosis. We identified one gene from a Maltose/Galactoside O-acetyltransferase family that originated by horizontal gene transfer from a bacterium to the common ancestor of C. orthopsilosis and C. parapsilosis. We report that TFB3, a component of the general transcription factor TFIIH, undergoes alternative splicing by intron retention in multiple Candida species. We also show that an intein in the vacuolar ATPase gene VMA1 is present in C. orthopsilosis but not C. parapsilosis, and has a patchy distribution in Candida species. Our results suggest that the difference in virulence between C. parapsilosis and C. orthopsilosis may be associated with expansion of gene families.

Type: Article
Title: Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1371/journal.pone.0035750
Publisher version: http://dx.doi.org/10.1371/journal.pone.0035750
Language: English
Additional information: © 2012 Riccombeni et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. PMCID: PMC3338533
Keywords: Amino Acid Sequence, Candida, Cluster Analysis, Genome, Fungal, Molecular Sequence Data, Phylogeny, Sequence Alignment, Sequence Analysis, DNA
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences
URI: https://discovery.ucl.ac.uk/id/eprint/1395585
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