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

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 g...

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Autores principales:	Alessandro Riccombeni, Genevieve Vidanes, Estelle Proux-Wéra, Kenneth H Wolfe, Geraldine Butler
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/9d1cd062f98340088d601507da282ad7
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spelling	oai:doaj.org-article:9d1cd062f98340088d601507da282ad72021-11-18T07:20:48ZSequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis.1932-620310.1371/journal.pone.0035750https://doaj.org/article/9d1cd062f98340088d601507da282ad72012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22563396/?tool=EBIhttps://doaj.org/toc/1932-6203Candida 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.Alessandro RiccombeniGenevieve VidanesEstelle Proux-WéraKenneth H WolfeGeraldine ButlerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 4, p e35750 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Alessandro Riccombeni Genevieve Vidanes Estelle Proux-Wéra Kenneth H Wolfe Geraldine Butler Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis.
description	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.
format	article
author	Alessandro Riccombeni Genevieve Vidanes Estelle Proux-Wéra Kenneth H Wolfe Geraldine Butler
author_facet	Alessandro Riccombeni Genevieve Vidanes Estelle Proux-Wéra Kenneth H Wolfe Geraldine Butler
author_sort	Alessandro Riccombeni
title	Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis.
title_short	Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis.
title_full	Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis.
title_fullStr	Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis.
title_full_unstemmed	Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis.
title_sort	sequence and analysis of the genome of the pathogenic yeast candida orthopsilosis.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/9d1cd062f98340088d601507da282ad7
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Sequence and analysis of the genome of the pathogenic yeast Candida orthopsilosis.

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