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Analysis of Ultra Low Genome Conservation in Clostridium difficile

Microarray-based comparative genome hybridisations (CGH) and genome sequencing of Clostridium difficile isolates have shown that the genomes of this species are highly variable. To further characterize their genome variation, we employed integration of data from CGH, genome sequencing and putative c...

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Autores principales: Scaria, Joy, Ponnala, Lalit, Janvilisri, Tavan, Yan, Weiwei, Mueller, Lukas A., Chang, Yung-Fu
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2999544/
https://www.ncbi.nlm.nih.gov/pubmed/21170335
http://dx.doi.org/10.1371/journal.pone.0015147
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author Scaria, Joy
Ponnala, Lalit
Janvilisri, Tavan
Yan, Weiwei
Mueller, Lukas A.
Chang, Yung-Fu
author_facet Scaria, Joy
Ponnala, Lalit
Janvilisri, Tavan
Yan, Weiwei
Mueller, Lukas A.
Chang, Yung-Fu
author_sort Scaria, Joy
collection PubMed
description Microarray-based comparative genome hybridisations (CGH) and genome sequencing of Clostridium difficile isolates have shown that the genomes of this species are highly variable. To further characterize their genome variation, we employed integration of data from CGH, genome sequencing and putative cellular pathways. Transcontinental strain comparison using CGH data confirmed the emergence of a human-specific hypervirulent cluster. However, there was no correlation between total toxin production and hypervirulent phenotype, indicating the possibility of involvement of additional factors towards hypervirulence. Calculation of C. difficile core and pan genome size using CGH and sequence data estimated that the core genome is composed of 947 to 1,033 genes and a pan genome comprised of 9,640 genes. The reconstruction, annotation and analysis of cellular pathways revealed highly conserved pathways despite large genome variation. However, few pathways such as tetrahydrofolate biosynthesis were found to be variable and could be contributing to adaptation towards virulence such as antibiotic resistance.
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spelling pubmed-29995442010-12-17 Analysis of Ultra Low Genome Conservation in Clostridium difficile Scaria, Joy Ponnala, Lalit Janvilisri, Tavan Yan, Weiwei Mueller, Lukas A. Chang, Yung-Fu PLoS One Research Article Microarray-based comparative genome hybridisations (CGH) and genome sequencing of Clostridium difficile isolates have shown that the genomes of this species are highly variable. To further characterize their genome variation, we employed integration of data from CGH, genome sequencing and putative cellular pathways. Transcontinental strain comparison using CGH data confirmed the emergence of a human-specific hypervirulent cluster. However, there was no correlation between total toxin production and hypervirulent phenotype, indicating the possibility of involvement of additional factors towards hypervirulence. Calculation of C. difficile core and pan genome size using CGH and sequence data estimated that the core genome is composed of 947 to 1,033 genes and a pan genome comprised of 9,640 genes. The reconstruction, annotation and analysis of cellular pathways revealed highly conserved pathways despite large genome variation. However, few pathways such as tetrahydrofolate biosynthesis were found to be variable and could be contributing to adaptation towards virulence such as antibiotic resistance. Public Library of Science 2010-12-08 /pmc/articles/PMC2999544/ /pubmed/21170335 http://dx.doi.org/10.1371/journal.pone.0015147 Text en Scaria et al. http://creativecommons.org/licenses/by/4.0/ 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 properly credited.
spellingShingle Research Article
Scaria, Joy
Ponnala, Lalit
Janvilisri, Tavan
Yan, Weiwei
Mueller, Lukas A.
Chang, Yung-Fu
Analysis of Ultra Low Genome Conservation in Clostridium difficile
title Analysis of Ultra Low Genome Conservation in Clostridium difficile
title_full Analysis of Ultra Low Genome Conservation in Clostridium difficile
title_fullStr Analysis of Ultra Low Genome Conservation in Clostridium difficile
title_full_unstemmed Analysis of Ultra Low Genome Conservation in Clostridium difficile
title_short Analysis of Ultra Low Genome Conservation in Clostridium difficile
title_sort analysis of ultra low genome conservation in clostridium difficile
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2999544/
https://www.ncbi.nlm.nih.gov/pubmed/21170335
http://dx.doi.org/10.1371/journal.pone.0015147
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