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Comparative Genomics of Mycoplasma: Analysis of Conserved Essential Genes and Diversity of the Pan-Genome

Mycoplasma, the smallest self-replicating organism with a minimal metabolism and little genomic redundancy, is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. This study employs comparative evolutionary analysis of twenty Mycoplasma genomes to gain...

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Autores principales: Liu, Wei, Fang, Liurong, Li, Mao, Li, Sha, Guo, Shaohua, Luo, Rui, Feng, Zhixin, Li, Bin, Zhou, Zhemin, Shao, Guoqing, Chen, Huanchun, Xiao, Shaobo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3335003/
https://www.ncbi.nlm.nih.gov/pubmed/22536428
http://dx.doi.org/10.1371/journal.pone.0035698
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author Liu, Wei
Fang, Liurong
Li, Mao
Li, Sha
Guo, Shaohua
Luo, Rui
Feng, Zhixin
Li, Bin
Zhou, Zhemin
Shao, Guoqing
Chen, Huanchun
Xiao, Shaobo
author_facet Liu, Wei
Fang, Liurong
Li, Mao
Li, Sha
Guo, Shaohua
Luo, Rui
Feng, Zhixin
Li, Bin
Zhou, Zhemin
Shao, Guoqing
Chen, Huanchun
Xiao, Shaobo
author_sort Liu, Wei
collection PubMed
description Mycoplasma, the smallest self-replicating organism with a minimal metabolism and little genomic redundancy, is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. This study employs comparative evolutionary analysis of twenty Mycoplasma genomes to gain an improved understanding of essential genes. By analyzing the core genome of mycoplasmas, we finally revealed the conserved essential genes set for mycoplasma survival. Further analysis showed that the core genome set has many characteristics in common with experimentally identified essential genes. Several key genes, which are related to DNA replication and repair and can be disrupted in transposon mutagenesis studies, may be critical for bacteria survival especially over long period natural selection. Phylogenomic reconstructions based on 3,355 homologous groups allowed robust estimation of phylogenetic relatedness among mycoplasma strains. To obtain deeper insight into the relative roles of molecular evolution in pathogen adaptation to their hosts, we also analyzed the positive selection pressures on particular sites and lineages. There appears to be an approximate correlation between the divergence of species and the level of positive selection detected in corresponding lineages.
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spelling pubmed-33350032012-04-25 Comparative Genomics of Mycoplasma: Analysis of Conserved Essential Genes and Diversity of the Pan-Genome Liu, Wei Fang, Liurong Li, Mao Li, Sha Guo, Shaohua Luo, Rui Feng, Zhixin Li, Bin Zhou, Zhemin Shao, Guoqing Chen, Huanchun Xiao, Shaobo PLoS One Research Article Mycoplasma, the smallest self-replicating organism with a minimal metabolism and little genomic redundancy, is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. This study employs comparative evolutionary analysis of twenty Mycoplasma genomes to gain an improved understanding of essential genes. By analyzing the core genome of mycoplasmas, we finally revealed the conserved essential genes set for mycoplasma survival. Further analysis showed that the core genome set has many characteristics in common with experimentally identified essential genes. Several key genes, which are related to DNA replication and repair and can be disrupted in transposon mutagenesis studies, may be critical for bacteria survival especially over long period natural selection. Phylogenomic reconstructions based on 3,355 homologous groups allowed robust estimation of phylogenetic relatedness among mycoplasma strains. To obtain deeper insight into the relative roles of molecular evolution in pathogen adaptation to their hosts, we also analyzed the positive selection pressures on particular sites and lineages. There appears to be an approximate correlation between the divergence of species and the level of positive selection detected in corresponding lineages. Public Library of Science 2012-04-20 /pmc/articles/PMC3335003/ /pubmed/22536428 http://dx.doi.org/10.1371/journal.pone.0035698 Text en Liu 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
Liu, Wei
Fang, Liurong
Li, Mao
Li, Sha
Guo, Shaohua
Luo, Rui
Feng, Zhixin
Li, Bin
Zhou, Zhemin
Shao, Guoqing
Chen, Huanchun
Xiao, Shaobo
Comparative Genomics of Mycoplasma: Analysis of Conserved Essential Genes and Diversity of the Pan-Genome
title Comparative Genomics of Mycoplasma: Analysis of Conserved Essential Genes and Diversity of the Pan-Genome
title_full Comparative Genomics of Mycoplasma: Analysis of Conserved Essential Genes and Diversity of the Pan-Genome
title_fullStr Comparative Genomics of Mycoplasma: Analysis of Conserved Essential Genes and Diversity of the Pan-Genome
title_full_unstemmed Comparative Genomics of Mycoplasma: Analysis of Conserved Essential Genes and Diversity of the Pan-Genome
title_short Comparative Genomics of Mycoplasma: Analysis of Conserved Essential Genes and Diversity of the Pan-Genome
title_sort comparative genomics of mycoplasma: analysis of conserved essential genes and diversity of the pan-genome
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3335003/
https://www.ncbi.nlm.nih.gov/pubmed/22536428
http://dx.doi.org/10.1371/journal.pone.0035698
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