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Pan-Genome Analyses of Geobacillus spp. Reveal Genetic Characteristics and Composting Potential

The genus Geobacillus is abundant in ecological diversity and is also well-known as an authoritative source for producing various thermostable enzymes. Although it is clear now that Geobacillus evolved from Bacillus, relatively little knowledge has been obtained regarding its evolutionary mechanism,...

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Autores principales: Wang, Mengmeng, Zhu, Han, Kong, Zhijian, Li, Tuo, Ma, Lei, Liu, Dongyang, Shen, Qirong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7246994/
https://www.ncbi.nlm.nih.gov/pubmed/32403359
http://dx.doi.org/10.3390/ijms21093393
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author Wang, Mengmeng
Zhu, Han
Kong, Zhijian
Li, Tuo
Ma, Lei
Liu, Dongyang
Shen, Qirong
author_facet Wang, Mengmeng
Zhu, Han
Kong, Zhijian
Li, Tuo
Ma, Lei
Liu, Dongyang
Shen, Qirong
author_sort Wang, Mengmeng
collection PubMed
description The genus Geobacillus is abundant in ecological diversity and is also well-known as an authoritative source for producing various thermostable enzymes. Although it is clear now that Geobacillus evolved from Bacillus, relatively little knowledge has been obtained regarding its evolutionary mechanism, which might also contribute to its ecological diversity and biotechnology potential. Here, a statistical comparison of thirty-two Geobacillus genomes was performed with a specific focus on pan- and core genomes. The pan-genome of this set of Geobacillus strains contained 14,913 genes, and the core genome contained 940 genes. The Clusters of Orthologous Groups (COG) and Carbohydrate-Active Enzymes (CAZymes) analysis revealed that the Geobacillus strains had huge potential industrial application in composting for agricultural waste management. Detailed comparative analyses showed that basic functional classes and housekeeping genes were conserved in the core genome, while genes associated with environmental interaction or energy metabolism were more enriched in the pan-genome. Therefore, the evolution of Geobacillus seems to be guided by environmental parameters. In addition, horizontal gene transfer (HGT) events among different Geobacillus species were detected. Altogether, pan-genome analysis was a useful method for detecting the evolutionary mechanism, and Geobacillus’ evolution was directed by the environment and HGT events.
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spelling pubmed-72469942020-06-02 Pan-Genome Analyses of Geobacillus spp. Reveal Genetic Characteristics and Composting Potential Wang, Mengmeng Zhu, Han Kong, Zhijian Li, Tuo Ma, Lei Liu, Dongyang Shen, Qirong Int J Mol Sci Article The genus Geobacillus is abundant in ecological diversity and is also well-known as an authoritative source for producing various thermostable enzymes. Although it is clear now that Geobacillus evolved from Bacillus, relatively little knowledge has been obtained regarding its evolutionary mechanism, which might also contribute to its ecological diversity and biotechnology potential. Here, a statistical comparison of thirty-two Geobacillus genomes was performed with a specific focus on pan- and core genomes. The pan-genome of this set of Geobacillus strains contained 14,913 genes, and the core genome contained 940 genes. The Clusters of Orthologous Groups (COG) and Carbohydrate-Active Enzymes (CAZymes) analysis revealed that the Geobacillus strains had huge potential industrial application in composting for agricultural waste management. Detailed comparative analyses showed that basic functional classes and housekeeping genes were conserved in the core genome, while genes associated with environmental interaction or energy metabolism were more enriched in the pan-genome. Therefore, the evolution of Geobacillus seems to be guided by environmental parameters. In addition, horizontal gene transfer (HGT) events among different Geobacillus species were detected. Altogether, pan-genome analysis was a useful method for detecting the evolutionary mechanism, and Geobacillus’ evolution was directed by the environment and HGT events. MDPI 2020-05-11 /pmc/articles/PMC7246994/ /pubmed/32403359 http://dx.doi.org/10.3390/ijms21093393 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Wang, Mengmeng
Zhu, Han
Kong, Zhijian
Li, Tuo
Ma, Lei
Liu, Dongyang
Shen, Qirong
Pan-Genome Analyses of Geobacillus spp. Reveal Genetic Characteristics and Composting Potential
title Pan-Genome Analyses of Geobacillus spp. Reveal Genetic Characteristics and Composting Potential
title_full Pan-Genome Analyses of Geobacillus spp. Reveal Genetic Characteristics and Composting Potential
title_fullStr Pan-Genome Analyses of Geobacillus spp. Reveal Genetic Characteristics and Composting Potential
title_full_unstemmed Pan-Genome Analyses of Geobacillus spp. Reveal Genetic Characteristics and Composting Potential
title_short Pan-Genome Analyses of Geobacillus spp. Reveal Genetic Characteristics and Composting Potential
title_sort pan-genome analyses of geobacillus spp. reveal genetic characteristics and composting potential
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7246994/
https://www.ncbi.nlm.nih.gov/pubmed/32403359
http://dx.doi.org/10.3390/ijms21093393
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