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Whole-Genome Sequencing of Corallococcus sp. Strain EGB Reveals the Genetic Determinants Linking Taxonomy and Predatory Behavior

Corallococcus sp. strain EGB is a Gram-negative myxobacteria isolated from saline soil, and has considerable potential for the biocontrol of phytopathogenic fungi. However, the detailed mechanisms related to development and predatory behavior are unclear. To obtain a comprehensive overview of geneti...

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Autores principales: Zhao, Yuqiang, Wang, Yanxin, Xia, Chengyao, Li, Xu, Ye, Xianfeng, Fan, Qiwen, Huang, Yan, Li, Zhoukun, Zhu, Cancan, Cui, Zhongli
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8466578/
https://www.ncbi.nlm.nih.gov/pubmed/34573403
http://dx.doi.org/10.3390/genes12091421
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author Zhao, Yuqiang
Wang, Yanxin
Xia, Chengyao
Li, Xu
Ye, Xianfeng
Fan, Qiwen
Huang, Yan
Li, Zhoukun
Zhu, Cancan
Cui, Zhongli
author_facet Zhao, Yuqiang
Wang, Yanxin
Xia, Chengyao
Li, Xu
Ye, Xianfeng
Fan, Qiwen
Huang, Yan
Li, Zhoukun
Zhu, Cancan
Cui, Zhongli
author_sort Zhao, Yuqiang
collection PubMed
description Corallococcus sp. strain EGB is a Gram-negative myxobacteria isolated from saline soil, and has considerable potential for the biocontrol of phytopathogenic fungi. However, the detailed mechanisms related to development and predatory behavior are unclear. To obtain a comprehensive overview of genetic features, the genome of strain EGB was sequenced, annotated, and compared with 10 other Corallococcus species. The strain EGB genome was assembled as a single circular chromosome of 9.4 Mb with 7916 coding genes. Phylogenomics analysis showed that strain EGB was most closely related to Corallococcus interemptor AB047A, and it was inferred to be a novel species within the Corallococcus genus. Comparative genomic analysis revealed that the pan-genome of Corallococcus genus was large and open. Only a small proportion of genes were specific to strain EGB, and most of them were annotated as hypothetical proteins. Subsequent analyses showed that strain EGB produced abundant extracellular enzymes such as chitinases and β-(1,3)-glucanases, and proteases to degrade the cell-wall components of phytopathogenic fungi. In addition, 35 biosynthetic gene clusters potentially coding for antimicrobial compounds were identified in the strain EGB, and the majority of them were present in the dispensable pan-genome with unexplored metabolites. Other genes related to secretion and regulation were also explored for strain EGB. This study opens new perspectives in the greater understanding of the predatory behavior of strain EGB, and facilitates a potential application in the biocontrol of fungal plant diseases in the future.
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spelling pubmed-84665782021-09-27 Whole-Genome Sequencing of Corallococcus sp. Strain EGB Reveals the Genetic Determinants Linking Taxonomy and Predatory Behavior Zhao, Yuqiang Wang, Yanxin Xia, Chengyao Li, Xu Ye, Xianfeng Fan, Qiwen Huang, Yan Li, Zhoukun Zhu, Cancan Cui, Zhongli Genes (Basel) Article Corallococcus sp. strain EGB is a Gram-negative myxobacteria isolated from saline soil, and has considerable potential for the biocontrol of phytopathogenic fungi. However, the detailed mechanisms related to development and predatory behavior are unclear. To obtain a comprehensive overview of genetic features, the genome of strain EGB was sequenced, annotated, and compared with 10 other Corallococcus species. The strain EGB genome was assembled as a single circular chromosome of 9.4 Mb with 7916 coding genes. Phylogenomics analysis showed that strain EGB was most closely related to Corallococcus interemptor AB047A, and it was inferred to be a novel species within the Corallococcus genus. Comparative genomic analysis revealed that the pan-genome of Corallococcus genus was large and open. Only a small proportion of genes were specific to strain EGB, and most of them were annotated as hypothetical proteins. Subsequent analyses showed that strain EGB produced abundant extracellular enzymes such as chitinases and β-(1,3)-glucanases, and proteases to degrade the cell-wall components of phytopathogenic fungi. In addition, 35 biosynthetic gene clusters potentially coding for antimicrobial compounds were identified in the strain EGB, and the majority of them were present in the dispensable pan-genome with unexplored metabolites. Other genes related to secretion and regulation were also explored for strain EGB. This study opens new perspectives in the greater understanding of the predatory behavior of strain EGB, and facilitates a potential application in the biocontrol of fungal plant diseases in the future. MDPI 2021-09-15 /pmc/articles/PMC8466578/ /pubmed/34573403 http://dx.doi.org/10.3390/genes12091421 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/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 (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zhao, Yuqiang
Wang, Yanxin
Xia, Chengyao
Li, Xu
Ye, Xianfeng
Fan, Qiwen
Huang, Yan
Li, Zhoukun
Zhu, Cancan
Cui, Zhongli
Whole-Genome Sequencing of Corallococcus sp. Strain EGB Reveals the Genetic Determinants Linking Taxonomy and Predatory Behavior
title Whole-Genome Sequencing of Corallococcus sp. Strain EGB Reveals the Genetic Determinants Linking Taxonomy and Predatory Behavior
title_full Whole-Genome Sequencing of Corallococcus sp. Strain EGB Reveals the Genetic Determinants Linking Taxonomy and Predatory Behavior
title_fullStr Whole-Genome Sequencing of Corallococcus sp. Strain EGB Reveals the Genetic Determinants Linking Taxonomy and Predatory Behavior
title_full_unstemmed Whole-Genome Sequencing of Corallococcus sp. Strain EGB Reveals the Genetic Determinants Linking Taxonomy and Predatory Behavior
title_short Whole-Genome Sequencing of Corallococcus sp. Strain EGB Reveals the Genetic Determinants Linking Taxonomy and Predatory Behavior
title_sort whole-genome sequencing of corallococcus sp. strain egb reveals the genetic determinants linking taxonomy and predatory behavior
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8466578/
https://www.ncbi.nlm.nih.gov/pubmed/34573403
http://dx.doi.org/10.3390/genes12091421
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