Genetic potential of the biocontrol agent pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 unraveled by genome sequencing and mining, comparative genomics and transcriptom...

Autores: Nelkner, Johanna; Torres Tejerizo, Gonzalo Arturo; Hassa, Julia; Lin, Timo Wentong; Witte, Julian; Verwaaijen, Bart; Winkler, Anika; Bunk, Boyke; Spröer, Cathrin; Overmann, Jörg; Grosch, Rita; Pühler, Alfred; Schlüter, Andreas
Año de publicación: 2019
Idioma: inglés
Tipo de recurso: artículo
Estado: versión publicada
Descripción: The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.
Fil: Nelkner, Johanna. Universitat Bielefeld. Center For Biotechnology; Alemania
Fil: Torres Tejerizo, Gonzalo Arturo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina
Fil: Hassa, Julia. Universitat Bielefeld. Center For Biotechnology; Alemania
Fil: Lin, Timo Wentong. Universitat Bielefeld. Center For Biotechnology; Alemania
Fil: Witte, Julian. Universitat Bielefeld. Center For Biotechnology; Alemania
Fil: Verwaaijen, Bart. Universitat Bielefeld. Center For Biotechnology; Alemania
Fil: Winkler, Anika. Universitat Bielefeld. Center For Biotechnology; Alemania
Fil: Bunk, Boyke. Leibniz - Institute Dsmzgerman Collection Of Microorgani; Alemania
Fil: Spröer, Cathrin. Leibniz - Institute Dsmzgerman Collection Of Microorgani; Alemania
Fil: Overmann, Jörg. Leibniz - Institute Dsmzgerman Collection Of Microorgani; Alemania
Fil: Grosch, Rita. Leibniz - Institute of Vegetable and Ornamental Crops; Alemania
Fil: Pühler, Alfred. Universitat Bielefeld. Center For Biotechnology; Alemania
Fil: Schlüter, Andreas. Universitat Bielefeld. Center For Biotechnology; Alemania
Materia: BIOCONTROL
COMPARATIVE GENOMICS
GENOME MINING
PLANT-GROWTH PROMOTION
PSEUDOMONASBRASSICACEARUM
RNA SEQUENCING
TRANSCRIPTOMICS
Nivel de accesibilidad: acceso abierto
Condiciones de uso: https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
Institución: Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador: oai:ri.conicet.gov.ar:11336/151981

Acceder

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network_acronym_str	CONICETDig
repository_id_str	3498
network_name_str	CONICET Digital (CONICET)
spelling	Genetic potential of the biocontrol agent pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 unraveled by genome sequencing and mining, comparative genomics and transcriptomicsNelkner, JohannaTorres Tejerizo, Gonzalo ArturoHassa, JuliaLin, Timo WentongWitte, JulianVerwaaijen, BartWinkler, AnikaBunk, BoykeSpröer, CathrinOvermann, JörgGrosch, RitaPühler, AlfredSchlüter, AndreasBIOCONTROLCOMPARATIVE GENOMICSGENOME MININGPLANT-GROWTH PROMOTIONPSEUDOMONASBRASSICACEARUMRNA SEQUENCINGTRANSCRIPTOMICShttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.Fil: Nelkner, Johanna. Universitat Bielefeld. Center For Biotechnology; AlemaniaFil: Torres Tejerizo, Gonzalo Arturo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Hassa, Julia. Universitat Bielefeld. Center For Biotechnology; AlemaniaFil: Lin, Timo Wentong. Universitat Bielefeld. Center For Biotechnology; AlemaniaFil: Witte, Julian. Universitat Bielefeld. Center For Biotechnology; AlemaniaFil: Verwaaijen, Bart. Universitat Bielefeld. Center For Biotechnology; AlemaniaFil: Winkler, Anika. Universitat Bielefeld. Center For Biotechnology; AlemaniaFil: Bunk, Boyke. Leibniz - Institute Dsmzgerman Collection Of Microorgani; AlemaniaFil: Spröer, Cathrin. Leibniz - Institute Dsmzgerman Collection Of Microorgani; AlemaniaFil: Overmann, Jörg. Leibniz - Institute Dsmzgerman Collection Of Microorgani; AlemaniaFil: Grosch, Rita. Leibniz - Institute of Vegetable and Ornamental Crops; AlemaniaFil: Pühler, Alfred. Universitat Bielefeld. Center For Biotechnology; AlemaniaFil: Schlüter, Andreas. Universitat Bielefeld. Center For Biotechnology; AlemaniaMDPI AG2019-08-09info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/151981Nelkner, Johanna; Torres Tejerizo, Gonzalo Arturo; Hassa, Julia; Lin, Timo Wentong; Witte, Julian; et al.; Genetic potential of the biocontrol agent pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 unraveled by genome sequencing and mining, comparative genomics and transcriptomics; MDPI AG; Genes; 10; 8; 09-8-2019; 1-292073-4425CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/2073-4425/10/8/601info:eu-repo/semantics/altIdentifier/doi/10.3390/genes10080601info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-11-26T08:47:02Zoai:ri.conicet.gov.ar:11336/151981instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-11-26 08:47:03.185CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv	Genetic potential of the biocontrol agent pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 unraveled by genome sequencing and mining, comparative genomics and transcriptomics
title	Genetic potential of the biocontrol agent pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 unraveled by genome sequencing and mining, comparative genomics and transcriptomics
spellingShingle	Genetic potential of the biocontrol agent pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 unraveled by genome sequencing and mining, comparative genomics and transcriptomics Nelkner, Johanna BIOCONTROL COMPARATIVE GENOMICS GENOME MINING PLANT-GROWTH PROMOTION PSEUDOMONASBRASSICACEARUM RNA SEQUENCING TRANSCRIPTOMICS
title_short	Genetic potential of the biocontrol agent pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 unraveled by genome sequencing and mining, comparative genomics and transcriptomics
title_full	Genetic potential of the biocontrol agent pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 unraveled by genome sequencing and mining, comparative genomics and transcriptomics
title_fullStr	Genetic potential of the biocontrol agent pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 unraveled by genome sequencing and mining, comparative genomics and transcriptomics
title_full_unstemmed	Genetic potential of the biocontrol agent pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 unraveled by genome sequencing and mining, comparative genomics and transcriptomics
title_sort	Genetic potential of the biocontrol agent pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 unraveled by genome sequencing and mining, comparative genomics and transcriptomics
dc.creator.none.fl_str_mv	Nelkner, Johanna Torres Tejerizo, Gonzalo Arturo Hassa, Julia Lin, Timo Wentong Witte, Julian Verwaaijen, Bart Winkler, Anika Bunk, Boyke Spröer, Cathrin Overmann, Jörg Grosch, Rita Pühler, Alfred Schlüter, Andreas
author	Nelkner, Johanna
author_facet	Nelkner, Johanna Torres Tejerizo, Gonzalo Arturo Hassa, Julia Lin, Timo Wentong Witte, Julian Verwaaijen, Bart Winkler, Anika Bunk, Boyke Spröer, Cathrin Overmann, Jörg Grosch, Rita Pühler, Alfred Schlüter, Andreas
author_role	author
author2	Torres Tejerizo, Gonzalo Arturo Hassa, Julia Lin, Timo Wentong Witte, Julian Verwaaijen, Bart Winkler, Anika Bunk, Boyke Spröer, Cathrin Overmann, Jörg Grosch, Rita Pühler, Alfred Schlüter, Andreas
author2_role	author author author author author author author author author author author author
dc.subject.none.fl_str_mv	BIOCONTROL COMPARATIVE GENOMICS GENOME MINING PLANT-GROWTH PROMOTION PSEUDOMONASBRASSICACEARUM RNA SEQUENCING TRANSCRIPTOMICS
topic	BIOCONTROL COMPARATIVE GENOMICS GENOME MINING PLANT-GROWTH PROMOTION PSEUDOMONASBRASSICACEARUM RNA SEQUENCING TRANSCRIPTOMICS
purl_subject.fl_str_mv	https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv	The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents. Fil: Nelkner, Johanna. Universitat Bielefeld. Center For Biotechnology; Alemania Fil: Torres Tejerizo, Gonzalo Arturo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; Argentina Fil: Hassa, Julia. Universitat Bielefeld. Center For Biotechnology; Alemania Fil: Lin, Timo Wentong. Universitat Bielefeld. Center For Biotechnology; Alemania Fil: Witte, Julian. Universitat Bielefeld. Center For Biotechnology; Alemania Fil: Verwaaijen, Bart. Universitat Bielefeld. Center For Biotechnology; Alemania Fil: Winkler, Anika. Universitat Bielefeld. Center For Biotechnology; Alemania Fil: Bunk, Boyke. Leibniz - Institute Dsmzgerman Collection Of Microorgani; Alemania Fil: Spröer, Cathrin. Leibniz - Institute Dsmzgerman Collection Of Microorgani; Alemania Fil: Overmann, Jörg. Leibniz - Institute Dsmzgerman Collection Of Microorgani; Alemania Fil: Grosch, Rita. Leibniz - Institute of Vegetable and Ornamental Crops; Alemania Fil: Pühler, Alfred. Universitat Bielefeld. Center For Biotechnology; Alemania Fil: Schlüter, Andreas. Universitat Bielefeld. Center For Biotechnology; Alemania
description	The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.
publishDate	2019
dc.date.none.fl_str_mv	2019-08-09
dc.type.none.fl_str_mv	info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo
format	article
status_str	publishedVersion
dc.identifier.none.fl_str_mv	http://hdl.handle.net/11336/151981 Nelkner, Johanna; Torres Tejerizo, Gonzalo Arturo; Hassa, Julia; Lin, Timo Wentong; Witte, Julian; et al.; Genetic potential of the biocontrol agent pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 unraveled by genome sequencing and mining, comparative genomics and transcriptomics; MDPI AG; Genes; 10; 8; 09-8-2019; 1-29 2073-4425 CONICET Digital CONICET
url	http://hdl.handle.net/11336/151981
identifier_str_mv	Nelkner, Johanna; Torres Tejerizo, Gonzalo Arturo; Hassa, Julia; Lin, Timo Wentong; Witte, Julian; et al.; Genetic potential of the biocontrol agent pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 unraveled by genome sequencing and mining, comparative genomics and transcriptomics; MDPI AG; Genes; 10; 8; 09-8-2019; 1-29 2073-4425 CONICET Digital CONICET
dc.language.none.fl_str_mv	eng
language	eng
dc.relation.none.fl_str_mv	info:eu-repo/semantics/altIdentifier/url/https://www.mdpi.com/2073-4425/10/8/601 info:eu-repo/semantics/altIdentifier/doi/10.3390/genes10080601
dc.rights.none.fl_str_mv	info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv	openAccess
rights_invalid_str_mv	https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv	application/pdf application/pdf
dc.publisher.none.fl_str_mv	MDPI AG
publisher.none.fl_str_mv	MDPI AG
dc.source.none.fl_str_mv	reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str	CONICET Digital (CONICET)
collection	CONICET Digital (CONICET)
instname_str	Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv	CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv	dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score	13.011256

Genetic potential of the biocontrol agent pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 unraveled by genome sequencing and mining, comparative genomics and transcriptom...

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