PoplarV1, Main, Exploration, bibRecord, 001918

Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis.

Identifieur interne : 001918 ( Main/Exploration ); précédent : 001917; suivant : 001919

Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis.

Auteurs : Se-Ran Jun [États-Unis] ; Trudy M. Wassenaar [Allemagne] ; Intawat Nookaew [États-Unis] ; Loren Hauser [États-Unis] ; Visanu Wanchai [États-Unis] ; Miriam Land [États-Unis] ; Collin M. Timm [États-Unis] ; Tse-Yuan S. Lu [États-Unis] ; Christopher W. Schadt [États-Unis] ; Mitchel J. Doktycz [États-Unis] ; Dale A. Pelletier [États-Unis] ; David W. Ussery [Pays-Bas]

Source :

Applied and environmental microbiology [ 1098-5336 ] ; 2016.

RBID : pubmed:26519390

Descripteurs français

KwdFr :
- Analyse de séquence d'ADN (MeSH), Génome bactérien (MeSH), Hybridation génomique comparative (MeSH), Phylogenèse (MeSH), Populus (microbiologie), Pseudomonas (classification), Pseudomonas (génétique), Pseudomonas (isolement et purification), Pseudomonas aeruginosa (génétique), Pseudomonas aeruginosa (isolement et purification), Pseudomonas fluorescens (classification), Pseudomonas fluorescens (génétique), Pseudomonas fluorescens (isolement et purification), Pseudomonas putida (génétique), Pseudomonas putida (isolement et purification), Racines de plante (microbiologie), Rhizosphère (MeSH), Variation génétique (MeSH).
MESH :
- génétique : Pseudomonas, Pseudomonas aeruginosa, Pseudomonas fluorescens, Pseudomonas putida.
- isolement et purification : Pseudomonas, Pseudomonas aeruginosa, Pseudomonas fluorescens, Pseudomonas putida.
- microbiologie : Populus, Racines de plante.
- classification : Analyse de séquence d'ADN, Génome bactérien, Hybridation génomique comparative, Phylogenèse, Pseudomonas, Pseudomonas fluorescens, Rhizosphère, Variation génétique.

English descriptors

KwdEn :
- Comparative Genomic Hybridization (MeSH), Genetic Variation (MeSH), Genome, Bacterial (MeSH), Phylogeny (MeSH), Plant Roots (microbiology), Populus (microbiology), Pseudomonas (classification), Pseudomonas (genetics), Pseudomonas (isolation & purification), Pseudomonas aeruginosa (genetics), Pseudomonas aeruginosa (isolation & purification), Pseudomonas fluorescens (classification), Pseudomonas fluorescens (genetics), Pseudomonas fluorescens (isolation & purification), Pseudomonas putida (genetics), Pseudomonas putida (isolation & purification), Rhizosphere (MeSH), Sequence Analysis, DNA (MeSH).
MESH :
- classification : Pseudomonas, Pseudomonas fluorescens.
- genetics : Pseudomonas, Pseudomonas aeruginosa, Pseudomonas fluorescens, Pseudomonas putida.
- isolation & purification : Pseudomonas, Pseudomonas aeruginosa, Pseudomonas fluorescens, Pseudomonas putida.
- microbiology : Plant Roots, Populus.
- Comparative Genomic Hybridization, Genetic Variation, Genome, Bacterial, Phylogeny, Rhizosphere, Sequence Analysis, DNA.

Abstract

The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000 Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides (eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All Pseudomonas aeruginosa genomes clustered together, and these were clearly distinct from other Pseudomonas species groups on the basis of pangenome and core genome analyses. In contrast, the genomes of Pseudomonas fluorescens were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21 Populus-associated isolates formed three distinct subgroups within the major P. fluorescens group, supported by pathway profile analysis, while two isolates were more closely related to Pseudomonas chlororaphis and Pseudomonas putida. Genes specific to Populus-associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrolase activity. This study justifies the need to sequence multiple isolates, especially from P. fluorescens, which displays the most genetic variation, in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing Pseudomonas strains for use to promote growth and increase disease resistance in plants.

DOI: 10.1128/AEM.02612-15
PubMed: 26519390
PubMed Central: PMC4702629

Affiliations:

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Le document en format XML

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<term>Phylogeny (MeSH)</term>
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<term>Populus (microbiology)</term>
<term>Pseudomonas (classification)</term>
<term>Pseudomonas (genetics)</term>
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<term>Pseudomonas fluorescens (isolation & purification)</term>
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<term>Pseudomonas putida (isolation & purification)</term>
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<term>Sequence Analysis, DNA (MeSH)</term>
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<term>Génome bactérien (MeSH)</term>
<term>Hybridation génomique comparative (MeSH)</term>
<term>Phylogenèse (MeSH)</term>
<term>Populus (microbiologie)</term>
<term>Pseudomonas (classification)</term>
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<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Pseudomonas</term>
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<keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Pseudomonas</term>
<term>Pseudomonas aeruginosa</term>
<term>Pseudomonas fluorescens</term>
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<keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Pseudomonas</term>
<term>Pseudomonas aeruginosa</term>
<term>Pseudomonas fluorescens</term>
<term>Pseudomonas putida</term>
</keywords>
<keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Populus</term>
<term>Racines de plante</term>
</keywords>
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<term>Populus</term>
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<front><div type="abstract" xml:lang="en">The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000 Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides (eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All Pseudomonas aeruginosa genomes clustered together, and these were clearly distinct from other Pseudomonas species groups on the basis of pangenome and core genome analyses. In contrast, the genomes of Pseudomonas fluorescens were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21 Populus-associated isolates formed three distinct subgroups within the major P. fluorescens group, supported by pathway profile analysis, while two isolates were more closely related to Pseudomonas chlororaphis and Pseudomonas putida. Genes specific to Populus-associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrolase activity. This study justifies the need to sequence multiple isolates, especially from P. fluorescens, which displays the most genetic variation, in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing Pseudomonas strains for use to promote growth and increase disease resistance in plants. </div>
</front>
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<Abstract><AbstractText>The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000 Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides (eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All Pseudomonas aeruginosa genomes clustered together, and these were clearly distinct from other Pseudomonas species groups on the basis of pangenome and core genome analyses. In contrast, the genomes of Pseudomonas fluorescens were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21 Populus-associated isolates formed three distinct subgroups within the major P. fluorescens group, supported by pathway profile analysis, while two isolates were more closely related to Pseudomonas chlororaphis and Pseudomonas putida. Genes specific to Populus-associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrolase activity. This study justifies the need to sequence multiple isolates, especially from P. fluorescens, which displays the most genetic variation, in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing Pseudomonas strains for use to promote growth and increase disease resistance in plants. </AbstractText>
<CopyrightInformation>Copyright © 2015 Jun et al.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Jun</LastName>
<ForeName>Se-Ran</ForeName>
<Initials>SR</Initials>
<AffiliationInfo><Affiliation>Joint Institute for Computational Sciences, University of Tennessee, Knoxville, Tennessee, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Wassenaar</LastName>
<ForeName>Trudy M</ForeName>
<Initials>TM</Initials>
<AffiliationInfo><Affiliation>Molecular Microbiology and Genomics Consultants, Zotzenheim, Germany.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Nookaew</LastName>
<ForeName>Intawat</ForeName>
<Initials>I</Initials>
<AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge Laboratory, Oak Ridge, Tennessee, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Hauser</LastName>
<ForeName>Loren</ForeName>
<Initials>L</Initials>
<AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge Laboratory, Oak Ridge, Tennessee, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Wanchai</LastName>
<ForeName>Visanu</ForeName>
<Initials>V</Initials>
<AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge Laboratory, Oak Ridge, Tennessee, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Land</LastName>
<ForeName>Miriam</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge Laboratory, Oak Ridge, Tennessee, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Timm</LastName>
<ForeName>Collin M</ForeName>
<Initials>CM</Initials>
<AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge Laboratory, Oak Ridge, Tennessee, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Lu</LastName>
<ForeName>Tse-Yuan S</ForeName>
<Initials>TY</Initials>
<AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge Laboratory, Oak Ridge, Tennessee, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Schadt</LastName>
<ForeName>Christopher W</ForeName>
<Initials>CW</Initials>
<AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge Laboratory, Oak Ridge, Tennessee, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Doktycz</LastName>
<ForeName>Mitchel J</ForeName>
<Initials>MJ</Initials>
<AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge Laboratory, Oak Ridge, Tennessee, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Pelletier</LastName>
<ForeName>Dale A</ForeName>
<Initials>DA</Initials>
<AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge Laboratory, Oak Ridge, Tennessee, USA.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Ussery</LastName>
<ForeName>David W</ForeName>
<Initials>DW</Initials>
<Identifier Source="ORCID">http://orcid.org/0000-0003-3632-5512</Identifier>
<AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge Laboratory, Oak Ridge, Tennessee, USA usserydw@ornl.gov.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2015</Year>
<Month>10</Month>
<Day>30</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>United States</Country>
<MedlineTA>Appl Environ Microbiol</MedlineTA>
<NlmUniqueID>7605801</NlmUniqueID>
<ISSNLinking>0099-2240</ISSNLinking>
</MedlineJournalInfo>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D055028" MajorTopicYN="N">Comparative Genomic Hybridization</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016680" MajorTopicYN="Y">Genome, Bacterial</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName>
<QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D011549" MajorTopicYN="N">Pseudomonas</DescriptorName>
<QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D011550" MajorTopicYN="N">Pseudomonas aeruginosa</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D011551" MajorTopicYN="N">Pseudomonas fluorescens</DescriptorName>
<QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016958" MajorTopicYN="N">Pseudomonas putida</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D058441" MajorTopicYN="N">Rhizosphere</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
</MeshHeading>
</MeshHeadingList>
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<Month>08</Month>
<Day>26</Day>
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<Month>10</Month>
<Day>21</Day>
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<Day>1</Day>
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<affiliations><list><country><li>Allemagne</li>
<li>Pays-Bas</li>
<li>États-Unis</li>
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<region><li>Tennessee</li>
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<name sortKey="Doktycz, Mitchel J" sort="Doktycz, Mitchel J" uniqKey="Doktycz M" first="Mitchel J" last="Doktycz">Mitchel J. Doktycz</name>
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<name sortKey="Land, Miriam" sort="Land, Miriam" uniqKey="Land M" first="Miriam" last="Land">Miriam Land</name>
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<name sortKey="Nookaew, Intawat" sort="Nookaew, Intawat" uniqKey="Nookaew I" first="Intawat" last="Nookaew">Intawat Nookaew</name>
<name sortKey="Pelletier, Dale A" sort="Pelletier, Dale A" uniqKey="Pelletier D" first="Dale A" last="Pelletier">Dale A. Pelletier</name>
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Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis.

Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis.

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