Genomic features of bacterial adaptation to plants.
Identifieur interne : 001362 ( Main/Exploration ); précédent : 001361; suivant : 001363Genomic features of bacterial adaptation to plants.
Auteurs : Asaf Levy [États-Unis] ; Isai Salas Gonzalez [États-Unis] ; Maximilian Mittelviefhaus [Suisse] ; Scott Clingenpeel [États-Unis] ; Sur Herrera Paredes [États-Unis] ; Jiamin Miao [États-Unis, République populaire de Chine] ; Kunru Wang [États-Unis] ; Giulia Devescovi [Italie] ; Kyra Stillman [États-Unis] ; Freddy Monteiro [États-Unis] ; Bryan Rangel Alvarez [États-Unis] ; Derek S. Lundberg [États-Unis] ; Tse-Yuan Lu [États-Unis] ; Sarah Lebeis [États-Unis] ; Zhao Jin [États-Unis] ; Meredith Mcdonald [États-Unis] ; Andrew P. Klein [États-Unis] ; Meghan E. Feltcher [États-Unis] ; Tijana Glavina Rio [États-Unis] ; Sarah R. Grant [États-Unis] ; Sharon L. Doty [États-Unis] ; Ruth E. Ley [Allemagne] ; Bingyu Zhao [États-Unis] ; Vittorio Venturi [Italie] ; Dale A. Pelletier [États-Unis] ; Julia A. Vorholt [Suisse] ; Susannah G. Tringe [États-Unis] ; Tanja Woyke [États-Unis] ; Jeffery L. Dangl [États-Unis]Source :
- Nature genetics [ 1546-1718 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
- croissance et développement : Bactéries.
- génétique : Bactéries, Interactions hôte-pathogène, Racines de plante.
- microbiologie : Plantes, Racines de plante.
- Adaptation physiologique, Génome bactérien, Génomique, Symbiose.
English descriptors
- KwdEn :
- MESH :
- genetics : Bacteria, Host-Pathogen Interactions, Plant Roots.
- growth & development : Bacteria.
- microbiology : Plant Roots, Plants.
- Adaptation, Physiological, Genome, Bacterial, Genomics, Symbiosis.
Abstract
Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly evolved genes that enable them to adapt to plant environments. However, the identities of such genes are mostly unknown, and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3,837 bacterial genomes to identify thousands of plant-associated gene clusters. Genomes of plant-associated bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant-associated genomes do. We experimentally validated candidates from two sets of plant-associated genes: one involved in plant colonization, and the other serving in microbe-microbe competition between plant-associated bacteria. We also identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes. This work expands the genome-based understanding of plant-microbe interactions and provides potential leads for efficient and sustainable agriculture through microbiome engineering.
DOI: 10.1038/s41588-017-0012-9
PubMed: 29255260
PubMed Central: PMC5957079
Affiliations:
- Allemagne, Italie, République populaire de Chine, Suisse, États-Unis
- Bade-Wurtemberg, Californie, Caroline du Nord, District de Tübingen, Maryland, Tennessee, Virginie, Washington (État), État de New York
- Ithaca (New York), Seattle, Tübingen
- Université Cornell, Université de Washington
Links toward previous steps (curation, corpus...)
Le document en format XML
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Ley</name><affiliation wicri:level="3"><nlm:affiliation>Max Planck Institute for Developmental Biology, Tübingen, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Developmental Biology, Tübingen</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Tübingen</region><settlement type="city">Tübingen</settlement></placeName></affiliation></author><author><name sortKey="Zhao, Bingyu" sort="Zhao, Bingyu" uniqKey="Zhao B" first="Bingyu" last="Zhao">Bingyu Zhao</name><affiliation wicri:level="2"><nlm:affiliation>Department of Horticulture, Virginia Tech, Blacksburg, VA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Horticulture, Virginia Tech, Blacksburg, VA</wicri:regionArea><placeName><region type="state">Virginie</region></placeName></affiliation></author><author><name sortKey="Venturi, Vittorio" sort="Venturi, Vittorio" uniqKey="Venturi V" first="Vittorio" last="Venturi">Vittorio Venturi</name><affiliation wicri:level="1"><nlm:affiliation>International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>International Centre for Genetic Engineering and Biotechnology, Trieste</wicri:regionArea><wicri:noRegion>Trieste</wicri:noRegion></affiliation></author><author><name sortKey="Pelletier, Dale A" sort="Pelletier, Dale A" uniqKey="Pelletier D" first="Dale A" last="Pelletier">Dale A. 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Center for Genome Sciences, University of North Carolina, Chapel Hill, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA. dangl@email.unc.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2017">2017</date><idno type="RBID">pubmed:29255260</idno><idno type="pmid">29255260</idno><idno type="doi">10.1038/s41588-017-0012-9</idno><idno type="pmc">PMC5957079</idno><idno type="wicri:Area/Main/Corpus">001030</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" 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wicri:level="2"><nlm:affiliation>Department of Biology, University of North Carolina, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, University of North Carolina, Chapel Hill, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Howard Hughes Medical Institute, Chevy Chase, MD, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Howard Hughes Medical Institute, Chevy Chase, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Mittelviefhaus, Maximilian" sort="Mittelviefhaus, Maximilian" uniqKey="Mittelviefhaus M" first="Maximilian" last="Mittelviefhaus">Maximilian Mittelviefhaus</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Microbiology, ETH Zurich, Zurich, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Institute of Microbiology, ETH Zurich, Zurich</wicri:regionArea><wicri:noRegion>Zurich</wicri:noRegion></affiliation></author><author><name sortKey="Clingenpeel, Scott" sort="Clingenpeel, Scott" uniqKey="Clingenpeel S" first="Scott" last="Clingenpeel">Scott Clingenpeel</name><affiliation wicri:level="2"><nlm:affiliation>DOE Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>DOE Joint Genome Institute, Walnut Creek, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Herrera Paredes, Sur" sort="Herrera Paredes, Sur" uniqKey="Herrera Paredes S" first="Sur" last="Herrera Paredes">Sur Herrera Paredes</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of North Carolina, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, University of North Carolina, Chapel Hill, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Howard Hughes Medical Institute, Chevy Chase, MD, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Howard Hughes Medical Institute, Chevy Chase, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, Stanford University, Stanford, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Miao, Jiamin" sort="Miao, Jiamin" uniqKey="Miao J" first="Jiamin" last="Miao">Jiamin Miao</name><affiliation wicri:level="2"><nlm:affiliation>Department of Horticulture, Virginia Tech, Blacksburg, VA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Horticulture, Virginia Tech, Blacksburg, VA</wicri:regionArea><placeName><region type="state">Virginie</region></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>The Grassland College, Gansu Agricultural University, Lanzhou, Gansu, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Grassland College, Gansu Agricultural University, Lanzhou, Gansu</wicri:regionArea><wicri:noRegion>Gansu</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Kunru" sort="Wang, Kunru" uniqKey="Wang K" first="Kunru" last="Wang">Kunru Wang</name><affiliation wicri:level="2"><nlm:affiliation>Department of Horticulture, Virginia Tech, Blacksburg, VA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Horticulture, Virginia Tech, Blacksburg, VA</wicri:regionArea><placeName><region type="state">Virginie</region></placeName></affiliation></author><author><name sortKey="Devescovi, Giulia" sort="Devescovi, Giulia" uniqKey="Devescovi G" first="Giulia" last="Devescovi">Giulia Devescovi</name><affiliation wicri:level="1"><nlm:affiliation>International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>International Centre for Genetic Engineering and Biotechnology, Trieste</wicri:regionArea><wicri:noRegion>Trieste</wicri:noRegion></affiliation></author><author><name sortKey="Stillman, Kyra" sort="Stillman, Kyra" uniqKey="Stillman K" first="Kyra" last="Stillman">Kyra Stillman</name><affiliation wicri:level="2"><nlm:affiliation>DOE Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>DOE Joint Genome Institute, Walnut Creek, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Monteiro, Freddy" sort="Monteiro, Freddy" uniqKey="Monteiro F" first="Freddy" last="Monteiro">Freddy Monteiro</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of North Carolina, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, University of North Carolina, Chapel Hill, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Howard Hughes Medical Institute, Chevy Chase, MD, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Howard Hughes Medical Institute, Chevy Chase, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Rangel Alvarez, Bryan" sort="Rangel Alvarez, Bryan" uniqKey="Rangel Alvarez B" first="Bryan" last="Rangel Alvarez">Bryan Rangel Alvarez</name><affiliation wicri:level="2"><nlm:affiliation>DOE Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>DOE Joint Genome Institute, Walnut Creek, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Lundberg, Derek S" sort="Lundberg, Derek S" uniqKey="Lundberg D" first="Derek S" last="Lundberg">Derek S. Lundberg</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of North Carolina, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, University of North Carolina, Chapel Hill, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Howard Hughes Medical Institute, Chevy Chase, MD, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Howard Hughes Medical Institute, Chevy Chase, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Lu, Tse Yuan" sort="Lu, Tse Yuan" uniqKey="Lu T" first="Tse-Yuan" last="Lu">Tse-Yuan Lu</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Lebeis, Sarah" sort="Lebeis, Sarah" uniqKey="Lebeis S" first="Sarah" last="Lebeis">Sarah Lebeis</name><affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology, University of Tennessee, Knoxville, TN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology, University of Tennessee, Knoxville, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Jin, Zhao" sort="Jin, Zhao" uniqKey="Jin Z" first="Zhao" last="Jin">Zhao Jin</name><affiliation wicri:level="4"><nlm:affiliation>Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY</wicri:regionArea><placeName><region type="state">État de New York</region><settlement type="city">Ithaca (New York)</settlement></placeName><orgName type="university">Université Cornell</orgName></affiliation></author><author><name sortKey="Mcdonald, Meredith" sort="Mcdonald, Meredith" uniqKey="Mcdonald M" first="Meredith" last="Mcdonald">Meredith Mcdonald</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of North Carolina, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, University of North Carolina, Chapel Hill, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Howard Hughes Medical Institute, Chevy Chase, MD, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Howard Hughes Medical Institute, Chevy Chase, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Klein, Andrew P" sort="Klein, Andrew P" uniqKey="Klein A" first="Andrew P" last="Klein">Andrew P. Klein</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of North Carolina, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, University of North Carolina, Chapel Hill, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Howard Hughes Medical Institute, Chevy Chase, MD, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Howard Hughes Medical Institute, Chevy Chase, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Feltcher, Meghan E" sort="Feltcher, Meghan E" uniqKey="Feltcher M" first="Meghan E" last="Feltcher">Meghan E. Feltcher</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of North Carolina, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, University of North Carolina, Chapel Hill, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Howard Hughes Medical Institute, Chevy Chase, MD, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Howard Hughes Medical Institute, Chevy Chase, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>BD Technologies and Innovation, Research Triangle Park, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>BD Technologies and Innovation, Research Triangle Park, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation></author><author><name sortKey="Rio, Tijana Glavina" sort="Rio, Tijana Glavina" uniqKey="Rio T" first="Tijana Glavina" last="Rio">Tijana Glavina Rio</name><affiliation wicri:level="2"><nlm:affiliation>DOE Joint Genome Institute, Walnut Creek, CA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>DOE Joint Genome Institute, Walnut Creek, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Grant, Sarah R" sort="Grant, Sarah R" uniqKey="Grant S" first="Sarah R" last="Grant">Sarah R. Grant</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of North Carolina, Chapel Hill, NC, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, University of North Carolina, Chapel Hill, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation></author><author><name sortKey="Doty, Sharon L" sort="Doty, Sharon L" uniqKey="Doty S" first="Sharon L" last="Doty">Sharon L. Doty</name><affiliation wicri:level="4"><nlm:affiliation>School of Environmental and Forest Sciences, University of Washington, Seattle, WA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Environmental and Forest Sciences, University of Washington, Seattle, WA</wicri:regionArea><placeName><region type="state">Washington (État)</region><settlement type="city">Seattle</settlement></placeName><orgName type="university">Université de Washington</orgName></affiliation></author><author><name sortKey="Ley, Ruth E" sort="Ley, Ruth E" uniqKey="Ley R" first="Ruth E" last="Ley">Ruth E. Ley</name><affiliation wicri:level="3"><nlm:affiliation>Max Planck Institute for Developmental Biology, Tübingen, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max Planck Institute for Developmental Biology, Tübingen</wicri:regionArea><placeName><region type="land" nuts="1">Bade-Wurtemberg</region><region type="district" nuts="2">District de Tübingen</region><settlement type="city">Tübingen</settlement></placeName></affiliation></author><author><name sortKey="Zhao, Bingyu" sort="Zhao, Bingyu" uniqKey="Zhao B" first="Bingyu" last="Zhao">Bingyu Zhao</name><affiliation wicri:level="2"><nlm:affiliation>Department of Horticulture, Virginia Tech, Blacksburg, VA, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Horticulture, Virginia Tech, Blacksburg, VA</wicri:regionArea><placeName><region type="state">Virginie</region></placeName></affiliation></author><author><name sortKey="Venturi, Vittorio" sort="Venturi, Vittorio" uniqKey="Venturi V" first="Vittorio" last="Venturi">Vittorio Venturi</name><affiliation wicri:level="1"><nlm:affiliation>International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>International Centre for Genetic Engineering and Biotechnology, Trieste</wicri:regionArea><wicri:noRegion>Trieste</wicri:noRegion></affiliation></author><author><name sortKey="Pelletier, Dale A" sort="Pelletier, Dale A" uniqKey="Pelletier D" first="Dale A" last="Pelletier">Dale A. Pelletier</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author><author><name sortKey="Vorholt, Julia A" sort="Vorholt, Julia A" uniqKey="Vorholt J" first="Julia A" last="Vorholt">Julia A. Vorholt</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Microbiology, ETH Zurich, Zurich, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Institute of Microbiology, ETH Zurich, Zurich</wicri:regionArea><wicri:noRegion>Zurich</wicri:noRegion></affiliation></author><author><name sortKey="Tringe, Susannah G" sort="Tringe, Susannah G" uniqKey="Tringe S" first="Susannah G" last="Tringe">Susannah G. Tringe</name><affiliation wicri:level="2"><nlm:affiliation>DOE Joint Genome Institute, Walnut Creek, CA, USA. sgtringe@lbl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>DOE Joint Genome Institute, Walnut Creek, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>School of Natural Sciences, University of California, Merced, Merced, CA, USA. sgtringe@lbl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Natural Sciences, University of California, Merced, Merced, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Woyke, Tanja" sort="Woyke, Tanja" uniqKey="Woyke T" first="Tanja" last="Woyke">Tanja Woyke</name><affiliation wicri:level="2"><nlm:affiliation>DOE Joint Genome Institute, Walnut Creek, CA, USA. twoyke@lbl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>DOE Joint Genome Institute, Walnut Creek, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>School of Natural Sciences, University of California, Merced, Merced, CA, USA. twoyke@lbl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>School of Natural Sciences, University of California, Merced, Merced, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Dangl, Jeffery L" sort="Dangl, Jeffery L" uniqKey="Dangl J" first="Jeffery L" last="Dangl">Jeffery L. Dangl</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biology, University of North Carolina, Chapel Hill, NC, USA. dangl@email.unc.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biology, University of North Carolina, Chapel Hill, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Howard Hughes Medical Institute, Chevy Chase, MD, USA. dangl@email.unc.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Howard Hughes Medical Institute, Chevy Chase, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>The Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC, USA. dangl@email.unc.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation><affiliation wicri:level="2"><nlm:affiliation>Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA. dangl@email.unc.edu.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC</wicri:regionArea><placeName><region type="state">Caroline du Nord</region></placeName></affiliation></author></analytic><series><title level="j">Nature genetics</title><idno type="eISSN">1546-1718</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adaptation, Physiological (MeSH)</term><term>Bacteria (genetics)</term><term>Bacteria (growth & development)</term><term>Genome, Bacterial (MeSH)</term><term>Genomics (MeSH)</term><term>Host-Pathogen Interactions (genetics)</term><term>Plant Roots (genetics)</term><term>Plant Roots (microbiology)</term><term>Plants (microbiology)</term><term>Symbiosis (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Adaptation physiologique (MeSH)</term><term>Bactéries (croissance et développement)</term><term>Bactéries (génétique)</term><term>Génome bactérien (MeSH)</term><term>Génomique (MeSH)</term><term>Interactions hôte-pathogène (génétique)</term><term>Plantes (microbiologie)</term><term>Racines de plante (génétique)</term><term>Racines de plante (microbiologie)</term><term>Symbiose (MeSH)</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Bactéries</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Bacteria</term><term>Host-Pathogen Interactions</term><term>Plant Roots</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Bactéries</term><term>Interactions hôte-pathogène</term><term>Racines de plante</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Plantes</term><term>Racines de plante</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Roots</term><term>Plants</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Adaptation, Physiological</term><term>Genome, Bacterial</term><term>Genomics</term><term>Symbiosis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Adaptation physiologique</term><term>Génome bactérien</term><term>Génomique</term><term>Symbiose</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly evolved genes that enable them to adapt to plant environments. However, the identities of such genes are mostly unknown, and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3,837 bacterial genomes to identify thousands of plant-associated gene clusters. Genomes of plant-associated bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant-associated genomes do. We experimentally validated candidates from two sets of plant-associated genes: one involved in plant colonization, and the other serving in microbe-microbe competition between plant-associated bacteria. We also identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes. This work expands the genome-based understanding of plant-microbe interactions and provides potential leads for efficient and sustainable agriculture through microbiome engineering.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29255260</PMID><DateCompleted><Year>2019</Year><Month>04</Month><Day>22</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>06</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1546-1718</ISSN><JournalIssue CitedMedium="Internet"><Volume>50</Volume><Issue>1</Issue><PubDate><Year>2017</Year><Month>12</Month><Day>18</Day></PubDate></JournalIssue><Title>Nature genetics</Title><ISOAbbreviation>Nat Genet</ISOAbbreviation></Journal><ArticleTitle>Genomic features of bacterial adaptation to plants.</ArticleTitle><Pagination><MedlinePgn>138-150</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/s41588-017-0012-9</ELocationID><Abstract><AbstractText>Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly evolved genes that enable them to adapt to plant environments. However, the identities of such genes are mostly unknown, and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3,837 bacterial genomes to identify thousands of plant-associated gene clusters. Genomes of plant-associated bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant-associated genomes do. We experimentally validated candidates from two sets of plant-associated genes: one involved in plant colonization, and the other serving in microbe-microbe competition between plant-associated bacteria. We also identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes. This work expands the genome-based understanding of plant-microbe interactions and provides potential leads for efficient and sustainable agriculture through microbiome engineering.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Levy</LastName><ForeName>Asaf</ForeName><Initials>A</Initials><Identifier Source="ORCID">http://orcid.org/0000-0003-2083-4072</Identifier><AffiliationInfo><Affiliation>DOE Joint Genome Institute, Walnut Creek, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Salas Gonzalez</LastName><ForeName>Isai</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Department of Biology, University of North Carolina, Chapel Hill, NC, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Howard Hughes Medical Institute, Chevy Chase, MD, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mittelviefhaus</LastName><ForeName>Maximilian</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Institute of Microbiology, ETH Zurich, Zurich, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Clingenpeel</LastName><ForeName>Scott</ForeName><Initials>S</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-6619-6320</Identifier><AffiliationInfo><Affiliation>DOE Joint Genome Institute, Walnut Creek, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Herrera Paredes</LastName><ForeName>Sur</ForeName><Initials>S</Initials><Identifier Source="ORCID">http://orcid.org/0000-0001-9246-8337</Identifier><AffiliationInfo><Affiliation>Department of Biology, University of North Carolina, Chapel Hill, NC, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Howard Hughes Medical Institute, Chevy Chase, MD, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Biology, Stanford University, Stanford, CA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Miao</LastName><ForeName>Jiamin</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Horticulture, Virginia Tech, Blacksburg, VA, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>The Grassland College, Gansu Agricultural University, Lanzhou, Gansu, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Kunru</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Horticulture, Virginia Tech, Blacksburg, VA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Devescovi</LastName><ForeName>Giulia</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>International Centre for Genetic Engineering and Biotechnology, Trieste, Italy.</Affiliation></AffiliationInfo></Author><Author 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sortKey="Clingenpeel, Scott" sort="Clingenpeel, Scott" uniqKey="Clingenpeel S" first="Scott" last="Clingenpeel">Scott Clingenpeel</name><name sortKey="Dangl, Jeffery L" sort="Dangl, Jeffery L" uniqKey="Dangl J" first="Jeffery L" last="Dangl">Jeffery L. Dangl</name><name sortKey="Dangl, Jeffery L" sort="Dangl, Jeffery L" uniqKey="Dangl J" first="Jeffery L" last="Dangl">Jeffery L. Dangl</name><name sortKey="Dangl, Jeffery L" sort="Dangl, Jeffery L" uniqKey="Dangl J" first="Jeffery L" last="Dangl">Jeffery L. Dangl</name><name sortKey="Dangl, Jeffery L" sort="Dangl, Jeffery L" uniqKey="Dangl J" first="Jeffery L" last="Dangl">Jeffery L. Dangl</name><name sortKey="Doty, Sharon L" sort="Doty, Sharon L" uniqKey="Doty S" first="Sharon L" last="Doty">Sharon L. Doty</name><name sortKey="Feltcher, Meghan E" sort="Feltcher, Meghan E" uniqKey="Feltcher M" first="Meghan E" last="Feltcher">Meghan E. Feltcher</name><name sortKey="Feltcher, Meghan E" sort="Feltcher, Meghan E" uniqKey="Feltcher M" first="Meghan E" last="Feltcher">Meghan E. Feltcher</name><name sortKey="Feltcher, Meghan E" sort="Feltcher, Meghan E" uniqKey="Feltcher M" first="Meghan E" last="Feltcher">Meghan E. Feltcher</name><name sortKey="Grant, Sarah R" sort="Grant, Sarah R" uniqKey="Grant S" first="Sarah R" last="Grant">Sarah R. Grant</name><name sortKey="Herrera Paredes, Sur" sort="Herrera Paredes, Sur" uniqKey="Herrera Paredes S" first="Sur" last="Herrera Paredes">Sur Herrera Paredes</name><name sortKey="Herrera Paredes, Sur" sort="Herrera Paredes, Sur" uniqKey="Herrera Paredes S" first="Sur" last="Herrera Paredes">Sur Herrera Paredes</name><name sortKey="Herrera Paredes, Sur" sort="Herrera Paredes, Sur" uniqKey="Herrera Paredes S" first="Sur" last="Herrera Paredes">Sur Herrera Paredes</name><name sortKey="Jin, Zhao" sort="Jin, Zhao" uniqKey="Jin Z" first="Zhao" last="Jin">Zhao Jin</name><name sortKey="Klein, Andrew P" sort="Klein, Andrew P" uniqKey="Klein A" first="Andrew P" last="Klein">Andrew P. Klein</name><name sortKey="Klein, Andrew P" sort="Klein, Andrew P" uniqKey="Klein A" first="Andrew P" last="Klein">Andrew P. Klein</name><name sortKey="Lebeis, Sarah" sort="Lebeis, Sarah" uniqKey="Lebeis S" first="Sarah" last="Lebeis">Sarah Lebeis</name><name sortKey="Lu, Tse Yuan" sort="Lu, Tse Yuan" uniqKey="Lu T" first="Tse-Yuan" last="Lu">Tse-Yuan Lu</name><name sortKey="Lundberg, Derek S" sort="Lundberg, Derek S" uniqKey="Lundberg D" first="Derek S" last="Lundberg">Derek S. Lundberg</name><name sortKey="Lundberg, Derek S" sort="Lundberg, Derek S" uniqKey="Lundberg D" first="Derek S" last="Lundberg">Derek S. 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Tringe</name><name sortKey="Tringe, Susannah G" sort="Tringe, Susannah G" uniqKey="Tringe S" first="Susannah G" last="Tringe">Susannah G. Tringe</name><name sortKey="Wang, Kunru" sort="Wang, Kunru" uniqKey="Wang K" first="Kunru" last="Wang">Kunru Wang</name><name sortKey="Woyke, Tanja" sort="Woyke, Tanja" uniqKey="Woyke T" first="Tanja" last="Woyke">Tanja Woyke</name><name sortKey="Woyke, Tanja" sort="Woyke, Tanja" uniqKey="Woyke T" first="Tanja" last="Woyke">Tanja Woyke</name><name sortKey="Zhao, Bingyu" sort="Zhao, Bingyu" uniqKey="Zhao B" first="Bingyu" last="Zhao">Bingyu Zhao</name></country><country name="Suisse"><noRegion><name sortKey="Mittelviefhaus, Maximilian" sort="Mittelviefhaus, Maximilian" uniqKey="Mittelviefhaus M" first="Maximilian" last="Mittelviefhaus">Maximilian Mittelviefhaus</name></noRegion><name sortKey="Vorholt, Julia A" sort="Vorholt, Julia A" uniqKey="Vorholt J" first="Julia A" last="Vorholt">Julia A. Vorholt</name></country><country name="République populaire de Chine"><noRegion><name sortKey="Miao, Jiamin" sort="Miao, Jiamin" uniqKey="Miao J" first="Jiamin" last="Miao">Jiamin Miao</name></noRegion></country><country name="Italie"><noRegion><name sortKey="Devescovi, Giulia" sort="Devescovi, Giulia" uniqKey="Devescovi G" first="Giulia" last="Devescovi">Giulia Devescovi</name></noRegion><name sortKey="Venturi, Vittorio" sort="Venturi, Vittorio" uniqKey="Venturi V" first="Vittorio" last="Venturi">Vittorio Venturi</name></country><country name="Allemagne"><region name="Bade-Wurtemberg"><name sortKey="Ley, Ruth E" sort="Ley, Ruth E" uniqKey="Ley R" first="Ruth E" last="Ley">Ruth E. Ley</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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