{"@context":{"@vocab":"https://cir.nii.ac.jp/schema/1.0/","rdfs":"http://www.w3.org/2000/01/rdf-schema#","dc":"http://purl.org/dc/elements/1.1/","dcterms":"http://purl.org/dc/terms/","foaf":"http://xmlns.com/foaf/0.1/","prism":"http://prismstandard.org/namespaces/basic/2.0/","cinii":"http://ci.nii.ac.jp/ns/1.0/","datacite":"https://schema.datacite.org/meta/kernel-4/","ndl":"http://ndl.go.jp/dcndl/terms/","jpcoar":"https://github.com/JPCOAR/schema/blob/master/2.0/"},"@id":"https://cir.nii.ac.jp/crid/1360565166755649280.json","@type":"Article","productIdentifier":[{"identifier":{"@type":"DOI","@value":"10.1038/ncomms11362"}},{"identifier":{"@type":"URI","@value":"https://www.nature.com/articles/ncomms11362.pdf"}},{"identifier":{"@type":"URI","@value":"https://www.nature.com/articles/ncomms11362"}},{"identifier":{"@type":"DOI","@value":"10.1038/ncomms13072"}},{"identifier":{"@type":"PMID","@value":"27681013"}},{"identifier":{"@type":"PMID","@value":"27150427"}},{"identifier":{"@type":"HANDLE","@value":"20.500.11755/b09fe60c-4e5b-4eba-b3fe-d585bb87c7bf"}},{"identifier":{"@type":"HANDLE","@value":"10033/620909"}},{"identifier":{"@type":"HANDLE","@value":"11858/00-001M-0000-002B-1613-F"}},{"identifier":{"@type":"HANDLE","@value":"11858/00-001M-0000-002B-1615-B"}}],"resourceType":"学術雑誌論文(journal article)","dc:title":[{"@value":"Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi"}],"description":[{"type":"abstract","notation":[{"@value":"<jats:title>Abstract</jats:title><jats:p>The sessile nature of plants forced them to evolve mechanisms to prioritize their responses to simultaneous stresses, including colonization by microbes or nutrient starvation. Here, we compare the genomes of a beneficial root endophyte, <jats:italic>Colletotrichum tofieldiae</jats:italic> and its pathogenic relative <jats:italic>C. incanum</jats:italic>, and examine the transcriptomes of both fungi and their plant host <jats:italic>Arabidopsis</jats:italic> during phosphate starvation. Although the two species diverged only 8.8 million years ago and have similar gene arsenals, we identify genomic signatures indicative of an evolutionary transition from pathogenic to beneficial lifestyles, including a narrowed repertoire of secreted effector proteins, expanded families of chitin-binding and secondary metabolism-related proteins, and limited activation of pathogenicity-related genes <jats:italic>in planta</jats:italic>. We show that beneficial responses are prioritized in <jats:italic>C. tofieldiae</jats:italic>-colonized roots under phosphate-deficient conditions, whereas defense responses are activated under phosphate-sufficient conditions. These immune responses are retained in phosphate-starved roots colonized by pathogenic <jats:italic>C. incanum</jats:italic>, illustrating the ability of plants to maximize survival in response to conflicting stresses.</jats:p>"}]}],"creator":[{"@id":"https://cir.nii.ac.jp/crid/1380284919968254465","@type":"Researcher","foaf:name":[{"@value":"Stéphane Hacquard"}]},{"@id":"https://cir.nii.ac.jp/crid/1380284919968254466","@type":"Researcher","foaf:name":[{"@value":"Barbara Kracher"}]},{"@id":"https://cir.nii.ac.jp/crid/1420564276161032320","@type":"Researcher","personIdentifier":[{"@type":"KAKEN_RESEARCHERS","@value":"20714504"},{"@type":"NRID","@value":"1000020714504"},{"@type":"NRID","@value":"9000018780376"},{"@type":"NRID","@value":"9000409505930"},{"@type":"NRID","@value":"9000404663900"},{"@type":"NRID","@value":"9000317167100"},{"@type":"NRID","@value":"9000399795906"},{"@type":"NRID","@value":"9000384267608"},{"@type":"RESEARCHMAP","@value":"https://researchmap.jp/7000018627"}],"foaf:name":[{"@value":"Kei Hiruma"}]},{"@id":"https://cir.nii.ac.jp/crid/1380284919968254467","@type":"Researcher","foaf:name":[{"@value":"Philipp C. Münch"}]},{"@id":"https://cir.nii.ac.jp/crid/1380284919968254601","@type":"Researcher","foaf:name":[{"@value":"Ruben Garrido-Oter"}]},{"@id":"https://cir.nii.ac.jp/crid/1380565166755649280","@type":"Researcher","foaf:name":[{"@value":"Michael R. Thon"}]},{"@id":"https://cir.nii.ac.jp/crid/1380284919968254593","@type":"Researcher","foaf:name":[{"@value":"Aaron Weimann"}]},{"@id":"https://cir.nii.ac.jp/crid/1380284919968254595","@type":"Researcher","foaf:name":[{"@value":"Ulrike Damm"}]},{"@id":"https://cir.nii.ac.jp/crid/1380284919968254468","@type":"Researcher","foaf:name":[{"@value":"Jean-Félix Dallery"}]},{"@id":"https://cir.nii.ac.jp/crid/1380284919968254602","@type":"Researcher","foaf:name":[{"@value":"Matthieu Hainaut"}]},{"@id":"https://cir.nii.ac.jp/crid/1380284919968254599","@type":"Researcher","foaf:name":[{"@value":"Bernard Henrissat"}]},{"@id":"https://cir.nii.ac.jp/crid/1380284919968254600","@type":"Researcher","foaf:name":[{"@value":"Olivier Lespinet"}]},{"@id":"https://cir.nii.ac.jp/crid/1380284919968254594","@type":"Researcher","foaf:name":[{"@value":"Soledad Sacristán"}]},{"@id":"https://cir.nii.ac.jp/crid/1380284919968254597","@type":"Researcher","foaf:name":[{"@value":"Emiel Ver Loren van Themaat"}]},{"@id":"https://cir.nii.ac.jp/crid/1380284919968254596","@type":"Researcher","foaf:name":[{"@value":"Eric Kemen"}]},{"@id":"https://cir.nii.ac.jp/crid/1380284919968254469","@type":"Researcher","foaf:name":[{"@value":"Alice C. McHardy"}]},{"@id":"https://cir.nii.ac.jp/crid/1380284919968254592","@type":"Researcher","foaf:name":[{"@value":"Paul Schulze-Lefert"}]},{"@id":"https://cir.nii.ac.jp/crid/1380284919968254598","@type":"Researcher","foaf:name":[{"@value":"Richard J. O’Connell"}]}],"contributor":[{"@id":"https://cir.nii.ac.jp/crid/1893679867484331149","@type":"Researcher","foaf:name":[{"@value":"Computational Biology of Infection Research [Braunschweig] ; Helmholtz Centre for Infection Research (HZI)"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331146","@type":"Researcher","foaf:name":[{"@value":"Max Von Pettenkofer Institute (MVP) ; Ludwig Maximilian University [Munich] = Ludwig Maximilians Universität München (LMU)"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331265","@type":"Researcher","foaf:name":[{"@value":"Cluster of Excellence on Plant Sciences (CEPLAS)"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331156","@type":"Researcher","foaf:name":[{"@value":"Algorithmische Bioinformatik [Düsseldorf] ; Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]"}]},{"@id":"https://cir.nii.ac.jp/crid/1890021790922491520","@type":"Researcher","foaf:name":[{"@value":"Centro Hispano-Luso de Investigaciones Agrarias, Departamento de Microbiología y Genétic ; Universidad de Salamanca [España] = University of Salamanca [Spain]"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331160","@type":"Researcher","foaf:name":[{"@value":"Fungal Biodiversity Centre"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331014","@type":"Researcher","foaf:name":[{"@value":"Institut de Biologie Intégrative de la Cellule (I2BC) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331145","@type":"Researcher","foaf:name":[{"@value":"BIOlogie et GEstion des Risques en agriculture (BIOGER) ; Institut National de la Recherche Agronomique (INRA)-AgroParisTech"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331170","@type":"Researcher","foaf:name":[{"@value":"Architecture et fonction des macromolécules biologiques (AFMB) ; Institut National de la Recherche Agronomique (INRA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331154","@type":"Researcher","foaf:name":[{"@value":"Laboratoire de Recherche en Imagerie : Méthodes d'imagerie des Échanges transcapillaires (LRI - EA4062) ; Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331141","@type":"Researcher","foaf:name":[{"@value":"BioInformatique Moléculaire (BIM) ; Département Biologie des Génomes (DBG) ; Institut de Biologie Intégrative de la Cellule (I2BC) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC) ; Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331269","@type":"Researcher","foaf:name":[{"@value":"German Centre for Infection Research - partner site Hamburg-Lübeck-Borstel-Riems (DZIF)"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331152","@type":"Researcher","foaf:name":[{"@value":"Department of Plant Microbe Interactions ; Max Planck Institute for Plant Breeding Research (MPIPZ)"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331175","@type":"Researcher","foaf:name":[{"@value":"Department of Biological Sciences ; King Abdulazziz University"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331276","@type":"Researcher","foaf:name":[{"@value":"Laboratoire de Recherche en Informatique (LRI) ; Université Paris-Sud - Paris 11 (UP11)-CentraleSupélec-Centre National de la Recherche Scientifique (CNRS)"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331008","@type":"Researcher","foaf:name":[{"@value":"Max Planck Society ; Agence Nationale de la Recherche [ANR-12-CHEX-0008-01] ; 'Cluster of Excellence on Plant Sciences' program - Deutsche Forschungsgemeinschaft ; German Center for Infection Research, DZIF ; Japan Society for the Promotion of Science"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331009","@type":"Researcher","foaf:name":[{"@value":"European Project: 323094,EC:FP7:ERC,ERC-2012-ADG_20120314,ROOTMICROBIOTA(2013)"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331011","@type":"Researcher","foaf:name":[{"@value":"BRICS, Braunschweiger Zentrum für Systembiologie, Rebenring 56, 38106 Braunschweig, Germany."}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331268","@type":"Researcher","foaf:name":[{"@value":"Centro de Biotechnologia y Genomica de Plantas (UPM-INIA) and ETSI Agronomos ; Universidad Politécnica de Madrid (UPM)"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331140","@type":"Researcher","foaf:name":[{"@value":"Hacquard, Stéphane"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331153","@type":"Researcher","foaf:name":[{"@value":"Kracher, Barbara"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331270","@type":"Researcher","foaf:name":[{"@value":"Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT) Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research (KAKENHI) 15K18645"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331137","@type":"Researcher","foaf:name":[{"@value":"German Center for Infection Research - Partner Site Bonn-Cologne (DZIF)"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331264","@type":"Researcher","foaf:name":[{"@value":"ANR-12-CHEX-0008,FUNAPP,Nouveaux rôles des appressoria de champignons pathogènes dans leurs interactions avec les plantes: détection des signaux de la plante et transfert d'effecteurs protéiques et de métabolites secondaires fongiques dans les cellules hôtes(2012)"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331012","@type":"Researcher","foaf:name":[{"@value":"Centro Hispano-Luso de Investigaciones Agrarias, Departamento de Microbiología y Genétic ; Universidad de Salamanca"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331148","@type":"Researcher","foaf:name":[{"@value":"BIOlogie et GEstion des Risques en agriculture (BIOGER) ; AgroParisTech-Institut National de la Recherche Agronomique (INRA)"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331142","@type":"Researcher","foaf:name":[{"@value":"Architecture et fonction des macromolécules biologiques (AFMB) ; Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Institut National de la Recherche Agronomique (INRA)"}]},{"@id":"https://cir.nii.ac.jp/crid/1890021790922491521","@type":"Researcher","foaf:name":[{"@value":"GRECH, Cécile"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331159","@type":"Researcher","foaf:name":[{"@value":"Department of Algorithmic Bioinformatics ; Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf]"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331161","@type":"Researcher","foaf:name":[{"@value":"Max Von Pettenkofer Institute (MVP) ; Ludwig-Maximilians-Universität München (LMU)"}]},{"@id":"https://cir.nii.ac.jp/crid/1893679867484331010","@type":"Researcher","foaf:name":[{"@value":"Cluster of Excellence on Plant Sciences  (CEPLAS)"}]}],"publication":{"publicationIdentifier":[{"@type":"EISSN","@value":"20411723"}],"prism:publicationName":[{"@value":"Nature Communications"}],"dc:publisher":[{"@value":"Springer Science and Business Media LLC"}],"prism:publicationDate":"2016-05-06","prism:volume":"7","prism:number":"1","prism:startingPage":"11362"},"reviewed":"false","dcterms:accessRights":"http://purl.org/coar/access_right/c_abf2","dc:rights":["https://creativecommons.org/licenses/by/4.0","https://creativecommons.org/licenses/by/4.0"],"url":[{"@id":"https://www.nature.com/articles/ncomms11362.pdf"},{"@id":"https://www.nature.com/articles/ncomms11362"}],"createdAt":"2016-05-06","modifiedAt":"2023-01-04","foaf:topic":[{"@id":"https://cir.nii.ac.jp/all?q=roots","dc:title":"roots"},{"@id":"https://cir.nii.ac.jp/all?q=Colletotrichum%20tofieldiae","dc:title":"Colletotrichum tofieldiae"},{"@id":"https://cir.nii.ac.jp/all?q=Arabidopsis%20thaliana","dc:title":"Arabidopsis thaliana"},{"@id":"https://cir.nii.ac.jp/all?q=plant%20innate%20immunity","dc:title":"plant innate immunity"},{"@id":"https://cir.nii.ac.jp/all?q=Science","dc:title":"Science"},{"@id":"https://cir.nii.ac.jp/all?q=%5BSDV%5DLife%20Sciences%20%5Bq-bio%5D","dc:title":"[SDV]Life Sciences [q-bio]"},{"@id":"https://cir.nii.ac.jp/all?q=Arabidopsis","dc:title":"Arabidopsis"},{"@id":"https://cir.nii.ac.jp/all?q=Chitin","dc:title":"Chitin"},{"@id":"https://cir.nii.ac.jp/all?q=Plant%20Roots","dc:title":"Plant Roots"},{"@id":"https://cir.nii.ac.jp/all?q=Article","dc:title":"Article"},{"@id":"https://cir.nii.ac.jp/all?q=Phosphates","dc:title":"Phosphates"},{"@id":"https://cir.nii.ac.jp/all?q=Colletotrichum","dc:title":"Colletotrichum"},{"@id":"https://cir.nii.ac.jp/all?q=Endophytes","dc:title":"Endophytes"},{"@id":"https://cir.nii.ac.jp/all?q=Colletotrichum%20tofieldiae%20;Colletotrichum%20incanum;Arabidopsis%20thaliana;endophyte%20;roots%20;plant%20innate%20immunity%20;genome;transcriptome;differential%20gene%20expression;symbiosis","dc:title":"Colletotrichum tofieldiae ;Colletotrichum incanum;Arabidopsis thaliana;endophyte ;roots ;plant innate immunity ;genome;transcriptome;differential gene expression;symbiosis"},{"@id":"https://cir.nii.ac.jp/all?q=Colletotrichum%20incanum","dc:title":"Colletotrichum incanum"},{"@id":"https://cir.nii.ac.jp/all?q=differential%20gene%20expression","dc:title":"differential gene expression"},{"@id":"https://cir.nii.ac.jp/all?q=Symbiosis","dc:title":"Symbiosis"},{"@id":"https://cir.nii.ac.jp/all?q=genome","dc:title":"genome"},{"@id":"https://cir.nii.ac.jp/all?q=580","dc:title":"580"},{"@id":"https://cir.nii.ac.jp/all?q=Q","dc:title":"Q"},{"@id":"https://cir.nii.ac.jp/all?q=ddc:no","dc:title":"ddc:no"},{"@id":"https://cir.nii.ac.jp/all?q=symbiosis","dc:title":"symbiosis"},{"@id":"https://cir.nii.ac.jp/all?q=%5BSDV%5D%20Life%20Sciences%20%5Bq-bio%5D","dc:title":"[SDV] Life Sciences [q-bio]"},{"@id":"https://cir.nii.ac.jp/all?q=Starvation","dc:title":"Starvation"},{"@id":"https://cir.nii.ac.jp/all?q=Erratum","dc:title":"Erratum"},{"@id":"https://cir.nii.ac.jp/all?q=Genome,%20Fungal","dc:title":"Genome, Fungal"},{"@id":"https://cir.nii.ac.jp/all?q=endophyte","dc:title":"endophyte"},{"@id":"https://cir.nii.ac.jp/all?q=transcriptome","dc:title":"transcriptome"}],"project":[{"@id":"https://cir.nii.ac.jp/crid/1040000781863698816","@type":"Project","projectIdentifier":[{"@type":"KAKEN","@value":"15K18645"},{"@type":"JGN","@value":"JP15K18645"},{"@type":"URI","@value":"https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-15K18645/"}],"notation":[{"@language":"ja","@value":"エンドファイト型コレトトリカム属菌の栄養条件依存的な植物成長促進機構の解明"},{"@language":"en","@value":"Revealing the mechanisms of nutrient status dependent Plant growth promotion effects by endophytic Colletotrichum species"}]}],"relatedProduct":[{"@id":"https://cir.nii.ac.jp/crid/1050292815315047680","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Multi-omics analysis on an agroecosystem reveals the significant role of organic nitrogen to increase agricultural crop yield"}]},{"@id":"https://cir.nii.ac.jp/crid/1360001113995903104","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Pattern recognition receptors and signaling in plant–microbe interactions"}]},{"@id":"https://cir.nii.ac.jp/crid/1360002218986213760","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"REAPR: a universal tool for genome assembly evaluation"}]},{"@id":"https://cir.nii.ac.jp/crid/1360011142938169216","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Versatile and open software for comparing large genomes"}]},{"@id":"https://cir.nii.ac.jp/crid/1360011143695987200","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Endophytic Life Strategies Decoded by Genome and Transcriptome Analyses of the Mutualistic Root Symbiont Piriformospora indica"}]},{"@id":"https://cir.nii.ac.jp/crid/1360011144720866304","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"WoLF PSORT: protein localization predictor"}]},{"@id":"https://cir.nii.ac.jp/crid/1360011146251037568","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Root Infection and Systemic Colonization of Maize by<i>Colletotrichum graminicola</i>"}]},{"@id":"https://cir.nii.ac.jp/crid/1360013168742381312","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"The Conserved Colletotrichum spp. Effector Candidate CEC3 Induces Nuclear Expansion and Cell Death in Plants"}]},{"@id":"https://cir.nii.ac.jp/crid/1360013168826428672","@type":"Article","resourceType":"preprint","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Guanosine-specific single-stranded ribonuclease effectors of a phytopathogenic fungus potentiate host immune responses"}]},{"@id":"https://cir.nii.ac.jp/crid/1360021389803207296","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"The disordered C-terminal tail of fungal LPMOs from phytopathogens mediates protein dimerization and impacts plant penetration"}]},{"@id":"https://cir.nii.ac.jp/crid/1360023717933240832","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"CLE peptide signaling in plant-microbe interactions"}]},{"@id":"https://cir.nii.ac.jp/crid/1360283693326539776","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of <i>Colletotrichum</i> fungi"}]},{"@id":"https://cir.nii.ac.jp/crid/1360285707399837056","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Beneficial associations between Brassicaceae plants and fungal endophytes under nutrient-limiting conditions: evolutionary origins and host–symbiont molecular mechanisms"}]},{"@id":"https://cir.nii.ac.jp/crid/1360287219295442688","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Roles of Plant-Derived Secondary Metabolites during Interactions with Pathogenic and Beneficial Microbes under Conditions of Environmental Stress"}]},{"@id":"https://cir.nii.ac.jp/crid/1360292617907946496","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"The carbohydrate-active enzymes database (CAZy) in 2013"}]},{"@id":"https://cir.nii.ac.jp/crid/1360292617907978752","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs"}]},{"@id":"https://cir.nii.ac.jp/crid/1360292618961304960","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Root-associated fungi of Arabidopsis thaliana and Microthlaspi perfoliatum"}]},{"@id":"https://cir.nii.ac.jp/crid/1360292619076125824","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"MEROPS: the peptidase database"}]},{"@id":"https://cir.nii.ac.jp/crid/1360292621475139712","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis"}]},{"@id":"https://cir.nii.ac.jp/crid/1360294647854474880","@type":"Article","resourceType":"preprint","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"The Conserved\n                  <i>Colletotrichum</i>\n                  spp. Effector CEC3 Induces Nuclear Expansion and Cell Death in Plants"}]},{"@id":"https://cir.nii.ac.jp/crid/1360302865725438592","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Guanosine‐specific single‐stranded ribonuclease effectors of a phytopathogenic fungus potentiate host immune responses"}]},{"@id":"https://cir.nii.ac.jp/crid/1360567184538898304","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Genomic Plasticity Mediated by Transposable Elements in the Plant Pathogenic Fungus Colletotrichum higginsianum"}]},{"@id":"https://cir.nii.ac.jp/crid/1360568468329318784","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Colletotrichum shisoi sp. nov., an anthracnose pathogen of Perilla frutescens in Japan: molecular phylogenetic, morphological and genomic evidence"}]},{"@id":"https://cir.nii.ac.jp/crid/1360572092709905408","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Continuous Spectrum of Lifestyles of Plant-Associated Fungi Under Fluctuating Environments: What Genetic Components Determine the Lifestyle Transition?"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574092886317824","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Fast gapped-read alignment with Bowtie 2"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574092888310272","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574092890795520","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574092892402176","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Automated generation of heuristics for biological sequence comparison"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574092893215104","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Repbase Update, a database of eukaryotic repetitive elements"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574094915390720","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574095958035968","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Mechanisms underlying beneficial plant–fungus interactions in mycorrhizal symbiosis"}]},{"@id":"https://cir.nii.ac.jp/crid/1360574096422901248","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Anthracnose of Japanese radish caused by Colletotrichum dematium"}]},{"@id":"https://cir.nii.ac.jp/crid/1360579814657223424","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Genome Resource of <i>Colletotrichum spaethianum</i>, the Causal Agent of Leaf Anthracnose in <i>Polygonatum falcatum</i>"}]},{"@id":"https://cir.nii.ac.jp/crid/1360584340707673728","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Modulation of plant immunity and biotic interactions under phosphate deficiency"}]},{"@id":"https://cir.nii.ac.jp/crid/1360846640782618368","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Root Endophyte Colletotrichum tofieldiae Confers Plant Fitness Benefits that Are Phosphate Status Dependent"}]},{"@id":"https://cir.nii.ac.jp/crid/1360846643280222720","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"<i>Colletotrichum higginsianum</i> extracellular LysM proteins play dual roles in appressorial function and suppression of chitin‐triggered plant immunity"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855567861517568","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Gene finding in novel genomes"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855567863120256","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"AUGUSTUS: ab initio prediction of alternative transcripts"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855567865731072","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855567866356096","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855567866476544","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"The Sequence Alignment/Map format and SAMtools"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855567867298304","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855567867368192","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855567868008448","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Full-length transcriptome assembly from RNA-Seq data without a reference genome"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855567868153856","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"A new mathematical model for relative quantification in real-time RT-PCR"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855567869826944","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Circos: An information aesthetic for comparative genomics"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855567870556032","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855567870558336","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"<tt>edgeR</tt>\n                    : a Bioconductor package for differential expression analysis of digital gene expression data"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855569525830912","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855570187618048","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Fungal Effectors and Plant Susceptibility"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855570483652224","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Inference of Gain and Loss Events from Phyletic Patterns Using Stochastic Mapping and Maximum Parsimony—A Simulation Study"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855570537966464","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Genetic Conversion of a Fungal Plant Pathogen to a Nonpathogenic, Endophytic Mutualist"}]},{"@id":"https://cir.nii.ac.jp/crid/1360855571025251200","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training"}]},{"@id":"https://cir.nii.ac.jp/crid/1360861707384587904","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Genomic resources of Colletotrichum fungi: development and application"}]},{"@id":"https://cir.nii.ac.jp/crid/1360869854377126400","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@value":"Uncovering the Host Range–Lifestyle Relationship in the Endophytic and Anthracnose Pathogenic Genus Colletotrichum"}]},{"@id":"https://cir.nii.ac.jp/crid/1361137044350290944","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"HTSeq—a Python framework to work with high-throughput sequencing data"}]},{"@id":"https://cir.nii.ac.jp/crid/1361137046063176960","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"The endophytic mycobiota of Arabidopsis thaliana"}]},{"@id":"https://cir.nii.ac.jp/crid/1361699993392486784","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Fungal endophytes: diversity and functional roles"}]},{"@id":"https://cir.nii.ac.jp/crid/1361699994666031744","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Protein homology detection by HMM–HMM comparison"}]},{"@id":"https://cir.nii.ac.jp/crid/1361699995274759680","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Mutualistic root endophytism is not associated with the reduction of saprotrophic traits and requires a noncompromised plant innate immunity"}]},{"@id":"https://cir.nii.ac.jp/crid/1361699995911925760","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Identification of primary and secondary metabolites with phosphorus status‐dependent abundance in <scp><i>A</i></scp><i>rabidopsis</i>, and of the transcription factor <scp>PHR</scp>1 as a major regulator of metabolic changes during phosphorus limitation"}]},{"@id":"https://cir.nii.ac.jp/crid/1361981468459990656","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Genesis: cluster analysis of microarray data"}]},{"@id":"https://cir.nii.ac.jp/crid/1362262943909540608","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Glucosinolate Metabolites Required for an\n                    <i>Arabidopsis</i>\n                    Innate Immune Response"}]},{"@id":"https://cir.nii.ac.jp/crid/1362262944335232128","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research"}]},{"@id":"https://cir.nii.ac.jp/crid/1362262945763258624","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"r8s: inferring absolute rates of molecular evolution and \ndivergence times in the absence of a molecular clock"}]},{"@id":"https://cir.nii.ac.jp/crid/1362262946167506688","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts"}]},{"@id":"https://cir.nii.ac.jp/crid/1362544418713542912","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species"}]},{"@id":"https://cir.nii.ac.jp/crid/1362544419184935808","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments"}]},{"@id":"https://cir.nii.ac.jp/crid/1362544419404116736","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation"}]},{"@id":"https://cir.nii.ac.jp/crid/1362544419854660352","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Transcriptome Responses to Combinations of Stresses in Arabidopsis"}]},{"@id":"https://cir.nii.ac.jp/crid/1362544420451982848","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Velvet: Algorithms for de novo short read assembly using de Bruijn graphs"}]},{"@id":"https://cir.nii.ac.jp/crid/1362825893419398784","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"cis-Element- and Transcriptome-Based Screening of Root Hair-Specific Genes and Their Functional Characterization in Arabidopsis"}]},{"@id":"https://cir.nii.ac.jp/crid/1362825893426141312","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"The rice endophyte Harpophora oryzae genome reveals evolution from a pathogen to a mutualistic endophyte"}]},{"@id":"https://cir.nii.ac.jp/crid/1362825894973658368","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Use of within-array replicate spots for assessing differential expression in microarray experiments"}]},{"@id":"https://cir.nii.ac.jp/crid/1362825896219929728","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists"}]},{"@id":"https://cir.nii.ac.jp/crid/1362825896386327424","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses"}]},{"@id":"https://cir.nii.ac.jp/crid/1363107369877236096","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Broad compatibility in fungal root symbioses"}]},{"@id":"https://cir.nii.ac.jp/crid/1363388843622582528","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Clearcut: a fast implementation of relaxed neighbor joining"}]},{"@id":"https://cir.nii.ac.jp/crid/1363388843885616384","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"What lies beneath: belowground defense strategies in plants"}]},{"@id":"https://cir.nii.ac.jp/crid/1363388844116832896","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Detecting Patches of Protein Sites of Influenza A Viruses under Positive Selection"}]},{"@id":"https://cir.nii.ac.jp/crid/1363388845563728000","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"The development of mycorrhizal infection in cucumber: effects of P supply on root growth, formation of entry points and growth of infection units"}]},{"@id":"https://cir.nii.ac.jp/crid/1363670318875915520","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"eggNOG v4.0: nested orthology inference across 3686 organisms"}]},{"@id":"https://cir.nii.ac.jp/crid/1363670319515233024","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"The transcription factor HIG1/MYB51 regulates indolic glucosinolate biosynthesis in <i>Arabidopsis thaliana</i>"}]},{"@id":"https://cir.nii.ac.jp/crid/1363951794543225472","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"A Glucosinolate Metabolism Pathway in Living Plant Cells Mediates Broad-Spectrum Antifungal Defense"}]},{"@id":"https://cir.nii.ac.jp/crid/1363951795968254976","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"The Role of WRKY Transcription Factors in Plant Immunity"}]},{"@id":"https://cir.nii.ac.jp/crid/1364233268243002752","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"PILER: identification and classification of genomic repeats"}]},{"@id":"https://cir.nii.ac.jp/crid/1364233269090572800","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Fungal endophytes in potato roots studied by traditional isolation and cultivation-independent DNA-based methods"}]},{"@id":"https://cir.nii.ac.jp/crid/1364233269977017344","@type":"Article","relationType":["references"],"jpcoar:relatedTitle":[{"@value":"Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice"}]},{"@id":"https://cir.nii.ac.jp/crid/1390845712966883328","@type":"Article","resourceType":"学術雑誌論文(journal article)","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"ja","@value":"リン栄養枯渇条件下での根圏糸状菌による植物生長促進"},{"@language":"en","@value":"Plant growth promotion by beneficial fungi in phosphate-starved conditions"},{"@language":"ja-Kana","@value":"リン エイヨウ コカツ ジョウケン カ デ ノ コンケン シジョウキン ニ ヨル ショクブツ セイチョウ ソクシン"}]},{"@id":"https://cir.nii.ac.jp/crid/1390868671488052480","@type":"Article","relationType":["isReferencedBy"],"jpcoar:relatedTitle":[{"@language":"en","@value":"Dynamic shifts in plant-microbe relationships"}]}],"dataSourceIdentifier":[{"@type":"CROSSREF","@value":"10.1038/ncomms11362"},{"@type":"KAKEN","@value":"PRODUCT-20312593"},{"@type":"OPENAIRE","@value":"doi_dedup___::68d777d5f2798d7feb96c3734bb269f4"},{"@type":"CROSSREF","@value":"10.1111/tpj.13808_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.1073/pnas.1917259117_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.3389/fmicb.2021.682155_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.1101/2021.10.13.464185_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.1073/pnas.2319998121_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.3389/fpls.2024.1481650_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.3390/microorganisms7090362_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.1111/nph.19582_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.5511/plantbiotechnology.25.0428a_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.1093/gbe/evz087_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.1038/s41598-019-50076-5_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.1007/978-3-030-57246-4_6_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.1094/phytofr-12-21-0082-a_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.1007/s10265-024-01546-z_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.1101/2021.03.18.435704_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.1111/nph.13994_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.3186/jjphytopath.84.78_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.1007/s10327-022-01097-y_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.3390/microorganisms13020428_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"},{"@type":"CROSSREF","@value":"10.1016/j.pbi.2018.04.009_references_DOI_PvfixNghXDQFY8UdW3nYUWJQEuW"}]}