RNA-seq Transcriptional Profiling of an Arbuscular Mycorrhiza Provides Insights into Regulated and Coordinated Gene Expression in Lotus japonicus and Rhizophagus irregularis.
Identifieur interne : 001432 ( Main/Exploration ); précédent : 001431; suivant : 001433RNA-seq Transcriptional Profiling of an Arbuscular Mycorrhiza Provides Insights into Regulated and Coordinated Gene Expression in Lotus japonicus and Rhizophagus irregularis.
Auteurs : Yoshihiro Handa [Japon] ; Hiroyo Nishide [Japon] ; Naoya Takeda [Japon] ; Yutaka Suzuki [Japon] ; Masayoshi Kawaguchi [Japon] ; Katsuharu Saito [Japon]Source :
- Plant & cell physiology [ 1471-9053 ] ; 2015.
Descripteurs français
- KwdFr :
- ARN des plantes (génétique), ARN fongique (génétique), Analyse de séquence d'ARN (MeSH), Données de séquences moléculaires (MeSH), Facteurs de transcription (génétique), Glomeromycota (physiologie), Loteae (génétique), Loteae (microbiologie), Mycorhizes (physiologie), Nodules racinaires de plante (génétique), Nodules racinaires de plante (microbiologie), Plant (génétique), Plant (microbiologie), Protéines fongiques (génétique), Protéines végétales (génétique), Racines de plante (génétique), Racines de plante (microbiologie), Régulation de l'expression des gènes végétaux (MeSH), Symbiose (MeSH), Séquence nucléotidique (MeSH), Séquençage nucléotidique à haut débit (MeSH), Transcriptome (MeSH).
- MESH :
- génétique : ARN des plantes, ARN fongique, Facteurs de transcription, Loteae, Nodules racinaires de plante, Plant, Protéines fongiques, Protéines végétales, Racines de plante.
- microbiologie : Loteae, Nodules racinaires de plante, Plant, Racines de plante.
- physiologie : Glomeromycota, Mycorhizes.
- Analyse de séquence d'ARN, Données de séquences moléculaires, Régulation de l'expression des gènes végétaux, Symbiose, Séquence nucléotidique, Séquençage nucléotidique à haut débit, Transcriptome.
English descriptors
- KwdEn :
- Base Sequence (MeSH), Fungal Proteins (genetics), Gene Expression Regulation, Plant (MeSH), Glomeromycota (physiology), High-Throughput Nucleotide Sequencing (MeSH), Lotus (genetics), Lotus (microbiology), Molecular Sequence Data (MeSH), Mycorrhizae (physiology), Plant Proteins (genetics), Plant Roots (genetics), Plant Roots (microbiology), RNA, Fungal (genetics), RNA, Plant (genetics), Root Nodules, Plant (genetics), Root Nodules, Plant (microbiology), Seedlings (genetics), Seedlings (microbiology), Sequence Analysis, RNA (MeSH), Symbiosis (MeSH), Transcription Factors (genetics), Transcriptome (MeSH).
- MESH :
- chemical , genetics : Fungal Proteins, Plant Proteins, RNA, Fungal, RNA, Plant, Transcription Factors.
- genetics : Lotus, Plant Roots, Root Nodules, Plant, Seedlings.
- microbiology : Lotus, Plant Roots, Root Nodules, Plant, Seedlings.
- physiology : Glomeromycota, Mycorrhizae.
- Base Sequence, Gene Expression Regulation, Plant, High-Throughput Nucleotide Sequencing, Molecular Sequence Data, Sequence Analysis, RNA, Symbiosis, Transcriptome.
Abstract
Gene expression during arbuscular mycorrhizal development is highly orchestrated in both plants and arbuscular mycorrhizal fungi. To elucidate the gene expression profiles of the symbiotic association, we performed a digital gene expression analysis of Lotus japonicus and Rhizophagus irregularis using a HiSeq 2000 next-generation sequencer with a Cufflinks assembly and de novo transcriptome assembly. There were 3,641 genes differentially expressed during arbuscular mycorrhizal development in L. japonicus, approximately 80% of which were up-regulated. The up-regulated genes included secreted proteins, transporters, proteins involved in lipid and amino acid metabolism, ribosomes and histones. We also detected many genes that were differentially expressed in small-secreted peptides and transcription factors, which may be involved in signal transduction or transcription regulation during symbiosis. Co-regulated genes between arbuscular mycorrhizal and root nodule symbiosis were not particularly abundant, but transcripts encoding for membrane traffic-related proteins, transporters and iron transport-related proteins were found to be highly co-up-regulated. In transcripts of arbuscular mycorrhizal fungi, expansion of cytochrome P450 was observed, which may contribute to various metabolic pathways required to accommodate roots and soil. The comprehensive gene expression data of both plants and arbuscular mycorrhizal fungi provide a powerful platform for investigating the functional and molecular mechanisms underlying arbuscular mycorrhizal symbiosis.
DOI: 10.1093/pcp/pcv071
PubMed: 26009592
Affiliations:
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(MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN des plantes (génétique)</term><term>ARN fongique (génétique)</term><term>Analyse de séquence d'ARN (MeSH)</term><term>Données de séquences moléculaires (MeSH)</term><term>Facteurs de transcription (génétique)</term><term>Glomeromycota (physiologie)</term><term>Loteae (génétique)</term><term>Loteae (microbiologie)</term><term>Mycorhizes (physiologie)</term><term>Nodules racinaires de plante (génétique)</term><term>Nodules racinaires de plante (microbiologie)</term><term>Plant (génétique)</term><term>Plant (microbiologie)</term><term>Protéines fongiques (génétique)</term><term>Protéines végétales (génétique)</term><term>Racines de plante (génétique)</term><term>Racines de plante (microbiologie)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Symbiose (MeSH)</term><term>Séquence nucléotidique (MeSH)</term><term>Séquençage nucléotidique à haut débit (MeSH)</term><term>Transcriptome (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Fungal Proteins</term><term>Plant Proteins</term><term>RNA, Fungal</term><term>RNA, Plant</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Lotus</term><term>Plant Roots</term><term>Root Nodules, Plant</term><term>Seedlings</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN des plantes</term><term>ARN fongique</term><term>Facteurs de transcription</term><term>Loteae</term><term>Nodules racinaires de plante</term><term>Plant</term><term>Protéines fongiques</term><term>Protéines végétales</term><term>Racines de plante</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Loteae</term><term>Nodules racinaires de plante</term><term>Plant</term><term>Racines de plante</term></keywords><keywords scheme="MESH" qualifier="microbiology" 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débit</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Gene expression during arbuscular mycorrhizal development is highly orchestrated in both plants and arbuscular mycorrhizal fungi. To elucidate the gene expression profiles of the symbiotic association, we performed a digital gene expression analysis of Lotus japonicus and Rhizophagus irregularis using a HiSeq 2000 next-generation sequencer with a Cufflinks assembly and de novo transcriptome assembly. There were 3,641 genes differentially expressed during arbuscular mycorrhizal development in L. japonicus, approximately 80% of which were up-regulated. The up-regulated genes included secreted proteins, transporters, proteins involved in lipid and amino acid metabolism, ribosomes and histones. We also detected many genes that were differentially expressed in small-secreted peptides and transcription factors, which may be involved in signal transduction or transcription regulation during symbiosis. Co-regulated genes between arbuscular mycorrhizal and root nodule symbiosis were not particularly abundant, but transcripts encoding for membrane traffic-related proteins, transporters and iron transport-related proteins were found to be highly co-up-regulated. In transcripts of arbuscular mycorrhizal fungi, expansion of cytochrome P450 was observed, which may contribute to various metabolic pathways required to accommodate roots and soil. The comprehensive gene expression data of both plants and arbuscular mycorrhizal fungi provide a powerful platform for investigating the functional and molecular mechanisms underlying arbuscular mycorrhizal symbiosis. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26009592</PMID><DateCompleted><Year>2016</Year><Month>07</Month><Day>01</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>02</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1471-9053</ISSN><JournalIssue CitedMedium="Internet"><Volume>56</Volume><Issue>8</Issue><PubDate><Year>2015</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Plant & cell physiology</Title><ISOAbbreviation>Plant Cell Physiol</ISOAbbreviation></Journal><ArticleTitle>RNA-seq Transcriptional Profiling of an Arbuscular Mycorrhiza Provides Insights into Regulated and Coordinated Gene Expression in Lotus japonicus and Rhizophagus irregularis.</ArticleTitle><Pagination><MedlinePgn>1490-511</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/pcp/pcv071</ELocationID><Abstract><AbstractText>Gene expression during arbuscular mycorrhizal development is highly orchestrated in both plants and arbuscular mycorrhizal fungi. To elucidate the gene expression profiles of the symbiotic association, we performed a digital gene expression analysis of Lotus japonicus and Rhizophagus irregularis using a HiSeq 2000 next-generation sequencer with a Cufflinks assembly and de novo transcriptome assembly. There were 3,641 genes differentially expressed during arbuscular mycorrhizal development in L. japonicus, approximately 80% of which were up-regulated. The up-regulated genes included secreted proteins, transporters, proteins involved in lipid and amino acid metabolism, ribosomes and histones. We also detected many genes that were differentially expressed in small-secreted peptides and transcription factors, which may be involved in signal transduction or transcription regulation during symbiosis. Co-regulated genes between arbuscular mycorrhizal and root nodule symbiosis were not particularly abundant, but transcripts encoding for membrane traffic-related proteins, transporters and iron transport-related proteins were found to be highly co-up-regulated. In transcripts of arbuscular mycorrhizal fungi, expansion of cytochrome P450 was observed, which may contribute to various metabolic pathways required to accommodate roots and soil. The comprehensive gene expression data of both plants and arbuscular mycorrhizal fungi provide a powerful platform for investigating the functional and molecular mechanisms underlying arbuscular mycorrhizal symbiosis. </AbstractText><CopyrightInformation>© The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Handa</LastName><ForeName>Yoshihiro</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nishide</LastName><ForeName>Hiroyo</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Data Integration and Analysis Facility, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Takeda</LastName><ForeName>Naoya</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Suzuki</LastName><ForeName>Yutaka</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kawaguchi</LastName><ForeName>Masayoshi</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Division of Symbiotic Systems, National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Saito</LastName><ForeName>Katsuharu</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Faculty of Agriculture, Shinshu University, Minamiminowa, Nagano 399-4598, Japan saitok@shinshu-u.ac.jp.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2015</Year><Month>05</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>Japan</Country><MedlineTA>Plant Cell Physiol</MedlineTA><NlmUniqueID>9430925</NlmUniqueID><ISSNLinking>0032-0781</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005656">Fungal Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012331">RNA, Fungal</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018749">RNA, Plant</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005656" MajorTopicYN="N">Fungal Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055137" MajorTopicYN="N">Glomeromycota</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000070116" MajorTopicYN="N">Lotus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012331" MajorTopicYN="N">RNA, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018749" MajorTopicYN="N">RNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D053204" MajorTopicYN="N">Root Nodules, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D036226" MajorTopicYN="N">Seedlings</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013559" MajorTopicYN="N">Symbiosis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="Y">Transcriptome</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Arbuscular mycorrhiza</Keyword><Keyword MajorTopicYN="N">Lotus japonicus</Keyword><Keyword MajorTopicYN="N">Rhizophagus irregularis</Keyword><Keyword MajorTopicYN="N">Root nodule</Keyword><Keyword MajorTopicYN="N">Symbiosis</Keyword><Keyword MajorTopicYN="N">Transcriptome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year><Month>12</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2015</Year><Month>05</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2015</Year><Month>5</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2015</Year><Month>5</Month><Day>27</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>7</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">26009592</ArticleId><ArticleId IdType="pii">pcv071</ArticleId><ArticleId IdType="doi">10.1093/pcp/pcv071</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Japon</li></country><region><li>Région de Kantō</li></region><settlement><li>Tokyo</li></settlement><orgName><li>Université de Tokyo</li></orgName></list><tree><country name="Japon"><noRegion><name sortKey="Handa, Yoshihiro" sort="Handa, Yoshihiro" uniqKey="Handa Y" first="Yoshihiro" last="Handa">Yoshihiro Handa</name></noRegion><name sortKey="Kawaguchi, Masayoshi" sort="Kawaguchi, Masayoshi" uniqKey="Kawaguchi M" first="Masayoshi" last="Kawaguchi">Masayoshi Kawaguchi</name><name sortKey="Nishide, Hiroyo" sort="Nishide, Hiroyo" uniqKey="Nishide H" first="Hiroyo" last="Nishide">Hiroyo Nishide</name><name sortKey="Saito, Katsuharu" sort="Saito, Katsuharu" uniqKey="Saito K" first="Katsuharu" last="Saito">Katsuharu Saito</name><name sortKey="Suzuki, Yutaka" sort="Suzuki, Yutaka" uniqKey="Suzuki Y" first="Yutaka" last="Suzuki">Yutaka Suzuki</name><name sortKey="Takeda, Naoya" sort="Takeda, Naoya" uniqKey="Takeda N" first="Naoya" last="Takeda">Naoya Takeda</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|texte= RNA-seq Transcriptional Profiling of an Arbuscular Mycorrhiza Provides Insights into Regulated and Coordinated Gene Expression in Lotus japonicus and Rhizophagus irregularis.
}}
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