Dual RNA-seq reveals large-scale non-conserved genotype × genotype-specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis.
Identifieur interne : 000586 ( Main/Exploration ); précédent : 000585; suivant : 000587Dual RNA-seq reveals large-scale non-conserved genotype × genotype-specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis.
Auteurs : Ivan D. Mateus [Suisse] ; Frédéric G. Masclaux [Suisse] ; Consolée Aletti [Suisse] ; Edward C. Rojas [Suisse] ; Romain Savary [Suisse] ; Cindy Dupuis [Suisse] ; Ian R. Sanders [Suisse]Source :
- The ISME journal [ 1751-7370 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Glomeromycota, Manihot, Mycorhizes, Symbiose.
- microbiologie : Manihot.
- Analyse de séquence d'ARN, Génotype, Transcription génétique.
English descriptors
- KwdEn :
- MESH :
- genetics : Glomeromycota, Manihot, Mycorrhizae, Symbiosis.
- microbiology : Manihot.
- Genotype, Sequence Analysis, RNA, Transcription, Genetic.
Abstract
Arbuscular mycorrhizal fungi (AMF) impact plant growth and are a major driver of plant diversity and productivity. We quantified the contribution of intra-specific genetic variability in cassava (Manihot esculenta) and Rhizophagus irregularis to gene reprogramming in symbioses using dual RNA-sequencing. A large number of cassava genes exhibited altered transcriptional responses to the fungus but transcription of most of these plant genes (72%) responded in a different direction or magnitude depending on the plant genotype. Two AMF isolates displayed large differences in their transcription, but the direction and magnitude of the transcriptional responses for a large number of these genes was also strongly influenced by the genotype of the plant host. This indicates that unlike the highly conserved plant genes necessary for the symbiosis establishment, most of the plant and fungal gene transcriptional responses are not conserved and are greatly influenced by plant and fungal genetic differences, even at the within-species level. The transcriptional variability detected allowed us to identify an extensive gene network showing the interplay in plant-fungal reprogramming in the symbiosis. Key genes illustrated that the two organisms jointly program their cytoskeleton organization during growth of the fungus inside roots. Our study reveals that plant and fungal genetic variation has a strong role in shaping the genetic reprograming in response to symbiosis, indicating considerable genotype × genotype interactions in the mycorrhizal symbiosis. Such variation needs to be considered in order to understand the molecular mechanisms between AMF and their plant hosts in natural communities.
DOI: 10.1038/s41396-018-0342-3
PubMed: 30647457
PubMed Central: PMC6474227
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Mateus</name><affiliation wicri:level="3"><nlm:affiliation>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne</wicri:regionArea><placeName><settlement type="city">Lausanne</settlement><region nuts="3" type="region">Canton de Vaud</region></placeName></affiliation></author><author><name sortKey="Masclaux, Frederic G" sort="Masclaux, Frederic G" uniqKey="Masclaux F" first="Frédéric G" last="Masclaux">Frédéric G. Masclaux</name><affiliation wicri:level="3"><nlm:affiliation>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne</wicri:regionArea><placeName><settlement type="city">Lausanne</settlement><region nuts="3" type="region">Canton de Vaud</region></placeName></affiliation><affiliation wicri:level="3"><nlm:affiliation>Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne</wicri:regionArea><placeName><settlement type="city">Lausanne</settlement><region nuts="3" type="region">Canton de Vaud</region></placeName></affiliation></author><author><name sortKey="Aletti, Consolee" sort="Aletti, Consolee" uniqKey="Aletti C" first="Consolée" last="Aletti">Consolée Aletti</name><affiliation wicri:level="3"><nlm:affiliation>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne</wicri:regionArea><placeName><settlement type="city">Lausanne</settlement><region nuts="3" type="region">Canton de Vaud</region></placeName></affiliation></author><author><name sortKey="Rojas, Edward C" sort="Rojas, Edward C" uniqKey="Rojas E" first="Edward C" last="Rojas">Edward C. Rojas</name><affiliation wicri:level="3"><nlm:affiliation>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne</wicri:regionArea><placeName><settlement type="city">Lausanne</settlement><region nuts="3" type="region">Canton de Vaud</region></placeName></affiliation></author><author><name sortKey="Savary, Romain" sort="Savary, Romain" uniqKey="Savary R" first="Romain" last="Savary">Romain Savary</name><affiliation wicri:level="3"><nlm:affiliation>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne</wicri:regionArea><placeName><settlement type="city">Lausanne</settlement><region nuts="3" type="region">Canton de Vaud</region></placeName></affiliation></author><author><name sortKey="Dupuis, Cindy" sort="Dupuis, Cindy" uniqKey="Dupuis C" first="Cindy" last="Dupuis">Cindy Dupuis</name><affiliation wicri:level="3"><nlm:affiliation>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne</wicri:regionArea><placeName><settlement type="city">Lausanne</settlement><region nuts="3" type="region">Canton de Vaud</region></placeName></affiliation></author><author><name sortKey="Sanders, Ian R" sort="Sanders, Ian R" uniqKey="Sanders I" first="Ian R" last="Sanders">Ian R. Sanders</name><affiliation wicri:level="3"><nlm:affiliation>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland. ian.sanders@unil.ch.</nlm:affiliation><country xml:lang="fr">Suisse</country><wicri:regionArea>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne</wicri:regionArea><placeName><settlement type="city">Lausanne</settlement><region nuts="3" type="region">Canton de Vaud</region></placeName></affiliation></author></analytic><series><title level="j">The ISME journal</title><idno type="eISSN">1751-7370</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Genotype (MeSH)</term><term>Glomeromycota (genetics)</term><term>Manihot (genetics)</term><term>Manihot (microbiology)</term><term>Mycorrhizae (genetics)</term><term>Sequence Analysis, RNA (MeSH)</term><term>Symbiosis (genetics)</term><term>Transcription, Genetic (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ARN (MeSH)</term><term>Glomeromycota (génétique)</term><term>Génotype (MeSH)</term><term>Manihot (génétique)</term><term>Manihot (microbiologie)</term><term>Mycorhizes (génétique)</term><term>Symbiose (génétique)</term><term>Transcription génétique (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Glomeromycota</term><term>Manihot</term><term>Mycorrhizae</term><term>Symbiosis</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Glomeromycota</term><term>Manihot</term><term>Mycorhizes</term><term>Symbiose</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Manihot</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Manihot</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genotype</term><term>Sequence Analysis, RNA</term><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ARN</term><term>Génotype</term><term>Transcription génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Arbuscular mycorrhizal fungi (AMF) impact plant growth and are a major driver of plant diversity and productivity. We quantified the contribution of intra-specific genetic variability in cassava (Manihot esculenta) and Rhizophagus irregularis to gene reprogramming in symbioses using dual RNA-sequencing. A large number of cassava genes exhibited altered transcriptional responses to the fungus but transcription of most of these plant genes (72%) responded in a different direction or magnitude depending on the plant genotype. Two AMF isolates displayed large differences in their transcription, but the direction and magnitude of the transcriptional responses for a large number of these genes was also strongly influenced by the genotype of the plant host. This indicates that unlike the highly conserved plant genes necessary for the symbiosis establishment, most of the plant and fungal gene transcriptional responses are not conserved and are greatly influenced by plant and fungal genetic differences, even at the within-species level. The transcriptional variability detected allowed us to identify an extensive gene network showing the interplay in plant-fungal reprogramming in the symbiosis. Key genes illustrated that the two organisms jointly program their cytoskeleton organization during growth of the fungus inside roots. Our study reveals that plant and fungal genetic variation has a strong role in shaping the genetic reprograming in response to symbiosis, indicating considerable genotype × genotype interactions in the mycorrhizal symbiosis. Such variation needs to be considered in order to understand the molecular mechanisms between AMF and their plant hosts in natural communities.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">30647457</PMID><DateCompleted><Year>2019</Year><Month>10</Month><Day>25</Day></DateCompleted><DateRevised><Year>2020</Year><Month>03</Month><Day>09</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1751-7370</ISSN><JournalIssue CitedMedium="Internet"><Volume>13</Volume><Issue>5</Issue><PubDate><Year>2019</Year><Month>05</Month></PubDate></JournalIssue><Title>The ISME journal</Title><ISOAbbreviation>ISME J</ISOAbbreviation></Journal><ArticleTitle>Dual RNA-seq reveals large-scale non-conserved genotype × genotype-specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis.</ArticleTitle><Pagination><MedlinePgn>1226-1238</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1038/s41396-018-0342-3</ELocationID><Abstract><AbstractText>Arbuscular mycorrhizal fungi (AMF) impact plant growth and are a major driver of plant diversity and productivity. We quantified the contribution of intra-specific genetic variability in cassava (Manihot esculenta) and Rhizophagus irregularis to gene reprogramming in symbioses using dual RNA-sequencing. A large number of cassava genes exhibited altered transcriptional responses to the fungus but transcription of most of these plant genes (72%) responded in a different direction or magnitude depending on the plant genotype. Two AMF isolates displayed large differences in their transcription, but the direction and magnitude of the transcriptional responses for a large number of these genes was also strongly influenced by the genotype of the plant host. This indicates that unlike the highly conserved plant genes necessary for the symbiosis establishment, most of the plant and fungal gene transcriptional responses are not conserved and are greatly influenced by plant and fungal genetic differences, even at the within-species level. The transcriptional variability detected allowed us to identify an extensive gene network showing the interplay in plant-fungal reprogramming in the symbiosis. Key genes illustrated that the two organisms jointly program their cytoskeleton organization during growth of the fungus inside roots. Our study reveals that plant and fungal genetic variation has a strong role in shaping the genetic reprograming in response to symbiosis, indicating considerable genotype × genotype interactions in the mycorrhizal symbiosis. Such variation needs to be considered in order to understand the molecular mechanisms between AMF and their plant hosts in natural communities.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Mateus</LastName><ForeName>Ivan D</ForeName><Initials>ID</Initials><AffiliationInfo><Affiliation>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Masclaux</LastName><ForeName>Frédéric G</ForeName><Initials>FG</Initials><AffiliationInfo><Affiliation>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Vital-IT, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Aletti</LastName><ForeName>Consolée</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rojas</LastName><ForeName>Edward C</ForeName><Initials>EC</Initials><AffiliationInfo><Affiliation>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Savary</LastName><ForeName>Romain</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dupuis</LastName><ForeName>Cindy</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Sanders</LastName><ForeName>Ian R</ForeName><Initials>IR</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-9591-8214</Identifier><AffiliationInfo><Affiliation>Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015, Lausanne, Switzerland. ian.sanders@unil.ch.</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>2019</Year><Month>01</Month><Day>15</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>ISME J</MedlineTA><NlmUniqueID>101301086</NlmUniqueID><ISSNLinking>1751-7362</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055137" MajorTopicYN="N">Glomeromycota</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002365" MajorTopicYN="N">Manihot</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013559" MajorTopicYN="N">Symbiosis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014158" MajorTopicYN="N">Transcription, Genetic</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>08</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>12</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2018</Year><Month>11</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>1</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>10</Month><Day>28</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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Mateus</name></region><name sortKey="Aletti, Consolee" sort="Aletti, Consolee" uniqKey="Aletti C" first="Consolée" last="Aletti">Consolée Aletti</name><name sortKey="Dupuis, Cindy" sort="Dupuis, Cindy" uniqKey="Dupuis C" first="Cindy" last="Dupuis">Cindy Dupuis</name><name sortKey="Masclaux, Frederic G" sort="Masclaux, Frederic G" uniqKey="Masclaux F" first="Frédéric G" last="Masclaux">Frédéric G. Masclaux</name><name sortKey="Masclaux, Frederic G" sort="Masclaux, Frederic G" uniqKey="Masclaux F" first="Frédéric G" last="Masclaux">Frédéric G. Masclaux</name><name sortKey="Rojas, Edward C" sort="Rojas, Edward C" uniqKey="Rojas E" first="Edward C" last="Rojas">Edward C. Rojas</name><name sortKey="Sanders, Ian R" sort="Sanders, Ian R" uniqKey="Sanders I" first="Ian R" last="Sanders">Ian R. 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