Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype Evolution.
Identifieur interne : 000562 ( Main/Exploration ); précédent : 000561; suivant : 000563Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype Evolution.
Auteurs : Lászl G. Nagy [Hongrie] ; Robert Riley [États-Unis] ; Philip J. Bergmann [États-Unis] ; Krisztina Krizsán [Hongrie] ; Francis M. Martin [France] ; Igor V. Grigoriev [États-Unis] ; Dan Cullen [États-Unis] ; David S. Hibbett [États-Unis]Source :
- Molecular biology and evolution [ 1537-1719 ] ; 2017.
Descripteurs français
- KwdFr :
- Bases de données d'acides nucléiques (MeSH), Biologie informatique (méthodes), Bois (microbiologie), Bois (métabolisme), Champignons (génétique), Champignons (métabolisme), Génome fongique (MeSH), Lignine (métabolisme), Maladies des plantes (microbiologie), Phylogenèse (MeSH), Protéines fongiques (génétique), Simulation numérique (MeSH), Études d'associations génétiques (MeSH), Évolution biologique (MeSH), Évolution moléculaire (MeSH).
- MESH :
- génétique : Champignons, Protéines fongiques.
- microbiologie : Bois, Maladies des plantes.
- métabolisme : Bois, Champignons, Lignine.
- méthodes : Biologie informatique.
- Bases de données d'acides nucléiques, Génome fongique, Phylogenèse, Simulation numérique, Études d'associations génétiques, Évolution biologique, Évolution moléculaire.
English descriptors
- KwdEn :
- Biological Evolution (MeSH), Computational Biology (methods), Computer Simulation (MeSH), Databases, Nucleic Acid (MeSH), Evolution, Molecular (MeSH), Fungal Proteins (genetics), Fungi (genetics), Fungi (metabolism), Genetic Association Studies (MeSH), Genome, Fungal (MeSH), Lignin (metabolism), Phylogeny (MeSH), Plant Diseases (microbiology), Wood (metabolism), Wood (microbiology).
- MESH :
- chemical , genetics : Fungal Proteins.
- genetics : Fungi.
- metabolism : Fungi, Lignin, Wood.
- methods : Computational Biology.
- microbiology : Plant Diseases, Wood.
- Biological Evolution, Computer Simulation, Databases, Nucleic Acid, Evolution, Molecular, Genetic Association Studies, Genome, Fungal, Phylogeny.
Abstract
Fungal decomposition of plant cell walls (PCW) is a complex process that has diverse industrial applications and huge impacts on the carbon cycle. White rot (WR) is a powerful mode of PCW decay in which lignin and carbohydrates are both degraded. Mechanistic studies of decay coupled with comparative genomic analyses have provided clues to the enzymatic components of WR systems and their evolutionary origins, but the complete suite of genes necessary for WR remains undetermined. Here, we use phylogenomic comparative methods, which we validate through simulations, to identify shifts in gene family diversification rates that are correlated with evolution of WR, using data from 62 fungal genomes. We detected 409 gene families that appear to be evolutionarily correlated with WR. The identified gene families encode well-characterized decay enzymes, e.g., fungal class II peroxidases and cellobiohydrolases, and enzymes involved in import and detoxification pathways, as well as 73 gene families that have no functional annotation. About 310 of the 409 identified gene families are present in the genome of the model WR fungus Phanerochaete chrysosporium and 192 of these (62%) have been shown to be upregulated under ligninolytic culture conditions, which corroborates the phylogeny-based functional inferences. These results illuminate the complexity of WR and suggest that its evolution has involved a general elaboration of the decay apparatus, including numerous gene families with as-yet unknown exact functions.
DOI: 10.1093/molbev/msw238
PubMed: 27834665
Affiliations:
- France, Hongrie, États-Unis
- Californie, Hauts-de-France, Massachusetts, Picardie, Wisconsin
- Champenoux
- Université Henri Poincaré
Links toward previous steps (curation, corpus...)
Le document en format XML
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Nagy</name><affiliation wicri:level="1"><nlm:affiliation>Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged, Hungary lnagy@brc.hu.</nlm:affiliation><country wicri:rule="url">Hongrie</country><wicri:regionArea>Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged</wicri:regionArea><wicri:noRegion>Szeged</wicri:noRegion></affiliation></author><author><name sortKey="Riley, Robert" sort="Riley, Robert" uniqKey="Riley R" first="Robert" last="Riley">Robert Riley</name><affiliation wicri:level="2"><nlm:affiliation>US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>US Department of Energy (DOE) Joint Genome Institute, Walnut Creek</wicri:cityArea></affiliation></author><author><name sortKey="Bergmann, Philip J" sort="Bergmann, Philip J" uniqKey="Bergmann P" first="Philip J" last="Bergmann">Philip J. 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Martin</name><affiliation wicri:level="4"><nlm:affiliation>Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 Université Henri Poincaré, Interactions Arbres/Micro-organismes, 02854 Champenoux, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 Université Henri Poincaré, Interactions Arbres/Micro-organismes, 02854 Champenoux</wicri:regionArea><placeName><region type="region" nuts="2">Hauts-de-France</region><region type="old region" nuts="2">Picardie</region><settlement type="city">Champenoux</settlement></placeName><orgName type="university">Université Henri Poincaré</orgName></affiliation></author><author><name sortKey="Grigoriev, Igor V" sort="Grigoriev, Igor V" uniqKey="Grigoriev I" first="Igor V" last="Grigoriev">Igor V. Grigoriev</name><affiliation wicri:level="2"><nlm:affiliation>US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>US Department of Energy (DOE) Joint Genome Institute, Walnut Creek</wicri:cityArea></affiliation></author><author><name sortKey="Cullen, Dan" sort="Cullen, Dan" uniqKey="Cullen D" first="Dan" last="Cullen">Dan Cullen</name><affiliation wicri:level="2"><nlm:affiliation>US Department of Agriculture (USDA) Forest Products Laboratory, Madison, WI.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Wisconsin</region></placeName><wicri:cityArea>US Department of Agriculture (USDA) Forest Products Laboratory, Madison</wicri:cityArea></affiliation></author><author><name sortKey="Hibbett, David S" sort="Hibbett, David S" uniqKey="Hibbett D" first="David S" last="Hibbett">David S. Hibbett</name><affiliation wicri:level="2"><nlm:affiliation>Biology Department, Clark University, Worcester, MA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Biology Department, Clark University, Worcester</wicri:cityArea></affiliation></author></analytic><series><title level="j">Molecular biology and evolution</title><idno type="eISSN">1537-1719</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Biological Evolution (MeSH)</term><term>Computational Biology (methods)</term><term>Computer Simulation (MeSH)</term><term>Databases, Nucleic Acid (MeSH)</term><term>Evolution, Molecular (MeSH)</term><term>Fungal Proteins (genetics)</term><term>Fungi (genetics)</term><term>Fungi (metabolism)</term><term>Genetic Association Studies (MeSH)</term><term>Genome, Fungal (MeSH)</term><term>Lignin (metabolism)</term><term>Phylogeny (MeSH)</term><term>Plant Diseases (microbiology)</term><term>Wood (metabolism)</term><term>Wood (microbiology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bases de données d'acides nucléiques (MeSH)</term><term>Biologie informatique (méthodes)</term><term>Bois (microbiologie)</term><term>Bois (métabolisme)</term><term>Champignons (génétique)</term><term>Champignons (métabolisme)</term><term>Génome fongique (MeSH)</term><term>Lignine (métabolisme)</term><term>Maladies des plantes (microbiologie)</term><term>Phylogenèse (MeSH)</term><term>Protéines fongiques (génétique)</term><term>Simulation numérique (MeSH)</term><term>Études d'associations génétiques (MeSH)</term><term>Évolution biologique (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Fungal Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fungi</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Champignons</term><term>Protéines fongiques</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Fungi</term><term>Lignin</term><term>Wood</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Bois</term><term>Maladies des plantes</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Diseases</term><term>Wood</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Bois</term><term>Champignons</term><term>Lignine</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Biologie informatique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Biological Evolution</term><term>Computer Simulation</term><term>Databases, Nucleic Acid</term><term>Evolution, Molecular</term><term>Genetic Association Studies</term><term>Genome, Fungal</term><term>Phylogeny</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données d'acides nucléiques</term><term>Génome fongique</term><term>Phylogenèse</term><term>Simulation numérique</term><term>Études d'associations génétiques</term><term>Évolution biologique</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Fungal decomposition of plant cell walls (PCW) is a complex process that has diverse industrial applications and huge impacts on the carbon cycle. White rot (WR) is a powerful mode of PCW decay in which lignin and carbohydrates are both degraded. Mechanistic studies of decay coupled with comparative genomic analyses have provided clues to the enzymatic components of WR systems and their evolutionary origins, but the complete suite of genes necessary for WR remains undetermined. Here, we use phylogenomic comparative methods, which we validate through simulations, to identify shifts in gene family diversification rates that are correlated with evolution of WR, using data from 62 fungal genomes. We detected 409 gene families that appear to be evolutionarily correlated with WR. The identified gene families encode well-characterized decay enzymes, e.g., fungal class II peroxidases and cellobiohydrolases, and enzymes involved in import and detoxification pathways, as well as 73 gene families that have no functional annotation. About 310 of the 409 identified gene families are present in the genome of the model WR fungus Phanerochaete chrysosporium and 192 of these (62%) have been shown to be upregulated under ligninolytic culture conditions, which corroborates the phylogeny-based functional inferences. These results illuminate the complexity of WR and suggest that its evolution has involved a general elaboration of the decay apparatus, including numerous gene families with as-yet unknown exact functions.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27834665</PMID><DateCompleted><Year>2017</Year><Month>07</Month><Day>14</Day></DateCompleted><DateRevised><Year>2018</Year><Month>03</Month><Day>28</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1537-1719</ISSN><JournalIssue CitedMedium="Internet"><Volume>34</Volume><Issue>1</Issue><PubDate><Year>2017</Year><Month>01</Month></PubDate></JournalIssue><Title>Molecular biology and evolution</Title><ISOAbbreviation>Mol Biol Evol</ISOAbbreviation></Journal><ArticleTitle>Genetic Bases of Fungal White Rot Wood Decay Predicted by Phylogenomic Analysis of Correlated Gene-Phenotype Evolution.</ArticleTitle><Pagination><MedlinePgn>35-44</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/molbev/msw238</ELocationID><Abstract><AbstractText>Fungal decomposition of plant cell walls (PCW) is a complex process that has diverse industrial applications and huge impacts on the carbon cycle. White rot (WR) is a powerful mode of PCW decay in which lignin and carbohydrates are both degraded. Mechanistic studies of decay coupled with comparative genomic analyses have provided clues to the enzymatic components of WR systems and their evolutionary origins, but the complete suite of genes necessary for WR remains undetermined. Here, we use phylogenomic comparative methods, which we validate through simulations, to identify shifts in gene family diversification rates that are correlated with evolution of WR, using data from 62 fungal genomes. We detected 409 gene families that appear to be evolutionarily correlated with WR. The identified gene families encode well-characterized decay enzymes, e.g., fungal class II peroxidases and cellobiohydrolases, and enzymes involved in import and detoxification pathways, as well as 73 gene families that have no functional annotation. About 310 of the 409 identified gene families are present in the genome of the model WR fungus Phanerochaete chrysosporium and 192 of these (62%) have been shown to be upregulated under ligninolytic culture conditions, which corroborates the phylogeny-based functional inferences. These results illuminate the complexity of WR and suggest that its evolution has involved a general elaboration of the decay apparatus, including numerous gene families with as-yet unknown exact functions.</AbstractText><CopyrightInformation>© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Nagy</LastName><ForeName>László G</ForeName><Initials>LG</Initials><AffiliationInfo><Affiliation>Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged, Hungary lnagy@brc.hu.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Riley</LastName><ForeName>Robert</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bergmann</LastName><ForeName>Philip J</ForeName><Initials>PJ</Initials><AffiliationInfo><Affiliation>Biology Department, Clark University, Worcester, MA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Krizsán</LastName><ForeName>Krisztina</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Synthetic and Systems Biology Unit, Institute of Biochemistry, BRC-HAS, Szeged, Hungary.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Martin</LastName><ForeName>Francis M</ForeName><Initials>FM</Initials><AffiliationInfo><Affiliation>Institut National de la Recherche Agronomique, Unité Mixte de Recherche 1136 Université Henri Poincaré, Interactions Arbres/Micro-organismes, 02854 Champenoux, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grigoriev</LastName><ForeName>Igor V</ForeName><Initials>IV</Initials><AffiliationInfo><Affiliation>US Department of Energy (DOE) Joint Genome Institute, Walnut Creek, CA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cullen</LastName><ForeName>Dan</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>US Department of Agriculture (USDA) Forest Products Laboratory, Madison, WI.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hibbett</LastName><ForeName>David S</ForeName><Initials>DS</Initials><AffiliationInfo><Affiliation>Biology Department, Clark University, Worcester, MA.</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><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>11</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Biol Evol</MedlineTA><NlmUniqueID>8501455</NlmUniqueID><ISSNLinking>0737-4038</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005656">Fungal Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>9005-53-2</RegistryNumber><NameOfSubstance UI="D008031">Lignin</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="CommentIn"><RefSource>Mol Biol Evol. 2017 Jan;34(1):241</RefSource><PMID Version="1">28053014</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D005075" MajorTopicYN="N">Biological Evolution</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="N">Computer Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D030561" MajorTopicYN="N">Databases, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005656" MajorTopicYN="N">Fungal Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005658" MajorTopicYN="N">Fungi</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D056726" MajorTopicYN="N">Genetic Association Studies</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016681" MajorTopicYN="N">Genome, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008031" MajorTopicYN="N">Lignin</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">bioinformatics</Keyword><Keyword MajorTopicYN="Y">comparative genomics</Keyword><Keyword MajorTopicYN="Y">fungal enzymes</Keyword><Keyword MajorTopicYN="Y">protein of unknown function</Keyword><Keyword MajorTopicYN="Y">wood-decay</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>11</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2017</Year><Month>7</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>11</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27834665</ArticleId><ArticleId IdType="pii">msw238</ArticleId><ArticleId IdType="doi">10.1093/molbev/msw238</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li><li>Hongrie</li><li>États-Unis</li></country><region><li>Californie</li><li>Hauts-de-France</li><li>Massachusetts</li><li>Picardie</li><li>Wisconsin</li></region><settlement><li>Champenoux</li></settlement><orgName><li>Université Henri Poincaré</li></orgName></list><tree><country name="Hongrie"><noRegion><name sortKey="Nagy, Laszl G" sort="Nagy, Laszl G" uniqKey="Nagy L" first="Lászl G" last="Nagy">Lászl G. Nagy</name></noRegion><name sortKey="Krizsan, Krisztina" sort="Krizsan, Krisztina" uniqKey="Krizsan K" first="Krisztina" last="Krizsán">Krisztina Krizsán</name></country><country name="États-Unis"><region name="Californie"><name sortKey="Riley, Robert" sort="Riley, Robert" uniqKey="Riley R" first="Robert" last="Riley">Robert Riley</name></region><name sortKey="Bergmann, Philip J" sort="Bergmann, Philip J" uniqKey="Bergmann P" first="Philip J" last="Bergmann">Philip J. Bergmann</name><name sortKey="Cullen, Dan" sort="Cullen, Dan" uniqKey="Cullen D" first="Dan" last="Cullen">Dan Cullen</name><name sortKey="Grigoriev, Igor V" sort="Grigoriev, Igor V" uniqKey="Grigoriev I" first="Igor V" last="Grigoriev">Igor V. Grigoriev</name><name sortKey="Hibbett, David S" sort="Hibbett, David S" uniqKey="Hibbett D" first="David S" last="Hibbett">David S. Hibbett</name></country><country name="France"><region name="Hauts-de-France"><name sortKey="Martin, Francis M" sort="Martin, Francis M" uniqKey="Martin F" first="Francis M" last="Martin">Francis M. Martin</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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