Comparative genomics of 40 edible and medicinal mushrooms provide an insight into the evolution of lignocellulose decomposition mechanisms.
Identifieur interne : 000309 ( Main/Exploration ); précédent : 000308; suivant : 000310Comparative genomics of 40 edible and medicinal mushrooms provide an insight into the evolution of lignocellulose decomposition mechanisms.
Auteurs : Qi An [République populaire de Chine] ; Xue-Jun Wu [République populaire de Chine] ; Yu-Cheng Dai [République populaire de Chine]Source :
- 3 Biotech [ 2190-572X ] ; 2019.
Abstract
Diversity comparison and phylogenetic analyses of carbohydrate-active enzymes (CAZymes), auxiliary activities (AAs) and cytochromes P450 among 40 fungi, which are based on different nutritional pathways, help clarify and explain their divergence and improvement of various life-styles. Molecular clock analyses allow us to understand the evolutionary and developmental rules in decomposition gene families. Our results suggested that fungi in different ecological types acquired an obvious preference on specific decomposing gene families during evolutionary selection. White rot and litter saprotrophic fungi possessed more complete types of varied degradation gene families and were superior in quantities. With evolution and development of lignocellulose decomposition mechanism, certain families (like CBM1, GH6, GH7, GH10, and CYP53) disappeared in brown rot fungi and symbiotic fungi. In addition, the earlier time of phylogenetic divergence determined the more integrated and larger decomposition families. And various gains and losses in gene quantity of varied decomposition families led in particularly phylogenetic clades or nodes, then accelerated in forming varied ecotypes of species.
DOI: 10.1007/s13205-019-1689-5
PubMed: 30944804
PubMed Central: PMC6439079
Affiliations:
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type="city">Pékin</settlement></placeName></affiliation><affiliation><nlm:affiliation>2Edible and Medicinal Fungi Research and Development Center, Universities/Colleges in Hebei Province, Langfang Normal University, Langfang, 065000 Hebei People's Republic of China.</nlm:affiliation><wicri:noCountry code="subField">065000 Hebei People's Republic of China</wicri:noCountry></affiliation></author><author><name sortKey="Wu, Xue Jun" sort="Wu, Xue Jun" uniqKey="Wu X" first="Xue-Jun" last="Wu">Xue-Jun Wu</name><affiliation wicri:level="3"><nlm:affiliation>1Institute of Microbiology, Beijing Forestry University, Beijing, 100083 People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>1Institute of Microbiology, Beijing Forestry University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Dai, Yu Cheng" sort="Dai, Yu Cheng" uniqKey="Dai Y" first="Yu-Cheng" last="Dai">Yu-Cheng Dai</name><affiliation wicri:level="3"><nlm:affiliation>1Institute of Microbiology, Beijing Forestry University, Beijing, 100083 People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>1Institute of Microbiology, Beijing Forestry University, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:affiliation>3Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, 35 Qinghuadong Road, Haidian District, Beijing, 100083 People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>3Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, 35 Qinghuadong Road, Haidian District, Beijing</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">3 Biotech</title><idno type="ISSN">2190-572X</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Diversity comparison and phylogenetic analyses of carbohydrate-active enzymes (CAZymes), auxiliary activities (AAs) and cytochromes P450 among 40 fungi, which are based on different nutritional pathways, help clarify and explain their divergence and improvement of various life-styles. Molecular clock analyses allow us to understand the evolutionary and developmental rules in decomposition gene families. Our results suggested that fungi in different ecological types acquired an obvious preference on specific decomposing gene families during evolutionary selection. White rot and litter saprotrophic fungi possessed more complete types of varied degradation gene families and were superior in quantities. With evolution and development of lignocellulose decomposition mechanism, certain families (like CBM1, GH6, GH7, GH10, and CYP53) disappeared in brown rot fungi and symbiotic fungi. In addition, the earlier time of phylogenetic divergence determined the more integrated and larger decomposition families. And various gains and losses in gene quantity of varied decomposition families led in particularly phylogenetic clades or nodes, then accelerated in forming varied ecotypes of species.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">30944804</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">2190-572X</ISSN><JournalIssue CitedMedium="Print"><Volume>9</Volume><Issue>4</Issue><PubDate><Year>2019</Year><Month>Apr</Month></PubDate></JournalIssue><Title>3 Biotech</Title><ISOAbbreviation>3 Biotech</ISOAbbreviation></Journal><ArticleTitle>Comparative genomics of 40 edible and medicinal mushrooms provide an insight into the evolution of lignocellulose decomposition mechanisms.</ArticleTitle><Pagination><MedlinePgn>157</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s13205-019-1689-5</ELocationID><Abstract><AbstractText>Diversity comparison and phylogenetic analyses of carbohydrate-active enzymes (CAZymes), auxiliary activities (AAs) and cytochromes P450 among 40 fungi, which are based on different nutritional pathways, help clarify and explain their divergence and improvement of various life-styles. Molecular clock analyses allow us to understand the evolutionary and developmental rules in decomposition gene families. Our results suggested that fungi in different ecological types acquired an obvious preference on specific decomposing gene families during evolutionary selection. White rot and litter saprotrophic fungi possessed more complete types of varied degradation gene families and were superior in quantities. With evolution and development of lignocellulose decomposition mechanism, certain families (like CBM1, GH6, GH7, GH10, and CYP53) disappeared in brown rot fungi and symbiotic fungi. In addition, the earlier time of phylogenetic divergence determined the more integrated and larger decomposition families. And various gains and losses in gene quantity of varied decomposition families led in particularly phylogenetic clades or nodes, then accelerated in forming varied ecotypes of species.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y" EqualContrib="Y"><LastName>An</LastName><ForeName>Qi</ForeName><Initials>Q</Initials><Identifier Source="ORCID">0000-0001-5917-2497</Identifier><AffiliationInfo><Affiliation>1Institute of Microbiology, Beijing Forestry University, Beijing, 100083 People's Republic of China.</Affiliation><Identifier Source="ISNI">0000 0001 1456 856X</Identifier><Identifier Source="GRID">grid.66741.32</Identifier></AffiliationInfo><AffiliationInfo><Affiliation>2Edible and Medicinal Fungi Research and Development Center, Universities/Colleges in Hebei Province, Langfang Normal University, Langfang, 065000 Hebei People's Republic of China.</Affiliation><Identifier Source="GRID">grid.440817.e</Identifier></AffiliationInfo></Author><Author ValidYN="Y" EqualContrib="Y"><LastName>Wu</LastName><ForeName>Xue-Jun</ForeName><Initials>XJ</Initials><AffiliationInfo><Affiliation>1Institute of Microbiology, Beijing Forestry University, Beijing, 100083 People's Republic of China.</Affiliation><Identifier Source="ISNI">0000 0001 1456 856X</Identifier><Identifier Source="GRID">grid.66741.32</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dai</LastName><ForeName>Yu-Cheng</ForeName><Initials>YC</Initials><Identifier Source="ORCID">0000-0002-6523-0320</Identifier><AffiliationInfo><Affiliation>1Institute of Microbiology, Beijing Forestry University, Beijing, 100083 People's Republic of China.</Affiliation><Identifier Source="ISNI">0000 0001 1456 856X</Identifier><Identifier Source="GRID">grid.66741.32</Identifier></AffiliationInfo><AffiliationInfo><Affiliation>3Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, 35 Qinghuadong Road, Haidian District, Beijing, 100083 People's Republic of China.</Affiliation><Identifier Source="ISNI">0000 0001 1456 856X</Identifier><Identifier Source="GRID">grid.66741.32</Identifier></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>03</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>3 Biotech</MedlineTA><NlmUniqueID>101565857</NlmUniqueID><ISSNLinking>2190-5738</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Degrading gene families</Keyword><Keyword MajorTopicYN="N">Eco-lifestyle</Keyword><Keyword MajorTopicYN="N">Edible and medical mushrooms</Keyword><Keyword MajorTopicYN="N">Gene evolution</Keyword><Keyword MajorTopicYN="N">Phylogeny</Keyword></KeywordList><CoiStatement>Compliance with ethical standardsThe authors declare that no conflicts of interest exist.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>12</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>03</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>4</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>4</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>4</Month><Day>5</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30944804</ArticleId><ArticleId IdType="doi">10.1007/s13205-019-1689-5</ArticleId><ArticleId IdType="pii">1689</ArticleId><ArticleId IdType="pmc">PMC6439079</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Mol Biol Evol. 2000 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An</name></noRegion><name sortKey="Dai, Yu Cheng" sort="Dai, Yu Cheng" uniqKey="Dai Y" first="Yu-Cheng" last="Dai">Yu-Cheng Dai</name><name sortKey="Dai, Yu Cheng" sort="Dai, Yu Cheng" uniqKey="Dai Y" first="Yu-Cheng" last="Dai">Yu-Cheng Dai</name><name sortKey="Wu, Xue Jun" sort="Wu, Xue Jun" uniqKey="Wu X" first="Xue-Jun" last="Wu">Xue-Jun Wu</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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