Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica.
Identifieur interne : 000424 ( Main/Exploration ); précédent : 000423; suivant : 000425Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus Flammulina elastica.
Auteurs : Young-Jin Park [Corée du Sud] ; Yong-Un Jeong [Corée du Sud] ; Won-Sik Kong [Corée du Sud]Source :
- International journal of molecular sciences [ 1422-0067 ] ; 2018.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ADN (MeSH), Bases de données génétiques (MeSH), Flammulina (enzymologie), Flammulina (génétique), Glycosidases (composition chimique), Glycosidases (génétique), Glycosidases (métabolisme), Glycosyltransferase (composition chimique), Glycosyltransferase (génétique), Glycosyltransferase (métabolisme), Génome fongique (MeSH), Phylogenèse (MeSH), Polysaccharide-lyases (composition chimique), Polysaccharide-lyases (génétique), Polysaccharide-lyases (métabolisme), Protéines fongiques (classification), Protéines fongiques (génétique), Protéines fongiques (métabolisme), Séquençage du génome entier (MeSH).
- MESH :
- classification : Protéines fongiques.
- composition chimique : Glycosidases, Glycosyltransferase, Polysaccharide-lyases.
- enzymologie : Flammulina.
- génétique : Flammulina, Glycosidases, Glycosyltransferase, Polysaccharide-lyases, Protéines fongiques.
- métabolisme : Glycosidases, Glycosyltransferase, Polysaccharide-lyases, Protéines fongiques.
- Analyse de séquence d'ADN, Bases de données génétiques, Génome fongique, Phylogenèse, Séquençage du génome entier.
English descriptors
- KwdEn :
- Databases, Genetic (MeSH), Flammulina (enzymology), Flammulina (genetics), Fungal Proteins (classification), Fungal Proteins (genetics), Fungal Proteins (metabolism), Genome, Fungal (MeSH), Glycoside Hydrolases (chemistry), Glycoside Hydrolases (genetics), Glycoside Hydrolases (metabolism), Glycosyltransferases (chemistry), Glycosyltransferases (genetics), Glycosyltransferases (metabolism), Phylogeny (MeSH), Polysaccharide-Lyases (chemistry), Polysaccharide-Lyases (genetics), Polysaccharide-Lyases (metabolism), Sequence Analysis, DNA (MeSH), Whole Genome Sequencing (MeSH).
- MESH :
- chemical , chemistry : Glycoside Hydrolases, Glycosyltransferases, Polysaccharide-Lyases.
- chemical , classification : Fungal Proteins.
- enzymology : Flammulina.
- genetics : Flammulina, Fungal Proteins, Glycoside Hydrolases, Glycosyltransferases, Polysaccharide-Lyases.
- chemical , metabolism : Fungal Proteins, Glycoside Hydrolases, Glycosyltransferases, Polysaccharide-Lyases.
- Databases, Genetic, Genome, Fungal, Phylogeny, Sequence Analysis, DNA, Whole Genome Sequencing.
Abstract
Next-generation sequencing (NGS) of the Flammulina elastica (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one F. elastica protein. Among the 12,536 predicted genes, F. elastica contained 24 species-specific genes, of which 17 genes were paralogous. CAZymes are divided into five classes: glycoside hydrolases (GHs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycosyltransferases (GTs), and auxiliary activities (AA). In the present study, annotation of the predicted amino acid sequences from F. elastica genes using the dbCAN CAZyme database revealed 508 CAZymes, including 82 AAs, 218 GHs, 89 GTs, 18 PLs, 59 CEs, and 42 carbohydrate binding modules in the F. elastica genome. Although the CAZyme repertoire of F. elastica was similar to those of other fungal species, the total number of GTs in F. elastica was larger than those of other basidiomycetes. This genome information elucidates newly identified wood-degrading machinery in F. elastica, offers opportunities to better understand this fungus, and presents possibilities for more detailed studies on lignocellulosic biomass degradation that may lead to future biotechnological and industrial applications.
DOI: 10.3390/ijms19082379
PubMed: 30104475
PubMed Central: PMC6121412
Affiliations:
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Institute of Horticultural and Herbal Science, Rural Development Administration, 92, Bisan-ro, Eumseong-gun 27709, Korea. wskong@korea.kr.</nlm:affiliation><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, 92, Bisan-ro, Eumseong-gun 27709</wicri:regionArea><wicri:noRegion>Eumseong-gun 27709</wicri:noRegion></affiliation></author></analytic><series><title level="j">International journal of molecular sciences</title><idno type="eISSN">1422-0067</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Databases, Genetic (MeSH)</term><term>Flammulina (enzymology)</term><term>Flammulina (genetics)</term><term>Fungal Proteins (classification)</term><term>Fungal Proteins (genetics)</term><term>Fungal Proteins (metabolism)</term><term>Genome, Fungal (MeSH)</term><term>Glycoside Hydrolases (chemistry)</term><term>Glycoside Hydrolases (genetics)</term><term>Glycoside Hydrolases (metabolism)</term><term>Glycosyltransferases (chemistry)</term><term>Glycosyltransferases (genetics)</term><term>Glycosyltransferases (metabolism)</term><term>Phylogeny (MeSH)</term><term>Polysaccharide-Lyases (chemistry)</term><term>Polysaccharide-Lyases (genetics)</term><term>Polysaccharide-Lyases (metabolism)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Whole Genome Sequencing (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN (MeSH)</term><term>Bases de données génétiques (MeSH)</term><term>Flammulina (enzymologie)</term><term>Flammulina (génétique)</term><term>Glycosidases (composition chimique)</term><term>Glycosidases (génétique)</term><term>Glycosidases (métabolisme)</term><term>Glycosyltransferase (composition chimique)</term><term>Glycosyltransferase (génétique)</term><term>Glycosyltransferase (métabolisme)</term><term>Génome fongique (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Polysaccharide-lyases (composition chimique)</term><term>Polysaccharide-lyases (génétique)</term><term>Polysaccharide-lyases (métabolisme)</term><term>Protéines fongiques (classification)</term><term>Protéines fongiques (génétique)</term><term>Protéines fongiques (métabolisme)</term><term>Séquençage du génome entier (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Glycoside Hydrolases</term><term>Glycosyltransferases</term><term>Polysaccharide-Lyases</term></keywords><keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>Fungal Proteins</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Protéines fongiques</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Glycosidases</term><term>Glycosyltransferase</term><term>Polysaccharide-lyases</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Flammulina</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Flammulina</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Flammulina</term><term>Fungal Proteins</term><term>Glycoside Hydrolases</term><term>Glycosyltransferases</term><term>Polysaccharide-Lyases</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Flammulina</term><term>Glycosidases</term><term>Glycosyltransferase</term><term>Polysaccharide-lyases</term><term>Protéines fongiques</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Fungal Proteins</term><term>Glycoside Hydrolases</term><term>Glycosyltransferases</term><term>Polysaccharide-Lyases</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Glycosidases</term><term>Glycosyltransferase</term><term>Polysaccharide-lyases</term><term>Protéines fongiques</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Genome, Fungal</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term><term>Whole Genome Sequencing</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Bases de données génétiques</term><term>Génome fongique</term><term>Phylogenèse</term><term>Séquençage du génome entier</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Next-generation sequencing (NGS) of the <i>Flammulina elastica</i> (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one <i>F. elastica</i> protein. Among the 12,536 predicted genes, <i>F. elastica</i> contained 24 species-specific genes, of which 17 genes were paralogous. CAZymes are divided into five classes: glycoside hydrolases (GHs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycosyltransferases (GTs), and auxiliary activities (AA). In the present study, annotation of the predicted amino acid sequences from <i>F. elastica</i> genes using the dbCAN CAZyme database revealed 508 CAZymes, including 82 AAs, 218 GHs, 89 GTs, 18 PLs, 59 CEs, and 42 carbohydrate binding modules in the <i>F. elastica</i> genome. Although the CAZyme repertoire of <i>F. elastica</i> was similar to those of other fungal species, the total number of GTs in <i>F. elastica</i> was larger than those of other basidiomycetes. This genome information elucidates newly identified wood-degrading machinery in <i>F. elastica</i>, offers opportunities to better understand this fungus, and presents possibilities for more detailed studies on lignocellulosic biomass degradation that may lead to future biotechnological and industrial applications.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30104475</PMID><DateCompleted><Year>2018</Year><Month>09</Month><Day>24</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>14</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1422-0067</ISSN><JournalIssue CitedMedium="Internet"><Volume>19</Volume><Issue>8</Issue><PubDate><Year>2018</Year><Month>Aug</Month><Day>13</Day></PubDate></JournalIssue><Title>International journal of molecular sciences</Title><ISOAbbreviation>Int J Mol Sci</ISOAbbreviation></Journal><ArticleTitle>Genome Sequencing and Carbohydrate-Active Enzyme (CAZyme) Repertoire of the White Rot Fungus <i>Flammulina elastica</i>.</ArticleTitle><ELocationID EIdType="pii" ValidYN="Y">E2379</ELocationID><ELocationID EIdType="doi" ValidYN="Y">10.3390/ijms19082379</ELocationID><Abstract><AbstractText>Next-generation sequencing (NGS) of the <i>Flammulina elastica</i> (wood-rotting basidiomycete) genome was performed to identify carbohydrate-active enzymes (CAZymes). The resulting assembly (31 kmer) revealed a total length of 35,045,521 bp (49.7% GC content). Using the AUGUSTUS tool, 12,536 total gene structures were predicted by ab initio gene prediction. An analysis of orthologs revealed that 6806 groups contained at least one <i>F. elastica</i> protein. Among the 12,536 predicted genes, <i>F. elastica</i> contained 24 species-specific genes, of which 17 genes were paralogous. CAZymes are divided into five classes: glycoside hydrolases (GHs), carbohydrate esterases (CEs), polysaccharide lyases (PLs), glycosyltransferases (GTs), and auxiliary activities (AA). In the present study, annotation of the predicted amino acid sequences from <i>F. elastica</i> genes using the dbCAN CAZyme database revealed 508 CAZymes, including 82 AAs, 218 GHs, 89 GTs, 18 PLs, 59 CEs, and 42 carbohydrate binding modules in the <i>F. elastica</i> genome. Although the CAZyme repertoire of <i>F. elastica</i> was similar to those of other fungal species, the total number of GTs in <i>F. elastica</i> was larger than those of other basidiomycetes. This genome information elucidates newly identified wood-degrading machinery in <i>F. elastica</i>, offers opportunities to better understand this fungus, and presents possibilities for more detailed studies on lignocellulosic biomass degradation that may lead to future biotechnological and industrial applications.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Park</LastName><ForeName>Young-Jin</ForeName><Initials>YJ</Initials><Identifier Source="ORCID">0000-0002-8392-4772</Identifier><AffiliationInfo><Affiliation>Department of Biomedical Chemistry, Research Institute for Biomedical & Health Science, College of Biomedical and Health Science, Konkuk University, 268 Chungwon-daero, Chungju-si 27478, Korea. yjpark@kku.ac.kr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jeong</LastName><ForeName>Yong-Un</ForeName><Initials>YU</Initials><AffiliationInfo><Affiliation>Department of Biomedical Chemistry, Research Institute for Biomedical & Health Science, College of Biomedical and Health Science, Konkuk University, 268 Chungwon-daero, Chungju-si 27478, Korea. s11034@kku.ac.kr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kong</LastName><ForeName>Won-Sik</ForeName><Initials>WS</Initials><AffiliationInfo><Affiliation>Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, 92, Bisan-ro, Eumseong-gun 27709, Korea. wskong@korea.kr.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>08</Month><Day>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Int J Mol Sci</MedlineTA><NlmUniqueID>101092791</NlmUniqueID><ISSNLinking>1422-0067</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005656">Fungal Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.4.-</RegistryNumber><NameOfSubstance UI="D016695">Glycosyltransferases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.2.1.-</RegistryNumber><NameOfSubstance UI="D006026">Glycoside Hydrolases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 4.2.2.-</RegistryNumber><NameOfSubstance UI="D011133">Polysaccharide-Lyases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D030541" MajorTopicYN="N">Databases, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055393" MajorTopicYN="N">Flammulina</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="N">enzymology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005656" MajorTopicYN="N">Fungal Proteins</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016681" MajorTopicYN="Y">Genome, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006026" MajorTopicYN="N">Glycoside Hydrolases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016695" MajorTopicYN="N">Glycosyltransferases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011133" MajorTopicYN="N">Polysaccharide-Lyases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000073336" MajorTopicYN="N">Whole Genome Sequencing</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Flammulina elastica</Keyword><Keyword MajorTopicYN="N">carbohydrate active enzyme</Keyword><Keyword MajorTopicYN="N">whole genome sequencing</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>07</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2018</Year><Month>07</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>08</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>8</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>8</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>9</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30104475</ArticleId><ArticleId IdType="pii">ijms19082379</ArticleId><ArticleId IdType="doi">10.3390/ijms19082379</ArticleId><ArticleId 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Sud</li></country></list><tree><country name="Corée du Sud"><noRegion><name sortKey="Park, Young Jin" sort="Park, Young Jin" uniqKey="Park Y" first="Young-Jin" last="Park">Young-Jin Park</name></noRegion><name sortKey="Jeong, Yong Un" sort="Jeong, Yong Un" uniqKey="Jeong Y" first="Yong-Un" last="Jeong">Yong-Un Jeong</name><name sortKey="Kong, Won Sik" sort="Kong, Won Sik" uniqKey="Kong W" first="Won-Sik" last="Kong">Won-Sik Kong</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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