Isolation source matters: sclerotia and ectomycorrhizal roots provide different views of genetic diversity in Cenococcum geophilum.
Identifieur interne : 000846 ( Main/Corpus ); précédent : 000845; suivant : 000847Isolation source matters: sclerotia and ectomycorrhizal roots provide different views of genetic diversity in Cenococcum geophilum.
Auteurs : Keisuke Obase ; Greg W. Douhan ; Yosuke Matsuda ; Matthew E. SmithSource :
- Mycologia [ 1557-2536 ]
English descriptors
- KwdEn :
- Ascomycota (genetics), DNA, Fungal (genetics), Forests (MeSH), Fungal Proteins (genetics), Genetic Variation (MeSH), Genotype (MeSH), Glyceraldehyde-3-Phosphate Dehydrogenases (genetics), Microsatellite Repeats (genetics), Mycorrhizae (genetics), Plant Roots (microbiology), Soil Microbiology (MeSH).
- MESH :
- chemical , genetics : DNA, Fungal, Fungal Proteins, Glyceraldehyde-3-Phosphate Dehydrogenases.
- genetics : Ascomycota, Microsatellite Repeats, Mycorrhizae.
- microbiology : Plant Roots.
- Forests, Genetic Variation, Genotype, Soil Microbiology.
Abstract
Cenococcum geophilum forms sclerotia and ectomycorrhizas with host plants in forest soils. We demonstrated the differences in genetic diversity of C. geophilum between cultured isolates from sclerotia and those from ectomycorrhizal roots in the same 73 soil samples based on glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene sequences and newly developed microsatellite markers. Based on GAPDH sequences, 759 cultured isolates (553 from sclerotia and 206 from ectomycorrhizas) were classified into 107 "genotypes" with sequence variation of up to 8.6%. The total number of GAPDH genotypes per soil sample ranged from 1 to 9, but genotypes that were shared between sclerotia and ectomycorrhizas were uncommon (0-3 per soil sample). More than 50% of GAPDH genotypes were unique to one source in most soil samples. Unique GAPDH genotypes were detected from either scleotia or ectomycorrhizal roots in most of the soil samples. Multilocus analysis using nine microsatellite markers provided additional resolution to differentiate fungal individuals and supported the results of GAPDH genotyping. The results indicated that sampling both sclerotia and ectomycorrhizal roots maximizes the detection of diversity at the soil core scale. On the other hand, when all isolates were viewed together, 82 GAPDH genotypes were unique to sclerotia whereas only 6 GAPDH genotypes were unique to ectomycorrhizas. Rarefaction analysis indicated that GAPDH genotypic diversity is significantly higher in sclerotia than ectomycorrhizal roots and the diversity within sclerotia is nearly the same as that of both sclerotia and ectomycorrhizas together. These findings suggest that sampling sclerotia alone is likely to detect the majority of GAPDH genotypes in Cenococcum at the regional scale. When deciding whether to sample sclerotia, ectomycorrhizas, or both types of tissues from Cenococcum, it is critical to consider the spatial scale and also the main questions and hypotheses of the study.
DOI: 10.1080/00275514.2018.1463130
PubMed: 29923792
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Isolation source matters: sclerotia and ectomycorrhizal roots provide different views of genetic diversity in Cenococcum geophilum.</title><author><name sortKey="Obase, Keisuke" sort="Obase, Keisuke" uniqKey="Obase K" first="Keisuke" last="Obase">Keisuke Obase</name><affiliation><nlm:affiliation>a Microbial Ecology Laboratory, Department of Mushroom Science and Forest Microbiology , Forestry and Forest Products Research Institute , 1 Matsunosato, Tsukuba , Ibaraki 305-8687 , Japan.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>b Department of Plant Pathology , University of Florida , 2523 Fifield Hall, Gainesville , Florida 32611-0680.</nlm:affiliation></affiliation></author><author><name sortKey="Douhan, Greg W" sort="Douhan, Greg W" uniqKey="Douhan G" first="Greg W" last="Douhan">Greg W. Douhan</name><affiliation><nlm:affiliation>c Department of Plant Pathology and Microbiology , University of California , Riverside , California 92521.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>d Cooperative Extension, Tulare County , University of California , Tulare , California 93274.</nlm:affiliation></affiliation></author><author><name sortKey="Matsuda, Yosuke" sort="Matsuda, Yosuke" uniqKey="Matsuda Y" first="Yosuke" last="Matsuda">Yosuke Matsuda</name><affiliation><nlm:affiliation>e Laboratory of Forest Mycology, Graduate School of Bioresources , Mie University , Kurimamachiya 1577, Tsu , Mie 514-8507 , Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Smith, Matthew E" sort="Smith, Matthew E" uniqKey="Smith M" first="Matthew E" last="Smith">Matthew E. Smith</name><affiliation><nlm:affiliation>b Department of Plant Pathology , University of Florida , 2523 Fifield Hall, Gainesville , Florida 32611-0680.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2018">2018 May-Jun</date><idno type="RBID">pubmed:29923792</idno><idno type="pmid">29923792</idno><idno type="doi">10.1080/00275514.2018.1463130</idno><idno type="wicri:Area/Main/Corpus">000846</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000846</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Isolation source matters: sclerotia and ectomycorrhizal roots provide different views of genetic diversity in Cenococcum geophilum.</title><author><name sortKey="Obase, Keisuke" sort="Obase, Keisuke" uniqKey="Obase K" first="Keisuke" last="Obase">Keisuke Obase</name><affiliation><nlm:affiliation>a Microbial Ecology Laboratory, Department of Mushroom Science and Forest Microbiology , Forestry and Forest Products Research Institute , 1 Matsunosato, Tsukuba , Ibaraki 305-8687 , Japan.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>b Department of Plant Pathology , University of Florida , 2523 Fifield Hall, Gainesville , Florida 32611-0680.</nlm:affiliation></affiliation></author><author><name sortKey="Douhan, Greg W" sort="Douhan, Greg W" uniqKey="Douhan G" first="Greg W" last="Douhan">Greg W. Douhan</name><affiliation><nlm:affiliation>c Department of Plant Pathology and Microbiology , University of California , Riverside , California 92521.</nlm:affiliation></affiliation><affiliation><nlm:affiliation>d Cooperative Extension, Tulare County , University of California , Tulare , California 93274.</nlm:affiliation></affiliation></author><author><name sortKey="Matsuda, Yosuke" sort="Matsuda, Yosuke" uniqKey="Matsuda Y" first="Yosuke" last="Matsuda">Yosuke Matsuda</name><affiliation><nlm:affiliation>e Laboratory of Forest Mycology, Graduate School of Bioresources , Mie University , Kurimamachiya 1577, Tsu , Mie 514-8507 , Japan.</nlm:affiliation></affiliation></author><author><name sortKey="Smith, Matthew E" sort="Smith, Matthew E" uniqKey="Smith M" first="Matthew E" last="Smith">Matthew E. Smith</name><affiliation><nlm:affiliation>b Department of Plant Pathology , University of Florida , 2523 Fifield Hall, Gainesville , Florida 32611-0680.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Mycologia</title><idno type="eISSN">1557-2536</idno></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Ascomycota (genetics)</term><term>DNA, Fungal (genetics)</term><term>Forests (MeSH)</term><term>Fungal Proteins (genetics)</term><term>Genetic Variation (MeSH)</term><term>Genotype (MeSH)</term><term>Glyceraldehyde-3-Phosphate Dehydrogenases (genetics)</term><term>Microsatellite Repeats (genetics)</term><term>Mycorrhizae (genetics)</term><term>Plant Roots (microbiology)</term><term>Soil Microbiology (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Fungal</term><term>Fungal Proteins</term><term>Glyceraldehyde-3-Phosphate Dehydrogenases</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Ascomycota</term><term>Microsatellite Repeats</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Roots</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Forests</term><term>Genetic Variation</term><term>Genotype</term><term>Soil Microbiology</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Cenococcum geophilum forms sclerotia and ectomycorrhizas with host plants in forest soils. We demonstrated the differences in genetic diversity of C. geophilum between cultured isolates from sclerotia and those from ectomycorrhizal roots in the same 73 soil samples based on glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene sequences and newly developed microsatellite markers. Based on GAPDH sequences, 759 cultured isolates (553 from sclerotia and 206 from ectomycorrhizas) were classified into 107 "genotypes" with sequence variation of up to 8.6%. The total number of GAPDH genotypes per soil sample ranged from 1 to 9, but genotypes that were shared between sclerotia and ectomycorrhizas were uncommon (0-3 per soil sample). More than 50% of GAPDH genotypes were unique to one source in most soil samples. Unique GAPDH genotypes were detected from either scleotia or ectomycorrhizal roots in most of the soil samples. Multilocus analysis using nine microsatellite markers provided additional resolution to differentiate fungal individuals and supported the results of GAPDH genotyping. The results indicated that sampling both sclerotia and ectomycorrhizal roots maximizes the detection of diversity at the soil core scale. On the other hand, when all isolates were viewed together, 82 GAPDH genotypes were unique to sclerotia whereas only 6 GAPDH genotypes were unique to ectomycorrhizas. Rarefaction analysis indicated that GAPDH genotypic diversity is significantly higher in sclerotia than ectomycorrhizal roots and the diversity within sclerotia is nearly the same as that of both sclerotia and ectomycorrhizas together. These findings suggest that sampling sclerotia alone is likely to detect the majority of GAPDH genotypes in Cenococcum at the regional scale. When deciding whether to sample sclerotia, ectomycorrhizas, or both types of tissues from Cenococcum, it is critical to consider the spatial scale and also the main questions and hypotheses of the study.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29923792</PMID><DateCompleted><Year>2019</Year><Month>07</Month><Day>12</Day></DateCompleted><DateRevised><Year>2019</Year><Month>07</Month><Day>12</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1557-2536</ISSN><JournalIssue CitedMedium="Internet"><Volume>110</Volume><Issue>3</Issue><PubDate><MedlineDate>2018 May-Jun</MedlineDate></PubDate></JournalIssue><Title>Mycologia</Title><ISOAbbreviation>Mycologia</ISOAbbreviation></Journal><ArticleTitle>Isolation source matters: sclerotia and ectomycorrhizal roots provide different views of genetic diversity in Cenococcum geophilum.</ArticleTitle><Pagination><MedlinePgn>473-481</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1080/00275514.2018.1463130</ELocationID><Abstract><AbstractText>Cenococcum geophilum forms sclerotia and ectomycorrhizas with host plants in forest soils. We demonstrated the differences in genetic diversity of C. geophilum between cultured isolates from sclerotia and those from ectomycorrhizal roots in the same 73 soil samples based on glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene sequences and newly developed microsatellite markers. Based on GAPDH sequences, 759 cultured isolates (553 from sclerotia and 206 from ectomycorrhizas) were classified into 107 "genotypes" with sequence variation of up to 8.6%. The total number of GAPDH genotypes per soil sample ranged from 1 to 9, but genotypes that were shared between sclerotia and ectomycorrhizas were uncommon (0-3 per soil sample). More than 50% of GAPDH genotypes were unique to one source in most soil samples. Unique GAPDH genotypes were detected from either scleotia or ectomycorrhizal roots in most of the soil samples. Multilocus analysis using nine microsatellite markers provided additional resolution to differentiate fungal individuals and supported the results of GAPDH genotyping. The results indicated that sampling both sclerotia and ectomycorrhizal roots maximizes the detection of diversity at the soil core scale. On the other hand, when all isolates were viewed together, 82 GAPDH genotypes were unique to sclerotia whereas only 6 GAPDH genotypes were unique to ectomycorrhizas. Rarefaction analysis indicated that GAPDH genotypic diversity is significantly higher in sclerotia than ectomycorrhizal roots and the diversity within sclerotia is nearly the same as that of both sclerotia and ectomycorrhizas together. These findings suggest that sampling sclerotia alone is likely to detect the majority of GAPDH genotypes in Cenococcum at the regional scale. When deciding whether to sample sclerotia, ectomycorrhizas, or both types of tissues from Cenococcum, it is critical to consider the spatial scale and also the main questions and hypotheses of the study.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Obase</LastName><ForeName>Keisuke</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>a Microbial Ecology Laboratory, Department of Mushroom Science and Forest Microbiology , Forestry and Forest Products Research Institute , 1 Matsunosato, Tsukuba , Ibaraki 305-8687 , Japan.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>b Department of Plant Pathology , University of Florida , 2523 Fifield Hall, Gainesville , Florida 32611-0680.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Douhan</LastName><ForeName>Greg W</ForeName><Initials>GW</Initials><AffiliationInfo><Affiliation>c Department of Plant Pathology and Microbiology , University of California , Riverside , California 92521.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>d Cooperative Extension, Tulare County , University of California , Tulare , California 93274.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Matsuda</LastName><ForeName>Yosuke</ForeName><Initials>Y</Initials><Identifier Source="ORCID">0000-0002-7001-3101</Identifier><AffiliationInfo><Affiliation>e Laboratory of Forest Mycology, Graduate School of Bioresources , Mie University , Kurimamachiya 1577, Tsu , Mie 514-8507 , Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Smith</LastName><ForeName>Matthew E</ForeName><Initials>ME</Initials><Identifier Source="ORCID">0000-0002-0878-0932</Identifier><AffiliationInfo><Affiliation>b Department of Plant Pathology , University of Florida , 2523 Fifield Hall, Gainesville , Florida 32611-0680.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>06</Month><Day>20</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mycologia</MedlineTA><NlmUniqueID>0400764</NlmUniqueID><ISSNLinking>0027-5514</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004271">DNA, Fungal</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005656">Fungal Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 1.2.1.-</RegistryNumber><NameOfSubstance UI="D005987">Glyceraldehyde-3-Phosphate Dehydrogenases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001203" MajorTopicYN="N">Ascomycota</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004271" MajorTopicYN="N">DNA, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D065928" MajorTopicYN="N">Forests</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005656" MajorTopicYN="N">Fungal Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="Y">Genetic Variation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005987" MajorTopicYN="N">Glyceraldehyde-3-Phosphate Dehydrogenases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="N">Microsatellite Repeats</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012988" MajorTopicYN="N">Soil Microbiology</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Anamorph</Keyword><Keyword MajorTopicYN="Y">ectomycorrhizal root</Keyword><Keyword MajorTopicYN="Y">genotype</Keyword><Keyword MajorTopicYN="Y">glyceraldehyde-3-phosphate dehydrogenase gene</Keyword><Keyword MajorTopicYN="Y">microsatellite</Keyword><Keyword MajorTopicYN="Y">sclerotium</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>6</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>7</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>6</Month><Day>21</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29923792</ArticleId><ArticleId IdType="doi">10.1080/00275514.2018.1463130</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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