The largest subunit of RNA polymerase II as a new marker gene to study assemblages of arbuscular mycorrhizal fungi in the field.
Identifieur interne : 001707 ( Main/Corpus ); précédent : 001706; suivant : 001708The largest subunit of RNA polymerase II as a new marker gene to study assemblages of arbuscular mycorrhizal fungi in the field.
Auteurs : Herbert Stockinger ; Marine Peyret-Guzzon ; Sally Koegel ; Marie-Lara Bouffaud ; Dirk RedeckerSource :
- PloS one [ 1932-6203 ] ; 2014.
English descriptors
- KwdEn :
- Agriculture (MeSH), DNA Barcoding, Taxonomic (MeSH), Exons (genetics), Genes, Fungal (MeSH), Glomeromycota (enzymology), Glomeromycota (genetics), Molecular Sequence Data (MeSH), Mycorrhizae (enzymology), Mycorrhizae (genetics), Phylogeny (MeSH), Principal Component Analysis (MeSH), Protein Subunits (genetics), RNA Polymerase II (genetics), Zea mays (microbiology).
- MESH :
- chemical , genetics : Protein Subunits, RNA Polymerase II.
- enzymology : Glomeromycota, Mycorrhizae.
- genetics : Exons, Glomeromycota, Mycorrhizae.
- microbiology : Zea mays.
- Agriculture, DNA Barcoding, Taxonomic, Genes, Fungal, Molecular Sequence Data, Phylogeny, Principal Component Analysis.
Abstract
Due to the potential of arbuscular mycorrhizal fungi (AMF, Glomeromycota) to improve plant growth and soil quality, the influence of agricultural practice on their diversity continues to be an important research question. Up to now studies of community diversity in AMF have exclusively been based on nuclear ribosomal gene regions, which in AMF show high intra-organism polymorphism, seriously complicating interpretation of these data. We designed specific PCR primers for 454 sequencing of a region of the largest subunit of RNA polymerase II gene, and established a new reference dataset comprising all major AMF lineages. This gene is known to be monomorphic within fungal isolates but shows an excellent barcode gap between species. We designed a primer set to amplify all known lineages of AMF and demonstrated its applicability in combination with high-throughput sequencing in a long-term tillage experiment. The PCR primers showed a specificity of 99.94% for glomeromycotan sequences. We found evidence of significant shifts of the AMF communities caused by soil management and showed that tillage effects on different AMF taxa are clearly more complex than previously thought. The high resolving power of high-throughput sequencing highlights the need for quantitative measurements to efficiently detect these effects.
DOI: 10.1371/journal.pone.0107783
PubMed: 25275381
PubMed Central: PMC4183475
Links to Exploration step
pubmed:25275381Le document en format XML
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Up to now studies of community diversity in AMF have exclusively been based on nuclear ribosomal gene regions, which in AMF show high intra-organism polymorphism, seriously complicating interpretation of these data. We designed specific PCR primers for 454 sequencing of a region of the largest subunit of RNA polymerase II gene, and established a new reference dataset comprising all major AMF lineages. This gene is known to be monomorphic within fungal isolates but shows an excellent barcode gap between species. We designed a primer set to amplify all known lineages of AMF and demonstrated its applicability in combination with high-throughput sequencing in a long-term tillage experiment. The PCR primers showed a specificity of 99.94% for glomeromycotan sequences. We found evidence of significant shifts of the AMF communities caused by soil management and showed that tillage effects on different AMF taxa are clearly more complex than previously thought. The high resolving power of high-throughput sequencing highlights the need for quantitative measurements to efficiently detect these effects. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25275381</PMID><DateCompleted><Year>2015</Year><Month>06</Month><Day>10</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><Issue>9</Issue><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>The largest subunit of RNA polymerase II as a new marker gene to study assemblages of arbuscular mycorrhizal fungi in the field.</ArticleTitle><Pagination><MedlinePgn>e107783</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0107783</ELocationID><Abstract><AbstractText>Due to the potential of arbuscular mycorrhizal fungi (AMF, Glomeromycota) to improve plant growth and soil quality, the influence of agricultural practice on their diversity continues to be an important research question. Up to now studies of community diversity in AMF have exclusively been based on nuclear ribosomal gene regions, which in AMF show high intra-organism polymorphism, seriously complicating interpretation of these data. We designed specific PCR primers for 454 sequencing of a region of the largest subunit of RNA polymerase II gene, and established a new reference dataset comprising all major AMF lineages. This gene is known to be monomorphic within fungal isolates but shows an excellent barcode gap between species. We designed a primer set to amplify all known lineages of AMF and demonstrated its applicability in combination with high-throughput sequencing in a long-term tillage experiment. The PCR primers showed a specificity of 99.94% for glomeromycotan sequences. We found evidence of significant shifts of the AMF communities caused by soil management and showed that tillage effects on different AMF taxa are clearly more complex than previously thought. The high resolving power of high-throughput sequencing highlights the need for quantitative measurements to efficiently detect these effects. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Stockinger</LastName><ForeName>Herbert</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Université de Bourgogne, UMR1347 Agroécologie, Dijon, France; INRA, UMR1347 Agroécologie, Dijon, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Peyret-Guzzon</LastName><ForeName>Marine</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>INRA, UMR1347 Agroécologie, Dijon, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Koegel</LastName><ForeName>Sally</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Botanical Institute, Basel, Switzerland.</Affiliation></AffiliationInfo></Author><Author 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