Combining nested PCR and restriction digest of the internal transcribed spacer region to characterize arbuscular mycorrhizal fungi on roots from the field.
Identifieur interne : 003871 ( Main/Curation ); précédent : 003870; suivant : 003872Combining nested PCR and restriction digest of the internal transcribed spacer region to characterize arbuscular mycorrhizal fungi on roots from the field.
Auteurs : Carsten Renker [Allemagne] ; Jochen Heinrichs ; Michael Kaldorf ; François BuscotSource :
- Mycorrhiza [ 0940-6360 ] ; 2003.
Descripteurs français
- KwdFr :
- ADN fongique (génétique), Alignement de séquences (MeSH), Ascomycota (génétique), Basidiomycota (génétique), Biodiversité (MeSH), Champignons (génétique), Chytridiomycota (génétique), Données de séquences moléculaires (MeSH), Espaceur de l'ADN ribosomique (génétique), Mycorhizes (génétique), Phylogenèse (MeSH), Racines de plante (microbiologie), Réaction de polymérisation en chaîne (MeSH), Séquence nucléotidique (MeSH), Type II site-specific deoxyribonuclease (MeSH).
- MESH :
- génétique : ADN fongique, Ascomycota, Basidiomycota, Champignons, Chytridiomycota, Espaceur de l'ADN ribosomique, Mycorhizes.
- microbiologie : Racines de plante.
- Alignement de séquences, Biodiversité, Données de séquences moléculaires, Phylogenèse, Réaction de polymérisation en chaîne, Séquence nucléotidique, Type II site-specific deoxyribonuclease.
English descriptors
- KwdEn :
- Ascomycota (genetics), Base Sequence (MeSH), Basidiomycota (genetics), Biodiversity (MeSH), Chytridiomycota (genetics), DNA, Fungal (genetics), DNA, Ribosomal Spacer (genetics), Deoxyribonucleases, Type II Site-Specific (MeSH), Fungi (genetics), Molecular Sequence Data (MeSH), Mycorrhizae (genetics), Phylogeny (MeSH), Plant Roots (microbiology), Polymerase Chain Reaction (MeSH), Sequence Alignment (MeSH).
- MESH :
- chemical , genetics : DNA, Fungal, DNA, Ribosomal Spacer.
- genetics : Ascomycota, Basidiomycota, Chytridiomycota, Fungi, Mycorrhizae.
- microbiology : Plant Roots.
- Base Sequence, Biodiversity, Deoxyribonucleases, Type II Site-Specific, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, Sequence Alignment.
Abstract
Identification of arbuscular mycorrhizal fungi (AMF) on roots is almost impossible with morphological methods and, due to the presence of contaminating fungi, it is also difficult with molecular biological techniques. To allow broad investigation of the population structure of AMF in the field, we have established a new method to selectively amplify the internal transcribed spacer (ITS) region of most AMF with a unique primer set. Based on available sequences of the rDNA, one primer pair specific for AMF and a few other fungal groups was designed and combined in a nested PCR with the already established primer pair ITS5/ITS4. Amplification from contaminating organisms was reduced by an AluI restriction after the first reaction of the nested PCR. The method was assessed at five different field sites representing different types of habitats. Members of all major groups within the Glomeromycota (except Archaeosporaceae) were detected at the different sites. Gigasporaceae also proved detectable with the method based on cultivated strains.
DOI: 10.1007/s00572-002-0214-5
PubMed: 12938031
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pubmed:12938031Le document en format XML
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<term>DNA, Ribosomal Spacer (genetics)</term>
<term>Deoxyribonucleases, Type II Site-Specific (MeSH)</term>
<term>Fungi (genetics)</term>
<term>Molecular Sequence Data (MeSH)</term>
<term>Mycorrhizae (genetics)</term>
<term>Phylogeny (MeSH)</term>
<term>Plant Roots (microbiology)</term>
<term>Polymerase Chain Reaction (MeSH)</term>
<term>Sequence Alignment (MeSH)</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>ADN fongique (génétique)</term>
<term>Alignement de séquences (MeSH)</term>
<term>Ascomycota (génétique)</term>
<term>Basidiomycota (génétique)</term>
<term>Biodiversité (MeSH)</term>
<term>Champignons (génétique)</term>
<term>Chytridiomycota (génétique)</term>
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<term>Espaceur de l'ADN ribosomique (génétique)</term>
<term>Mycorhizes (génétique)</term>
<term>Phylogenèse (MeSH)</term>
<term>Racines de plante (microbiologie)</term>
<term>Réaction de polymérisation en chaîne (MeSH)</term>
<term>Séquence nucléotidique (MeSH)</term>
<term>Type II site-specific deoxyribonuclease (MeSH)</term>
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<term>Basidiomycota</term>
<term>Chytridiomycota</term>
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<term>Chytridiomycota</term>
<term>Espaceur de l'ADN ribosomique</term>
<term>Mycorhizes</term>
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<keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term>
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<term>Deoxyribonucleases, Type II Site-Specific</term>
<term>Molecular Sequence Data</term>
<term>Phylogeny</term>
<term>Polymerase Chain Reaction</term>
<term>Sequence Alignment</term>
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<keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term>
<term>Biodiversité</term>
<term>Données de séquences moléculaires</term>
<term>Phylogenèse</term>
<term>Réaction de polymérisation en chaîne</term>
<term>Séquence nucléotidique</term>
<term>Type II site-specific deoxyribonuclease</term>
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<front><div type="abstract" xml:lang="en">Identification of arbuscular mycorrhizal fungi (AMF) on roots is almost impossible with morphological methods and, due to the presence of contaminating fungi, it is also difficult with molecular biological techniques. To allow broad investigation of the population structure of AMF in the field, we have established a new method to selectively amplify the internal transcribed spacer (ITS) region of most AMF with a unique primer set. Based on available sequences of the rDNA, one primer pair specific for AMF and a few other fungal groups was designed and combined in a nested PCR with the already established primer pair ITS5/ITS4. Amplification from contaminating organisms was reduced by an AluI restriction after the first reaction of the nested PCR. The method was assessed at five different field sites representing different types of habitats. Members of all major groups within the Glomeromycota (except Archaeosporaceae) were detected at the different sites. Gigasporaceae also proved detectable with the method based on cultivated strains.</div>
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<Abstract><AbstractText>Identification of arbuscular mycorrhizal fungi (AMF) on roots is almost impossible with morphological methods and, due to the presence of contaminating fungi, it is also difficult with molecular biological techniques. To allow broad investigation of the population structure of AMF in the field, we have established a new method to selectively amplify the internal transcribed spacer (ITS) region of most AMF with a unique primer set. Based on available sequences of the rDNA, one primer pair specific for AMF and a few other fungal groups was designed and combined in a nested PCR with the already established primer pair ITS5/ITS4. Amplification from contaminating organisms was reduced by an AluI restriction after the first reaction of the nested PCR. The method was assessed at five different field sites representing different types of habitats. Members of all major groups within the Glomeromycota (except Archaeosporaceae) were detected at the different sites. Gigasporaceae also proved detectable with the method based on cultivated strains.</AbstractText>
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