MycorrhizaeV1, Main, Exploration, bibRecord, 000F93

Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions of Rhizophagus irregularis and Gigaspora margarita is high and isolate-dependent.

Identifieur interne : 000F93 ( Main/Exploration ); précédent : 000F92; suivant : 000F94

Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions of Rhizophagus irregularis and Gigaspora margarita is high and isolate-dependent.

Auteurs : Odile Thiéry [Estonie] ; Martti Vasar [Estonie] ; Teele Jairus [Estonie] ; John Davison [Estonie] ; Christophe Roux [France] ; Paula-Ann Kivistik [Estonie] ; Andres Metspalu [Estonie] ; Lili Milani [Estonie] ; Ülle Saks [Estonie] ; Mari Moora [Estonie] ; Martin Zobel [Estonie] ; Maarja Öpik [Estonie]

Source :

Molecular ecology [ 1365-294X ] ; 2016.

RBID : pubmed:27092961

Descripteurs français

English descriptors

KwdEn :
- DNA, Fungal (genetics), DNA, Ribosomal Spacer (genetics), Genetic Variation (MeSH), Glomeromycota (classification), Glomeromycota (genetics), High-Throughput Nucleotide Sequencing (MeSH), Mycorrhizae (genetics), Polymorphism, Single Nucleotide (MeSH), Ribosome Subunits, Large (genetics), Ribosome Subunits, Small (genetics), Sequence Analysis, DNA (MeSH).
MESH :
- chemical , genetics : DNA, Fungal, DNA, Ribosomal Spacer.
- classification : Glomeromycota.
- genetics : Glomeromycota, Mycorrhizae, Ribosome Subunits, Large, Ribosome Subunits, Small.
- Genetic Variation, High-Throughput Nucleotide Sequencing, Polymorphism, Single Nucleotide, Sequence Analysis, DNA.

Abstract

Arbuscular mycorrhizal (AM) fungi are known to exhibit high intra-organism genetic variation. However, information about intra- vs. interspecific variation among the genes commonly used in diversity surveys is limited. Here, the nuclear small subunit (SSU) rRNA gene, internal transcribed spacer (ITS) region and large subunit (LSU) rRNA gene portions were sequenced from 3 to 5 individual spores from each of two isolates of Rhizophagus irregularis and Gigaspora margarita. A total of 1482 Sanger sequences (0.5 Mb) from 239 clones were obtained, spanning ~4370 bp of the ribosomal operon when concatenated. Intrasporal and intra-isolate sequence variation was high for all three regions even though variant numbers were not exhausted by sequencing 12-40 clones per isolate. Intra-isolate nucleotide variation levels followed the expected order of ITS > LSU > SSU, but the values were strongly dependent on isolate identity. Single nucleotide polymorphism (SNP) densities over 4 SNP/kb in the ribosomal operon were detected in all four isolates. Automated operational taxonomic unit picking within the sequence set of known identity overestimated species richness with almost all cut-off levels, markers and isolates. Average intraspecific sequence similarity values were 99%, 96% and 94% for amplicons in SSU, LSU and ITS, respectively. The suitability of the central part of the SSU as a marker for AM fungal community surveys was further supported by its level of nucleotide variation, which is similar to that of the ITS region; its alignability across the entire phylum; its appropriate length for next-generation sequencing; and its ease of amplification in single-step PCR.

DOI: 10.1111/mec.13655
PubMed: 27092961

Affiliations:

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<term>Glomeromycota (classification)</term>
<term>Glomeromycota (genetics)</term>
<term>High-Throughput Nucleotide Sequencing (MeSH)</term>
<term>Mycorrhizae (genetics)</term>
<term>Polymorphism, Single Nucleotide (MeSH)</term>
<term>Ribosome Subunits, Large (genetics)</term>
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<term>Analyse de séquence d'ADN (MeSH)</term>
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<term>Glomeromycota (classification)</term>
<term>Glomeromycota (génétique)</term>
<term>Grande sous-unité du ribosome (génétique)</term>
<term>Mycorhizes (génétique)</term>
<term>Petite sous-unité du ribosome (génétique)</term>
<term>Polymorphisme de nucléotide simple (MeSH)</term>
<term>Séquençage nucléotidique à haut débit (MeSH)</term>
<term>Variation génétique (MeSH)</term>
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<term>DNA, Ribosomal Spacer</term>
</keywords>
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</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Glomeromycota</term>
<term>Mycorrhizae</term>
<term>Ribosome Subunits, Large</term>
<term>Ribosome Subunits, Small</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN fongique</term>
<term>Espaceur de l'ADN ribosomique</term>
<term>Glomeromycota</term>
<term>Grande sous-unité du ribosome</term>
<term>Mycorhizes</term>
<term>Petite sous-unité du ribosome</term>
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<keywords scheme="MESH" xml:lang="en"><term>Genetic Variation</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Polymorphisme de nucléotide simple</term>
<term>Séquençage nucléotidique à haut débit</term>
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<front><div type="abstract" xml:lang="en">Arbuscular mycorrhizal (AM) fungi are known to exhibit high intra-organism genetic variation. However, information about intra- vs. interspecific variation among the genes commonly used in diversity surveys is limited. Here, the nuclear small subunit (SSU) rRNA gene, internal transcribed spacer (ITS) region and large subunit (LSU) rRNA gene portions were sequenced from 3 to 5 individual spores from each of two isolates of Rhizophagus irregularis and Gigaspora margarita. A total of 1482 Sanger sequences (0.5 Mb) from 239 clones were obtained, spanning ~4370 bp of the ribosomal operon when concatenated. Intrasporal and intra-isolate sequence variation was high for all three regions even though variant numbers were not exhausted by sequencing 12-40 clones per isolate. Intra-isolate nucleotide variation levels followed the expected order of ITS > LSU > SSU, but the values were strongly dependent on isolate identity. Single nucleotide polymorphism (SNP) densities over 4 SNP/kb in the ribosomal operon were detected in all four isolates. Automated operational taxonomic unit picking within the sequence set of known identity overestimated species richness with almost all cut-off levels, markers and isolates. Average intraspecific sequence similarity values were 99%, 96% and 94% for amplicons in SSU, LSU and ITS, respectively. The suitability of the central part of the SSU as a marker for AM fungal community surveys was further supported by its level of nucleotide variation, which is similar to that of the ITS region; its alignability across the entire phylum; its appropriate length for next-generation sequencing; and its ease of amplification in single-step PCR.</div>
</front>
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<DateCompleted><Year>2017</Year>
<Month>06</Month>
<Day>07</Day>
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<Month>02</Month>
<Day>05</Day>
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<Title>Molecular ecology</Title>
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<ArticleTitle>Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions of Rhizophagus irregularis and Gigaspora margarita is high and isolate-dependent.</ArticleTitle>
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<Abstract><AbstractText>Arbuscular mycorrhizal (AM) fungi are known to exhibit high intra-organism genetic variation. However, information about intra- vs. interspecific variation among the genes commonly used in diversity surveys is limited. Here, the nuclear small subunit (SSU) rRNA gene, internal transcribed spacer (ITS) region and large subunit (LSU) rRNA gene portions were sequenced from 3 to 5 individual spores from each of two isolates of Rhizophagus irregularis and Gigaspora margarita. A total of 1482 Sanger sequences (0.5 Mb) from 239 clones were obtained, spanning ~4370 bp of the ribosomal operon when concatenated. Intrasporal and intra-isolate sequence variation was high for all three regions even though variant numbers were not exhausted by sequencing 12-40 clones per isolate. Intra-isolate nucleotide variation levels followed the expected order of ITS > LSU > SSU, but the values were strongly dependent on isolate identity. Single nucleotide polymorphism (SNP) densities over 4 SNP/kb in the ribosomal operon were detected in all four isolates. Automated operational taxonomic unit picking within the sequence set of known identity overestimated species richness with almost all cut-off levels, markers and isolates. Average intraspecific sequence similarity values were 99%, 96% and 94% for amplicons in SSU, LSU and ITS, respectively. The suitability of the central part of the SSU as a marker for AM fungal community surveys was further supported by its level of nucleotide variation, which is similar to that of the ITS region; its alignability across the entire phylum; its appropriate length for next-generation sequencing; and its ease of amplification in single-step PCR.</AbstractText>
<CopyrightInformation>© 2016 John Wiley & Sons Ltd.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Thiéry</LastName>
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</Author>
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</AffiliationInfo>
</Author>
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</AffiliationInfo>
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</MeshHeading>
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</MeshHeading>
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</MeshHeading>
<MeshHeading><DescriptorName UI="D054679" MajorTopicYN="N">Ribosome Subunits, Small</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
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</MeshHeading>
</MeshHeadingList>
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<Keyword MajorTopicYN="Y">qiime</Keyword>
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<Keyword MajorTopicYN="Y">sequence-based identification</Keyword>
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<Day>17</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="revised"><Year>2016</Year>
<Month>03</Month>
<Day>29</Day>
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<PubMedPubDate PubStatus="accepted"><Year>2016</Year>
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</pubmed>
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<li>France</li>
</country>
<region><li>Midi-Pyrénées</li>
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</region>
<settlement><li>Castanet-Tolosan</li>
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<tree><country name="Estonie"><noRegion><name sortKey="Thiery, Odile" sort="Thiery, Odile" uniqKey="Thiery O" first="Odile" last="Thiéry">Odile Thiéry</name>
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<name sortKey="Jairus, Teele" sort="Jairus, Teele" uniqKey="Jairus T" first="Teele" last="Jairus">Teele Jairus</name>
<name sortKey="Kivistik, Paula Ann" sort="Kivistik, Paula Ann" uniqKey="Kivistik P" first="Paula-Ann" last="Kivistik">Paula-Ann Kivistik</name>
<name sortKey="Metspalu, Andres" sort="Metspalu, Andres" uniqKey="Metspalu A" first="Andres" last="Metspalu">Andres Metspalu</name>
<name sortKey="Milani, Lili" sort="Milani, Lili" uniqKey="Milani L" first="Lili" last="Milani">Lili Milani</name>
<name sortKey="Moora, Mari" sort="Moora, Mari" uniqKey="Moora M" first="Mari" last="Moora">Mari Moora</name>
<name sortKey="Opik, Maarja" sort="Opik, Maarja" uniqKey="Opik M" first="Maarja" last="Öpik">Maarja Öpik</name>
<name sortKey="Saks, Ulle" sort="Saks, Ulle" uniqKey="Saks U" first="Ülle" last="Saks">Ülle Saks</name>
<name sortKey="Vasar, Martti" sort="Vasar, Martti" uniqKey="Vasar M" first="Martti" last="Vasar">Martti Vasar</name>
<name sortKey="Zobel, Martin" sort="Zobel, Martin" uniqKey="Zobel M" first="Martin" last="Zobel">Martin Zobel</name>
</country>
<country name="France"><region name="Occitanie (région administrative)"><name sortKey="Roux, Christophe" sort="Roux, Christophe" uniqKey="Roux C" first="Christophe" last="Roux">Christophe Roux</name>
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</record>

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   |texte=   Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions of Rhizophagus irregularis and Gigaspora margarita is high and isolate-dependent.
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Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions of Rhizophagus irregularis and Gigaspora margarita is high and isolate-dependent.

Sequence variation in nuclear ribosomal small subunit, internal transcribed spacer and large subunit regions of Rhizophagus irregularis and Gigaspora margarita is high and isolate-dependent.

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