Comparative analysis of mitochondrial genomes of Rhizophagus irregularis - syn. Glomus irregulare - reveals a polymorphism induced by variability generating elements.
Identifieur interne : 001E58 ( Main/Corpus ); précédent : 001E57; suivant : 001E59Comparative analysis of mitochondrial genomes of Rhizophagus irregularis - syn. Glomus irregulare - reveals a polymorphism induced by variability generating elements.
Auteurs : Damien Formey ; Marion Molès ; Alexandra Haouy ; Bruno Savelli ; Olivier Bouchez ; Guillaume Bécard ; Christophe RouxSource :
- The New phytologist [ 1469-8137 ] ; 2012.
English descriptors
- KwdEn :
- DNA-Directed DNA Polymerase (genetics), Genome, Mitochondrial (MeSH), Glomeromycota (genetics), Inverted Repeat Sequences (MeSH), Microsatellite Repeats (MeSH), Mycorrhizae (genetics), Open Reading Frames (MeSH), Phylogeny (MeSH), Polymorphism, Single Nucleotide (MeSH), Sequence Analysis, DNA (methods).
- MESH :
- chemical , genetics : DNA-Directed DNA Polymerase.
- genetics : Glomeromycota, Mycorrhizae.
- methods : Sequence Analysis, DNA.
- Genome, Mitochondrial, Inverted Repeat Sequences, Microsatellite Repeats, Open Reading Frames, Phylogeny, Polymorphism, Single Nucleotide.
Abstract
Arbuscular mycorrhizal (AM) fungi are involved in one of the most widespread plant-fungus interactions. A number of studies on the population dynamics of AM fungi have used mitochondrial (mt) DNA sequences, and yet mt AM fungus genomes are poorly known. To date, four mt genomes of three species of AM fungi are available, among which are two from Rhizophagus irregularis. In order to study intra- and interstrain mt genome variability of R. irregularis, we sequenced and de novo assembled four additional mt genomes of this species. We used 454 pyrosequencing and Illumina technologies to directly sequence mt genomes from total genomic DNA. The mt genomes are unique within each strain. Interstrain divergences in genome size, as a result of highly polymorphic intergenic and intronic sequences, were observed. The polymorphism is brought about by three types of variability generating element (VGE): homing endonucleases, DNA polymerase domain-containing open reading frames and small inverted repeats. Based on VGE positioning, mt sequences and nuclear markers, two subclades of R. irregularis were characterized. The discovery of VGEs highlights the great intraspecific plasticity of the R. irregularis mt genome. VGEs allow the design of powerful mt markers for the typing and monitoring of R. irregularis strains in genetic and population studies.
DOI: 10.1111/j.1469-8137.2012.04283.x
PubMed: 22967288
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pubmed:22967288Le document en format XML
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Glomus irregulare - reveals a polymorphism induced by variability generating elements.</title><author><name sortKey="Formey, Damien" sort="Formey, Damien" uniqKey="Formey D" first="Damien" last="Formey">Damien Formey</name><affiliation><nlm:affiliation>Université de Toulouse, Castanet-Tolosan Cedex, France.</nlm:affiliation></affiliation></author><author><name sortKey="Moles, Marion" sort="Moles, Marion" uniqKey="Moles M" first="Marion" last="Molès">Marion Molès</name></author><author><name sortKey="Haouy, Alexandra" sort="Haouy, Alexandra" uniqKey="Haouy A" first="Alexandra" last="Haouy">Alexandra Haouy</name></author><author><name sortKey="Savelli, Bruno" sort="Savelli, Bruno" uniqKey="Savelli B" first="Bruno" last="Savelli">Bruno Savelli</name></author><author><name sortKey="Bouchez, Olivier" sort="Bouchez, Olivier" uniqKey="Bouchez O" first="Olivier" last="Bouchez">Olivier Bouchez</name></author><author><name sortKey="Becard, Guillaume" sort="Becard, Guillaume" uniqKey="Becard G" first="Guillaume" last="Bécard">Guillaume Bécard</name></author><author><name sortKey="Roux, Christophe" sort="Roux, Christophe" uniqKey="Roux C" first="Christophe" last="Roux">Christophe Roux</name></author></analytic><series><title level="j">The New phytologist</title><idno type="eISSN">1469-8137</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA-Directed DNA Polymerase (genetics)</term><term>Genome, Mitochondrial (MeSH)</term><term>Glomeromycota (genetics)</term><term>Inverted Repeat Sequences (MeSH)</term><term>Microsatellite Repeats (MeSH)</term><term>Mycorrhizae (genetics)</term><term>Open Reading Frames (MeSH)</term><term>Phylogeny (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Sequence Analysis, DNA (methods)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA-Directed DNA Polymerase</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Glomeromycota</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genome, Mitochondrial</term><term>Inverted Repeat Sequences</term><term>Microsatellite Repeats</term><term>Open Reading Frames</term><term>Phylogeny</term><term>Polymorphism, Single Nucleotide</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Arbuscular mycorrhizal (AM) fungi are involved in one of the most widespread plant-fungus interactions. A number of studies on the population dynamics of AM fungi have used mitochondrial (mt) DNA sequences, and yet mt AM fungus genomes are poorly known. To date, four mt genomes of three species of AM fungi are available, among which are two from Rhizophagus irregularis. In order to study intra- and interstrain mt genome variability of R. irregularis, we sequenced and de novo assembled four additional mt genomes of this species. We used 454 pyrosequencing and Illumina technologies to directly sequence mt genomes from total genomic DNA. The mt genomes are unique within each strain. Interstrain divergences in genome size, as a result of highly polymorphic intergenic and intronic sequences, were observed. The polymorphism is brought about by three types of variability generating element (VGE): homing endonucleases, DNA polymerase domain-containing open reading frames and small inverted repeats. Based on VGE positioning, mt sequences and nuclear markers, two subclades of R. irregularis were characterized. The discovery of VGEs highlights the great intraspecific plasticity of the R. irregularis mt genome. VGEs allow the design of powerful mt markers for the typing and monitoring of R. irregularis strains in genetic and population studies.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22967288</PMID><DateCompleted><Year>2013</Year><Month>04</Month><Day>25</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1469-8137</ISSN><JournalIssue CitedMedium="Internet"><Volume>196</Volume><Issue>4</Issue><PubDate><Year>2012</Year><Month>Dec</Month></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>Comparative analysis of mitochondrial genomes of Rhizophagus irregularis - syn. Glomus irregulare - reveals a polymorphism induced by variability generating elements.</ArticleTitle><Pagination><MedlinePgn>1217-27</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/j.1469-8137.2012.04283.x</ELocationID><Abstract><AbstractText>Arbuscular mycorrhizal (AM) fungi are involved in one of the most widespread plant-fungus interactions. A number of studies on the population dynamics of AM fungi have used mitochondrial (mt) DNA sequences, and yet mt AM fungus genomes are poorly known. To date, four mt genomes of three species of AM fungi are available, among which are two from Rhizophagus irregularis. In order to study intra- and interstrain mt genome variability of R. irregularis, we sequenced and de novo assembled four additional mt genomes of this species. We used 454 pyrosequencing and Illumina technologies to directly sequence mt genomes from total genomic DNA. The mt genomes are unique within each strain. Interstrain divergences in genome size, as a result of highly polymorphic intergenic and intronic sequences, were observed. The polymorphism is brought about by three types of variability generating element (VGE): homing endonucleases, DNA polymerase domain-containing open reading frames and small inverted repeats. Based on VGE positioning, mt sequences and nuclear markers, two subclades of R. irregularis were characterized. The discovery of VGEs highlights the great intraspecific plasticity of the R. irregularis mt genome. VGEs allow the design of powerful mt markers for the typing and monitoring of R. irregularis strains in genetic and population studies.</AbstractText><CopyrightInformation>© 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Formey</LastName><ForeName>Damien</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Université de Toulouse, Castanet-Tolosan Cedex, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Molès</LastName><ForeName>Marion</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Haouy</LastName><ForeName>Alexandra</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Savelli</LastName><ForeName>Bruno</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Bouchez</LastName><ForeName>Olivier</ForeName><Initials>O</Initials></Author><Author ValidYN="Y"><LastName>Bécard</LastName><ForeName>Guillaume</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Roux</LastName><ForeName>Christophe</ForeName><Initials>C</Initials></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>2012</Year><Month>09</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>New Phytol</MedlineTA><NlmUniqueID>9882884</NlmUniqueID><ISSNLinking>0028-646X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>EC 2.7.7.7</RegistryNumber><NameOfSubstance UI="D004259">DNA-Directed DNA Polymerase</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="CommentIn"><RefSource>New Phytol. 2012 Dec;196(4):963-5</RefSource><PMID Version="1">23121186</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D004259" MajorTopicYN="N">DNA-Directed DNA Polymerase</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D054629" MajorTopicYN="Y">Genome, Mitochondrial</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055137" MajorTopicYN="N">Glomeromycota</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D055029" MajorTopicYN="N">Inverted Repeat Sequences</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018895" MajorTopicYN="N">Microsatellite Repeats</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D038821" MajorTopicYN="N">Mycorrhizae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016366" MajorTopicYN="N">Open Reading Frames</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2012</Year><Month>06</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2012</Year><Month>07</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2012</Year><Month>9</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2012</Year><Month>9</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2013</Year><Month>4</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">22967288</ArticleId><ArticleId IdType="doi">10.1111/j.1469-8137.2012.04283.x</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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