Studying genome heterogeneity within the arbuscular mycorrhizal fungal cytoplasm.
Identifieur interne : 001593 ( Main/Corpus ); précédent : 001592; suivant : 001594Studying genome heterogeneity within the arbuscular mycorrhizal fungal cytoplasm.
Auteurs : Eva Boon ; Sébastien Halary ; Eric Bapteste ; Mohamed HijriSource :
- Genome biology and evolution [ 1759-6653 ] ; 2015.
English descriptors
- KwdEn :
- Alleles (MeSH), Base Sequence (MeSH), Cluster Analysis (MeSH), Computer Simulation (MeSH), Cytoplasm (genetics), Evolution, Molecular (MeSH), Gene Dosage (MeSH), Genetic Markers (MeSH), Genetic Variation (MeSH), Genome Size (MeSH), Genome, Fungal (MeSH), Glomeromycota (genetics), Glomeromycota (isolation & purification), Molecular Sequence Annotation (MeSH), Mutation (genetics), Mycorrhizae (genetics), Mycorrhizae (isolation & purification), Polymorphism, Genetic (MeSH), Real-Time Polymerase Chain Reaction (MeSH), Repetitive Sequences, Nucleic Acid (genetics), Reproducibility of Results (MeSH).
- MESH :
- chemical : Genetic Markers.
- genetics : Cytoplasm, Glomeromycota, Mutation, Mycorrhizae, Repetitive Sequences, Nucleic Acid.
- isolation & purification : Glomeromycota, Mycorrhizae.
- Alleles, Base Sequence, Cluster Analysis, Computer Simulation, Evolution, Molecular, Gene Dosage, Genetic Variation, Genome Size, Genome, Fungal, Molecular Sequence Annotation, Polymorphism, Genetic, Real-Time Polymerase Chain Reaction, Reproducibility of Results.
Abstract
Although heterokaryons have been reported in nature, multicellular organisms are generally assumed genetically homogeneous. Here, we investigate the case of arbuscular mycorrhizal fungi (AMF) that form symbiosis with plant roots. The growth advantages they confer to their hosts are of great potential benefit to sustainable agricultural practices. However, measuring genetic diversity for these coenocytes is a major challenge: Within the same cytoplasm, AMF contain thousands of nuclei and show extremely high levels of genetic variation for some loci. The extent and physical location of polymorphism within and between AMF genomes is unclear. We used two complementary strategies to estimate genetic diversity in AMF, investigating polymorphism both on a genome scale and in putative single copy loci. First, we used data from whole-genome pyrosequencing of four AMF isolates to describe genetic diversity, based on a conservative network-based clustering approach. AMF isolates showed marked differences in genome-wide diversity patterns in comparison to a panel of control fungal genomes. This clustering approach further allowed us to provide conservative estimates of Rhizophagus spp. genomes sizes. Second, we designed new putative single copy genomic markers, which we investigated by massive parallel amplicon sequencing for two Rhizophagus irregularis and one Rhizophagus sp. isolates. Most loci showed high polymorphism, with up to 103 alleles per marker. This polymorphism could be distributed within or between nuclei. However, we argue that the Rhizophagus isolates under study might be heterokaryotic, at least for the putative single copy markers we studied. Considering that genetic information is the main resource for identification of AMF, we suggest that special attention is warranted for the study of these ecologically important organisms.
DOI: 10.1093/gbe/evv002
PubMed: 25573960
PubMed Central: PMC4350173
Links to Exploration step
pubmed:25573960Le document en format XML
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wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">001593</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Studying genome heterogeneity within the arbuscular mycorrhizal fungal cytoplasm.</title><author><name sortKey="Boon, Eva" sort="Boon, Eva" uniqKey="Boon E" first="Eva" last="Boon">Eva Boon</name><affiliation><nlm:affiliation>Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Quebec, Canada eric.bapteste@snv.jussieu.fr mohamed.hijri@umontreal.ca.</nlm:affiliation></affiliation></author><author><name sortKey="Halary, Sebastien" sort="Halary, Sebastien" uniqKey="Halary S" first="Sébastien" last="Halary">Sébastien Halary</name><affiliation><nlm:affiliation>Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Quebec, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Bapteste, Eric" sort="Bapteste, Eric" uniqKey="Bapteste E" first="Eric" last="Bapteste">Eric Bapteste</name><affiliation><nlm:affiliation>CNRS, UMR7138, Institut de Biologie Paris-Seine, Paris, France Sorbonne Universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), Paris, France eric.bapteste@snv.jussieu.fr mohamed.hijri@umontreal.ca.</nlm:affiliation></affiliation></author><author><name sortKey="Hijri, Mohamed" sort="Hijri, Mohamed" uniqKey="Hijri M" first="Mohamed" last="Hijri">Mohamed Hijri</name><affiliation><nlm:affiliation>Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Quebec, Canada eric.bapteste@snv.jussieu.fr mohamed.hijri@umontreal.ca.</nlm:affiliation></affiliation></author></analytic><series><title level="j">Genome biology and evolution</title><idno type="eISSN">1759-6653</idno><imprint><date when="2015" type="published">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alleles (MeSH)</term><term>Base Sequence (MeSH)</term><term>Cluster Analysis (MeSH)</term><term>Computer Simulation (MeSH)</term><term>Cytoplasm (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Dosage (MeSH)</term><term>Genetic Markers (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genome Size (MeSH)</term><term>Genome, Fungal (MeSH)</term><term>Glomeromycota (genetics)</term><term>Glomeromycota (isolation & purification)</term><term>Molecular Sequence Annotation (MeSH)</term><term>Mutation (genetics)</term><term>Mycorrhizae (genetics)</term><term>Mycorrhizae (isolation & purification)</term><term>Polymorphism, Genetic (MeSH)</term><term>Real-Time Polymerase Chain Reaction (MeSH)</term><term>Repetitive Sequences, Nucleic Acid (genetics)</term><term>Reproducibility of Results (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cytoplasm</term><term>Glomeromycota</term><term>Mutation</term><term>Mycorrhizae</term><term>Repetitive Sequences, Nucleic Acid</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Glomeromycota</term><term>Mycorrhizae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alleles</term><term>Base Sequence</term><term>Cluster Analysis</term><term>Computer Simulation</term><term>Evolution, Molecular</term><term>Gene Dosage</term><term>Genetic Variation</term><term>Genome Size</term><term>Genome, Fungal</term><term>Molecular Sequence Annotation</term><term>Polymorphism, Genetic</term><term>Real-Time Polymerase Chain Reaction</term><term>Reproducibility of Results</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Although heterokaryons have been reported in nature, multicellular organisms are generally assumed genetically homogeneous. Here, we investigate the case of arbuscular mycorrhizal fungi (AMF) that form symbiosis with plant roots. The growth advantages they confer to their hosts are of great potential benefit to sustainable agricultural practices. However, measuring genetic diversity for these coenocytes is a major challenge: Within the same cytoplasm, AMF contain thousands of nuclei and show extremely high levels of genetic variation for some loci. The extent and physical location of polymorphism within and between AMF genomes is unclear. We used two complementary strategies to estimate genetic diversity in AMF, investigating polymorphism both on a genome scale and in putative single copy loci. First, we used data from whole-genome pyrosequencing of four AMF isolates to describe genetic diversity, based on a conservative network-based clustering approach. AMF isolates showed marked differences in genome-wide diversity patterns in comparison to a panel of control fungal genomes. This clustering approach further allowed us to provide conservative estimates of Rhizophagus spp. genomes sizes. Second, we designed new putative single copy genomic markers, which we investigated by massive parallel amplicon sequencing for two Rhizophagus irregularis and one Rhizophagus sp. isolates. Most loci showed high polymorphism, with up to 103 alleles per marker. This polymorphism could be distributed within or between nuclei. However, we argue that the Rhizophagus isolates under study might be heterokaryotic, at least for the putative single copy markers we studied. Considering that genetic information is the main resource for identification of AMF, we suggest that special attention is warranted for the study of these ecologically important organisms.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25573960</PMID><DateCompleted><Year>2015</Year><Month>09</Month><Day>28</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1759-6653</ISSN><JournalIssue CitedMedium="Internet"><Volume>7</Volume><Issue>2</Issue><PubDate><Year>2015</Year><Month>Jan</Month><Day>07</Day></PubDate></JournalIssue><Title>Genome biology and evolution</Title><ISOAbbreviation>Genome Biol Evol</ISOAbbreviation></Journal><ArticleTitle>Studying genome heterogeneity within the arbuscular mycorrhizal fungal cytoplasm.</ArticleTitle><Pagination><MedlinePgn>505-21</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/gbe/evv002</ELocationID><Abstract><AbstractText>Although heterokaryons have been reported in nature, multicellular organisms are generally assumed genetically homogeneous. Here, we investigate the case of arbuscular mycorrhizal fungi (AMF) that form symbiosis with plant roots. The growth advantages they confer to their hosts are of great potential benefit to sustainable agricultural practices. However, measuring genetic diversity for these coenocytes is a major challenge: Within the same cytoplasm, AMF contain thousands of nuclei and show extremely high levels of genetic variation for some loci. The extent and physical location of polymorphism within and between AMF genomes is unclear. We used two complementary strategies to estimate genetic diversity in AMF, investigating polymorphism both on a genome scale and in putative single copy loci. First, we used data from whole-genome pyrosequencing of four AMF isolates to describe genetic diversity, based on a conservative network-based clustering approach. AMF isolates showed marked differences in genome-wide diversity patterns in comparison to a panel of control fungal genomes. This clustering approach further allowed us to provide conservative estimates of Rhizophagus spp. genomes sizes. Second, we designed new putative single copy genomic markers, which we investigated by massive parallel amplicon sequencing for two Rhizophagus irregularis and one Rhizophagus sp. isolates. Most loci showed high polymorphism, with up to 103 alleles per marker. This polymorphism could be distributed within or between nuclei. However, we argue that the Rhizophagus isolates under study might be heterokaryotic, at least for the putative single copy markers we studied. Considering that genetic information is the main resource for identification of AMF, we suggest that special attention is warranted for the study of these ecologically important organisms.</AbstractText><CopyrightInformation>© The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Boon</LastName><ForeName>Eva</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Quebec, Canada eric.bapteste@snv.jussieu.fr mohamed.hijri@umontreal.ca.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Halary</LastName><ForeName>Sébastien</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Quebec, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bapteste</LastName><ForeName>Eric</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>CNRS, UMR7138, Institut de Biologie Paris-Seine, Paris, France Sorbonne Universités, 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