Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria‐rich microbiome
Identifieur interne : 001970 ( Main/Exploration ); précédent : 001969; suivant : 001971Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria‐rich microbiome
Auteurs : C. Alisha Quandt [États-Unis] ; Annegret Kohler [France] ; Cedar N. Hesse [États-Unis] ; Thomas J. Sharpton [États-Unis] ; Francis Martin [France] ; Joseph W. Spatafora [États-Unis]Source :
- Environmental Microbiology [ 1462-2912 ] ; 2015-08.
Abstract
Many obligate symbiotic fungi are difficult to maintain in culture, and there is a growing need for alternative approaches to obtaining tissue and subsequent genomic assemblies from such species. In this study, the genome of Elaphomyces granulatus was sequenced from sporocarp tissue. The genome assembly remains on many contigs, but gene space is estimated to be mostly complete. Phylogenetic analyses revealed that the Elaphomyces lineage is most closely related to Talaromyces and Trichocomaceae s.s. The genome of E. granulatus is reduced in carbohydrate‐active enzymes, despite a large expansion in genome size, both of which are consistent with what is seen in Tuber melanosporum, the other sequenced ectomycorrhizal ascomycete. A large number of transposable elements are predicted in the E. granulatus genome, especially Gypsy‐like long terminal repeats, and there has also been an expansion in helicases. The metagenome is a complex community dominated by bacteria in Bradyrhizobiaceae, and there is evidence to suggest that the community may be reduced in functional capacity as estimated by KEGG pathways. Through the sequencing of sporocarp tissue, this study has provided insights into Elaphomyces phylogenetics, genomics, metagenomics and the evolution of the ectomycorrhizal association.
Url:
DOI: 10.1111/1462-2920.12840
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Istex, to step Corpus: 002412
- to stream Istex, to step Curation: 002412
- to stream Istex, to step Checkpoint: 000114
- to stream Main, to step Merge: 001975
- to stream Main, to step Curation: 001970
Le document en format XML
<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria‐rich microbiome</title><author><name sortKey="Quandt, C Alisha" sort="Quandt, C Alisha" uniqKey="Quandt C" first="C. Alisha" last="Quandt">C. Alisha Quandt</name></author><author><name sortKey="Kohler, Annegret" sort="Kohler, Annegret" uniqKey="Kohler A" first="Annegret" last="Kohler">Annegret Kohler</name></author><author><name sortKey="Hesse, Cedar N" sort="Hesse, Cedar N" uniqKey="Hesse C" first="Cedar N." last="Hesse">Cedar N. Hesse</name></author><author><name sortKey="Sharpton, Thomas J" sort="Sharpton, Thomas J" uniqKey="Sharpton T" first="Thomas J." last="Sharpton">Thomas J. Sharpton</name></author><author><name sortKey="Martin, Francis" sort="Martin, Francis" uniqKey="Martin F" first="Francis" last="Martin">Francis Martin</name></author><author><name sortKey="Spatafora, Joseph W" sort="Spatafora, Joseph W" uniqKey="Spatafora J" first="Joseph W." last="Spatafora">Joseph W. Spatafora</name></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:2CAF4A26852BBE28AC587387A1A8DFC37C06A8A0</idno><date when="2015" year="2015">2015</date><idno type="doi">10.1111/1462-2920.12840</idno><idno type="url">https://api.istex.fr/ark:/67375/WNG-03FN1VHQ-3/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">002412</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">002412</idno><idno type="wicri:Area/Istex/Curation">002412</idno><idno type="wicri:Area/Istex/Checkpoint">000114</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Checkpoint">000114</idno><idno type="wicri:doubleKey">1462-2912:2015:Quandt C:metagenome:sequence:of</idno><idno type="wicri:Area/Main/Merge">001975</idno><idno type="wicri:Area/Main/Curation">001970</idno><idno type="wicri:Area/Main/Exploration">001970</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main">Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria‐rich microbiome</title><author><name sortKey="Quandt, C Alisha" sort="Quandt, C Alisha" uniqKey="Quandt C" first="C. Alisha" last="Quandt">C. Alisha Quandt</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Botany and Plant Pathology, Oregon State University, OR, 97331, Corvallis</wicri:regionArea><wicri:noRegion>Corvallis</wicri:noRegion></affiliation><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Current Address: Department of Ecology and Evolutionary Biology, University of Michigan, MI, Ann Arbor</wicri:regionArea><wicri:noRegion>Ann Arbor</wicri:noRegion></affiliation><affiliation wicri:level="1"><country wicri:rule="url">États-Unis</country></affiliation></author><author><name sortKey="Kohler, Annegret" sort="Kohler, Annegret" uniqKey="Kohler A" first="Annegret" last="Kohler">Annegret Kohler</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>Institut National de la Recherché Agronomique, Centre de Nancy, Champenoux</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Champenoux</settlement></placeName></affiliation></author><author><name sortKey="Hesse, Cedar N" sort="Hesse, Cedar N" uniqKey="Hesse C" first="Cedar N." last="Hesse">Cedar N. Hesse</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Bioscience Division, Los Alamos National Laboratory, NM, Los Alamos</wicri:regionArea><wicri:noRegion>Los Alamos</wicri:noRegion></affiliation></author><author><name sortKey="Sharpton, Thomas J" sort="Sharpton, Thomas J" uniqKey="Sharpton T" first="Thomas J." last="Sharpton">Thomas J. Sharpton</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Microbiology, Oregon State University, 97331, Corvallis, OR</wicri:regionArea><wicri:noRegion>OR</wicri:noRegion></affiliation><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Statistics, Oregon State University, OR, 97331, Corvallis</wicri:regionArea><wicri:noRegion>Corvallis</wicri:noRegion></affiliation></author><author><name sortKey="Martin, Francis" sort="Martin, Francis" uniqKey="Martin F" first="Francis" last="Martin">Francis Martin</name><affiliation wicri:level="3"><country xml:lang="fr">France</country><wicri:regionArea>Institut National de la Recherché Agronomique, Centre de Nancy, Champenoux</wicri:regionArea><placeName><region type="region" nuts="2">Grand Est</region><region type="old region" nuts="2">Lorraine (région)</region><settlement type="city">Champenoux</settlement></placeName></affiliation></author><author><name sortKey="Spatafora, Joseph W" sort="Spatafora, Joseph W" uniqKey="Spatafora J" first="Joseph W." last="Spatafora">Joseph W. Spatafora</name><affiliation wicri:level="1"><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Botany and Plant Pathology, Oregon State University, OR, 97331, Corvallis</wicri:regionArea><wicri:noRegion>Corvallis</wicri:noRegion></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Environmental Microbiology</title><title level="j" type="alt">ENVIRONMENTAL MICROBIOLOGY</title><idno type="ISSN">1462-2912</idno><idno type="eISSN">1462-2920</idno><imprint><biblScope unit="vol">17</biblScope><biblScope unit="issue">8</biblScope><biblScope unit="page" from="2952">2952</biblScope><biblScope unit="page" to="2968">2968</biblScope><biblScope unit="page-count">17</biblScope><date type="published" when="2015-08">2015-08</date></imprint><idno type="ISSN">1462-2912</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1462-2912</idno></seriesStmt></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract">Many obligate symbiotic fungi are difficult to maintain in culture, and there is a growing need for alternative approaches to obtaining tissue and subsequent genomic assemblies from such species. In this study, the genome of Elaphomyces granulatus was sequenced from sporocarp tissue. The genome assembly remains on many contigs, but gene space is estimated to be mostly complete. Phylogenetic analyses revealed that the Elaphomyces lineage is most closely related to Talaromyces and Trichocomaceae s.s. The genome of E. granulatus is reduced in carbohydrate‐active enzymes, despite a large expansion in genome size, both of which are consistent with what is seen in Tuber melanosporum, the other sequenced ectomycorrhizal ascomycete. A large number of transposable elements are predicted in the E. granulatus genome, especially Gypsy‐like long terminal repeats, and there has also been an expansion in helicases. The metagenome is a complex community dominated by bacteria in Bradyrhizobiaceae, and there is evidence to suggest that the community may be reduced in functional capacity as estimated by KEGG pathways. Through the sequencing of sporocarp tissue, this study has provided insights into Elaphomyces phylogenetics, genomics, metagenomics and the evolution of the ectomycorrhizal association.</div></front></TEI><affiliations><list><country><li>France</li><li>États-Unis</li></country><region><li>Grand Est</li><li>Lorraine (région)</li></region><settlement><li>Champenoux</li></settlement></list><tree><country name="États-Unis"><noRegion><name sortKey="Quandt, C Alisha" sort="Quandt, C Alisha" uniqKey="Quandt C" first="C. Alisha" last="Quandt">C. Alisha Quandt</name></noRegion><name sortKey="Hesse, Cedar N" sort="Hesse, Cedar N" uniqKey="Hesse C" first="Cedar N." last="Hesse">Cedar N. Hesse</name><name sortKey="Quandt, C Alisha" sort="Quandt, C Alisha" uniqKey="Quandt C" first="C. Alisha" last="Quandt">C. Alisha Quandt</name><name sortKey="Quandt, C Alisha" sort="Quandt, C Alisha" uniqKey="Quandt C" first="C. Alisha" last="Quandt">C. Alisha Quandt</name><name sortKey="Sharpton, Thomas J" sort="Sharpton, Thomas J" uniqKey="Sharpton T" first="Thomas J." last="Sharpton">Thomas J. Sharpton</name><name sortKey="Sharpton, Thomas J" sort="Sharpton, Thomas J" uniqKey="Sharpton T" first="Thomas J." last="Sharpton">Thomas J. Sharpton</name><name sortKey="Spatafora, Joseph W" sort="Spatafora, Joseph W" uniqKey="Spatafora J" first="Joseph W." last="Spatafora">Joseph W. Spatafora</name></country><country name="France"><region name="Grand Est"><name sortKey="Kohler, Annegret" sort="Kohler, Annegret" uniqKey="Kohler A" first="Annegret" last="Kohler">Annegret Kohler</name></region><name sortKey="Martin, Francis" sort="Martin, Francis" uniqKey="Martin F" first="Francis" last="Martin">Francis Martin</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001970 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 001970 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= ISTEX:2CAF4A26852BBE28AC587387A1A8DFC37C06A8A0
|texte= Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria‐rich microbiome
}}
| This area was generated with Dilib version V0.6.33. |  |