Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome.
Identifieur interne : 001523 ( Main/Corpus ); précédent : 001522; suivant : 001524Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome.
Auteurs : C Alisha Quandt ; Annegret Kohler ; Cedar N. Hesse ; Thomas J. Sharpton ; Francis Martin ; Joseph W. SpataforaSource :
- Environmental microbiology [ 1462-2920 ] ; 2015.
English descriptors
- KwdEn :
- Base Sequence (MeSH), Bradyrhizobiaceae (classification), Bradyrhizobiaceae (genetics), DNA Transposable Elements (genetics), DNA, Fungal (genetics), Eurotiales (classification), Eurotiales (genetics), Fruiting Bodies, Fungal (genetics), Genome, Fungal (genetics), Metagenome (MeSH), Metagenomics (MeSH), Microbiota (genetics), Mycorrhizae (genetics), Phylogeny (MeSH), Sequence Analysis, DNA (MeSH), Talaromyces (genetics).
- MESH :
- chemical , genetics : DNA Transposable Elements, DNA, Fungal.
- classification : Bradyrhizobiaceae, Eurotiales.
- genetics : Bradyrhizobiaceae, Eurotiales, Fruiting Bodies, Fungal, Genome, Fungal, Microbiota, Mycorrhizae, Talaromyces.
- Base Sequence, Metagenome, Metagenomics, Phylogeny, Sequence Analysis, DNA.
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.
DOI: 10.1111/1462-2920.12840
PubMed: 25753751
Links to Exploration step
pubmed:25753751Le document en format XML
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<author><name sortKey="Hesse, Cedar N" sort="Hesse, Cedar N" uniqKey="Hesse C" first="Cedar N" last="Hesse">Cedar N. Hesse</name>
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<series><title level="j">Environmental microbiology</title>
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<term>Bradyrhizobiaceae (classification)</term>
<term>Bradyrhizobiaceae (genetics)</term>
<term>DNA Transposable Elements (genetics)</term>
<term>DNA, Fungal (genetics)</term>
<term>Eurotiales (classification)</term>
<term>Eurotiales (genetics)</term>
<term>Fruiting Bodies, Fungal (genetics)</term>
<term>Genome, Fungal (genetics)</term>
<term>Metagenome (MeSH)</term>
<term>Metagenomics (MeSH)</term>
<term>Microbiota (genetics)</term>
<term>Mycorrhizae (genetics)</term>
<term>Phylogeny (MeSH)</term>
<term>Sequence Analysis, DNA (MeSH)</term>
<term>Talaromyces (genetics)</term>
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<term>DNA, Fungal</term>
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<term>Eurotiales</term>
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<term>Genome, Fungal</term>
<term>Microbiota</term>
<term>Mycorrhizae</term>
<term>Talaromyces</term>
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<keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term>
<term>Metagenome</term>
<term>Metagenomics</term>
<term>Phylogeny</term>
<term>Sequence Analysis, DNA</term>
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<front><div type="abstract" xml:lang="en">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>
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<Abstract><AbstractText>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. </AbstractText>
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