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Metagenome sequence of E laphomyces granulatus from sporocarp tissue reveals A scomycota ectomycorrhizal fingerprints of genome expansion and a P roteobacteria ‐rich microbiome
Author(s) -
Quandt C. Alisha,
Kohler Annegret,
Hesse Cedar N.,
Sharpton Thomas J.,
Martin Francis,
Spatafora Joseph W.
Publication year - 2015
Publication title -
environmental microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.954
H-Index - 188
eISSN - 1462-2920
pISSN - 1462-2912
DOI - 10.1111/1462-2920.12840
Subject(s) - biology , genome , obligate , metagenomics , phylogenetic tree , phylogenetics , transposable element , evolutionary biology , genetics , gene , botany
Summary 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 E laphomyces 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 E laphomyces lineage is most closely related to T alaromyces and T richocomaceae s.s. The genome of E . granulatu s is reduced in carbohydrate‐active enzymes, despite a large expansion in genome size, both of which are consistent with what is seen in T uber melanosporum , the other sequenced ectomycorrhizal ascomycete. A large number of transposable elements are predicted in the E . granulatus genome, especially G ypsy‐like long terminal repeats, and there has also been an expansion in helicases. The metagenome is a complex community dominated by bacteria in B radyrhizobiaceae , 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 E laphomyces phylogenetics, genomics, metagenomics and the evolution of the ectomycorrhizal association.