Metagenome sequence of Elaphomyces granulatus from sporocarp tissue reveals Ascomycota ectomycorrhizal fingerprints of genome expansion and a Proteobacteria-rich microbiome

Environmental Microbiology
C Alisha QuandtJoseph W Spatafora

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, metagenomic...Continue Reading

References

Mar 28, 2002·Nucleic Acids Research·A J EnrightC A Ouzounis
Mar 11, 2003·Glycobiology·Alan D ElbeinDavid Carroll
Mar 27, 2003·International Journal of Systematic and Evolutionary Microbiology·Valeria BianciottoPeter Vandamme
Aug 21, 2003·Lancet·Patricia RenestoDidier Raoult
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Jun 24, 2004·Proceedings of the National Academy of Sciences of the United States of America·Bastien BoussauSiv G E Andersson
Sep 28, 2004·Mycological Research·Patrik InderbitzinMary L Berbee
Jun 2, 2005·FEMS Microbiology Letters·Elena BarbieriVilberto Stocchi
Jun 18, 2005·Bioinformatics·Alkes L PricePavel A Pevzner
Dec 3, 2005·Nature Reviews. Microbiology·Nancy P KellerJoan W Bennett
Nov 1, 1993·Applied and Environmental Microbiology·D L CrawfordM A Ousley
Apr 22, 2006·The New Phytologist·Leho TedersooRasmus Kjøller
May 4, 2006·The Journal of Biological Chemistry·Smita S Patel, Ilker Donmez
Aug 12, 2006·International Journal of Systematic and Evolutionary Microbiology·Elena BustiStefano Donadio
Mar 29, 2007·The New Phytologist·Mónica Fajardo LópezUwe Nehls
May 10, 2007·Mycologia·David M GeiserAndré Aptroot
May 17, 2007·The New Phytologist·Nina A LehrMika T Tarkka
Aug 10, 2007·Environmental Microbiology·Elena BarbieriVilberto Stocchi
Sep 7, 2007·The New Phytologist·P Frey-KlettM Tarkka
Nov 6, 2007·International Journal of Systematic and Evolutionary Microbiology·Laila P Partida-MartinezChristian Hertweck
Nov 21, 2007·Genome Research·Brandi L CantarelMark Yandell
Apr 12, 2008·PLoS Genetics·Natalie D FedorovaWilliam C Nierman
Sep 2, 2008·Genome Research·Vardges Ter-HovhannisyanMark Borodovsky
Sep 30, 2008·Nature Biotechnology·Marco A van den BergRoel A L Bovenberg
Oct 8, 2008·Nucleic Acids Research·Brandi L CantarelBernard Henrissat
Nov 1, 2008·Current Opinion in Microbiology·Ellen M Fox, Barbara J Howlett
Dec 2, 2008·Nucleic Acids Research·Genis ParraIan Korf
Feb 10, 2009·Applied and Environmental Microbiology·Naomi L WardCheryl R Kuske

❮ Previous
Next ❯

Citations

Mar 15, 2016·Frontiers in Microbiology·Annika C MosierJillian F Banfield
Mar 3, 2018·Genome Research·Patrick T WestJillian F Banfield
Jan 13, 2018·Environmental Microbiology Reports·Mohammad BahramMartin Ryberg
May 8, 2018·Canadian Journal of Microbiology·J M Rinta-KantoS Timonen
Nov 30, 2018·The New Phytologist·Ying ChangJoseph W Spatafora
Mar 20, 2020·Genome Research·Lin-Xing ChenJillian F Banfield
Sep 17, 2017·Microbiology Spectrum·Joseph W SpataforaMeredith Blackwell
Jul 11, 2021·Current Biology : CB·Rachel A KochM Catherine Aime
Sep 9, 2021·Environmental Microbiology Reports·Hong-Yan BaiYong Jia
Oct 5, 2021·Frontiers in Microbiology·Teppo Rämä, C Alisha Quandt

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.