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Wood decay under anoxia by the brown-rot fungus Fomitopsis pinicola

The degradation of dead wood by basidiomycete fungi relies on Fenton chemistry under aerobic conditions. Here, Röllig et al. show that these fungi can also thrive and degrade wood in anoxia, switching from a Fenton chemistry-based process to the secretion of plant cell wall-active enzymes.

Robert Röllig
Annie Lebreton
Jean-Guy Berrin
ResearchOpen Access09 Aug 2025
Nature Communications

Volume: 16, P: 1-13
Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

De novo assembly of 23 Aspergillus section Nigri and 6 Aspergillus niger genome sequences allows for inter- and intraspecies comparisons and prediction of secondary metabolite gene clusters.

Tammi C. Vesth
Jane L. Nybo
Mikael R. Andersen
ResearchOpen Access22 Oct 2018
Nature Genetics

Volume: 50, P: 1688-1695
Bacteroidetes use thousands of enzyme combinations to break down glycans

Bacteroidetes genomes contain polysaccharide utilization loci (PULs), each of which encodes enzymes for the breakdown of one particular glycan. By analyzing the enzyme composition of 13,537 PULs, the authors suggest that the natural glycan diversity is orders of magnitude lower than previously proposed.

Pascal Lapébie
Vincent Lombard
Bernard Henrissat
ResearchOpen Access03 May 2019
Nature Communications

Volume: 10, P: 1-7
Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi

Asian soybean rust caused by Phakopsora pachyrhizi is an important plant pathogen, but an accurate genome assembly for this fungus has been lacking. This study sequenced three independent P. pachyrhizi isolates and generated reference quality assemblies and genome annotations, representing a critical step for further in-depth studies of this pathogen and the development of new methods of control.

Yogesh K. Gupta
Francismar C. Marcelino-Guimarães
H. Peter van Esse
ResearchOpen Access01 Apr 2023
Nature Communications

Volume: 14, P: 1-16
Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria

The fungal genus Armillaria includes virulent necrotrophic pathogens, unusual wood decayers and the largest terrestrial organisms on Earth. Sahu et al. suggest that horizontal gene transfer contributed to the evolution of some of these unique traits.

Neha Sahu
Boris Indic
László G. Nagy
Research07 Aug 2023
Nature Microbiology

Volume: 8, P: 1668-1681
Genetic determinants of endophytism in the Arabidopsis root mycobiome

Plant roots host diverse fungal communities that affect plant health. Here, Mesny et al. use comparative genomics and transcriptomics of fungal isolates from the Arabidopsis thaliana root mycobiota, together with root colonization assays, to identify genetic determinants of endophytism.

Fantin Mesny
Shingo Miyauchi
Stéphane Hacquard
ResearchOpen Access10 Dec 2021
Nature Communications

Volume: 12, P: 1-15
Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Mycorrhizal symbioses have evolved repeatedly in diverse fungal lineages. A large phylogenomic analysis sheds light on genomic changes associated with transitions from saprotrophy to symbiosis, including divergent genetic innovations underlying the convergent origins of the ectomycorrhizal guild.

Shingo Miyauchi
Enikő Kiss
Francis M. Martin
ResearchOpen Access12 Oct 2020
Nature Communications

Volume: 11, P: 1-17
Snow- and ice-ecosystem cleaning capability of the pucciniomycotinous yeast Phenoliferia psychrophenolica

Phenoliferia psychrophenolica, isolated from red snow, harbors a genome rich in ice-binding proteins and carbohydrate-active enzymes, and metabolizes pigments from snow and glacier algae, potentially linking the decline of algal blooms to cryospheric carbon fluxes.

Jade A. Ezzedine
Pierre Guenzi-Tiberi
Eric Maréchal
ResearchOpen Access21 Jul 2025
Communications Biology

Volume: 8, P: 1-15
Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Rumen microbiome biology gets a boost with the release of 410 high-quality reference genomes from the Hungate1000 project.

Rekha Seshadri
Sinead C Leahy
William J Kelly
ResearchOpen Access19 Mar 2018
Nature Biotechnology

Volume: 36, P: 359-367
Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses

An extensive comparative genomic analysis of thermophilic, thermotolerant, and mesophilic fungi genomes is used to define features of thermophily and shows the power of integrating phylogenetic analysis with machine learning and AlphaFold2 to obtain insights into the evolutionary origins of a specific physiology.

Andrei S. Steindorff
Maria Victoria Aguilar-Pontes
Igor V. Grigoriev
ResearchOpen Access12 Sept 2024
Communications Biology

Volume: 7, P: 1-11
Niche differentiation and evolution of the wood decay machinery in the invasive fungus Serpula lacrymans

Jaqueline Hess
Sudhagar V. Balasundaram
Inger Skrede
ResearchOpen Access19 Oct 2020
The ISME Journal

Volume: 15, P: 592-604

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Wood decay under anoxia by the brown-rot fungus Fomitopsis pinicola

Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

Bacteroidetes use thousands of enzyme combinations to break down glycans

Major proliferation of transposable elements shaped the genome of the soybean rust pathogen Phakopsora pachyrhizi

Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria

Genetic determinants of endophytism in the Arabidopsis root mycobiome

Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits

Snow- and ice-ecosystem cleaning capability of the pucciniomycotinous yeast Phenoliferia psychrophenolica

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

Comparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses

Niche differentiation and evolution of the wood decay machinery in the invasive fungus Serpula lacrymans

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