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Rapid Divergence of Genome Architectures Following the Origin of an Ectomycorrhizal Symbiosis in the Genus Amanita

https://doi.org/10.1093/molbev/msy179
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Molecular Mycorrhizal Symbiosis
inferredcites →https://doi.org/10.1002/9781118951446.ch6openalex-snapshot
The evolution of the mycorrhizal lifestyles – a genomic perspective
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Parallel Acceleration of Evolutionary Rates in Symbiont Genes Underlying Host Nutrition
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ProtTest-HPC: Fast Selection of Best-Fit Models of Protein Evolution
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Correlations Between Bacterial Ecology and Mobile DNA
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Ectomycorrhizal lifestyle in fungi: global diversity, distribution, and evolution of phylogenetic lineages
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Mycorrhizal Symbiosis
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The Natural Histories of Species and Their Genomes
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Carbohydrate-Binding Modules of Fungal Cellulases
inferredcites →https://doi.org/10.1016/j.abb.2017.06.023openalex-snapshot
The family of berberine bridge enzyme-like enzymes: A treasure-trove of oxidative reactions
inferredcites →https://doi.org/10.1016/j.bbapap.2010.06.020openalex-snapshot
Cytochrome P450 enzymes in the fungal kingdom
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A Secreted Effector Protein of Laccaria bicolor Is Required for Symbiosis Development
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Reduced genomic potential for secreted plant cell-wall-degrading enzymes in the ectomycorrhizal fungus Amanita bisporigera, based on the secretome of Trichoderma reesei
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Take a Trip Through the Plant and Fungal Transportome of Mycorrhiza
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Convergence in Multispecies Interactions
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Isolation and analysis of a gene bbe1 encoding the berberine bridge enzyme from the California poppy Eschscholzia californica
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Selective recruitment of bacteria during embryogenesis of an earthworm
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A saponin-detoxifying enzyme mediates suppression of plant defences
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The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis
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Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis
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Full-length transcriptome assembly from RNA-Seq data without a reference genome
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Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum
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Comparative genomics reveals convergent rates of evolution in ant–plant mutualisms
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Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists
inferredcites →https://doi.org/10.1038/nmeth.1527openalex-snapshot
Limitations of next-generation genome sequence assembly
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SignalP 4.0: discriminating signal peptides from transmembrane regions
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Mechanisms of change in gene copy number
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The fungus that came in from the cold: dry rot’s pre-adapted ability to invade buildings
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Specialized plant biochemistry drives gene clustering in fungi
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An ancient family of lytic polysaccharide monooxygenases with roles in arthropod development and biomass digestion
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Parallel genome reduction in symbionts descended from closely related free-living bacteria
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Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria
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Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi
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An algorithm for progressive multiple alignment of sequences with insertions
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High-quality draft assemblies of mammalian genomes from massively parallel sequence data
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Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis
inferredcites →https://doi.org/10.1073/pnas.1322671111openalex-snapshot
Effector MiSSP7 of the mutualistic fungus Laccaria bicolor stabilizes the Populus JAZ6 protein and represses jasmonic acid (JA) responsive genes
inferredcites →https://doi.org/10.1073/pnas.1400592111openalex-snapshot
Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi
inferredcites →https://doi.org/10.1073/pnas.93.7.2873openalex-snapshot
Accelerated evolution and Muller's rachet in endosymbiotic bacteria.
inferredcites →https://doi.org/10.1073/pnas.94.21.11422openalex-snapshot
Accelerated evolution as a consequence of transitions to mutualism
inferredcites →https://doi.org/10.1074/jbc.m115.659631openalex-snapshot
Oxidation of Monolignols by Members of the Berberine Bridge Enzyme Family Suggests a Role in Plant Cell Wall Metabolism
inferredcites →https://doi.org/10.1080/15572536.2006.11832627openalex-snapshot
Major clades of Agaricales: a multilocus phylogenetic overview
inferredcites →https://doi.org/10.1086/302221openalex-snapshot
Concerted Evolution: Molecular Mechanism and Biological Implications
inferredcites →https://doi.org/10.1093/bioinformatics/bti310openalex-snapshot
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btl140openalex-snapshot
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
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Using native and syntenically mapped cDNA alignments to improve de novo gene finding
inferredcites →https://doi.org/10.1093/bioinformatics/btp348openalex-snapshot
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btr088openalex-snapshot
ProtTest 3: fast selection of best-fit models of protein evolution
inferredcites →https://doi.org/10.1093/bioinformatics/bts386openalex-snapshot
Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees
inferredcites →https://doi.org/10.1093/bioinformatics/btu031openalex-snapshot
InterProScan 5: genome-scale protein function classification
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btv351openalex-snapshot
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
inferredcites →https://doi.org/10.1093/gbe/evr124openalex-snapshot
Causes and Consequences of Genome Expansion in Fungi
inferredcites →https://doi.org/10.1093/gbe/evt210openalex-snapshot
Genome Degeneration and Adaptation in a Nascent Stage of Symbiosis
inferredcites →https://doi.org/10.1093/gbe/evu121openalex-snapshot
Transposable Element Dynamics among Asymbiotic and Ectomycorrhizal Amanita Fungi
inferredcites →https://doi.org/10.1093/gbe/evu251openalex-snapshot
Diversity and Variability of NOD-Like Receptors in Fungi
inferredcites →https://doi.org/10.1093/gbe/evw140openalex-snapshot
Species- and Strain-Specific Adaptation of the HSP70 Super Family in Pathogenic Trypanosomatids
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Population Genomic Analysis of a Pitviper Reveals Microevolutionary Forces Underlying Venom Chemistry
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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
inferredcites →https://doi.org/10.1093/nar/gkj063openalex-snapshot
The PROSITE database
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WoLF PSORT: protein localization predictor
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The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
inferredcites →https://doi.org/10.1093/nar/gkt1178openalex-snapshot
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inferredcites →https://doi.org/10.1093/nar/gkv1248openalex-snapshot
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The Mutualist Laccaria bicolor Expresses a Core Gene Regulon During the Colonization of Diverse Host Plants and a Variable Regulon to Counteract Host-Specific Defenses
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Populus trichocarpa and Populus deltoides Exhibit Different Metabolomic Responses to Colonization by the Symbiotic Fungus Laccaria bicolor
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Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training
inferredcites →https://doi.org/10.1101/gr.161968.113openalex-snapshot
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inferredcites →https://doi.org/10.1101/gr.1917404openalex-snapshot
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Metatranscriptomic analysis of ectomycorrhizal roots reveals genes associated with P iloderma– P inus symbiosis: improved methodologies for assessing gene expression in situ
inferredcites →https://doi.org/10.1111/1462-2920.13670openalex-snapshot
The ectomycorrhizal basidiomycete Hebeloma cylindrosporum undergoes early waves of transcriptional reprogramming prior to symbiotic structures differentiation
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The ectomycorrhizal fungus Paxillus involutus converts organic matter in plant litter using a trimmed brown‐rot mechanism involving Fenton chemistry
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Polymorphism at the ribosomal DNA ITS and its relation to postglacial re‐colonization routes of the Perigord truffle Tuber melanosporum
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The evolution of plant–insect mutualisms
inferredcites →https://doi.org/10.1111/j.1469-8137.2009.02774.xopenalex-snapshot
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POPULATION STRUCTURE, LEVELS OF SELECTION, AND THE EVOLUTION OF INTRACELLULAR SYMBIONTS
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Horizontal transfer of carbohydrate metabolism genes into ectomycorrhizal A manita
inferredcites →https://doi.org/10.1111/nph.13722openalex-snapshot
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inferredcites →https://doi.org/10.1126/science.1221748openalex-snapshot
The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes
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Plant-Polysaccharide-Degrading Enzymes from Basidiomycetes
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A NEW GENERATION OF HOMOLOGY SEARCH TOOLS BASED ON PROBABILISTIC INFERENCE
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Comparative analysis of fungal protein kinases and associated domains
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Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans
inferredcites →https://doi.org/10.1186/1471-2164-14-555openalex-snapshot
Functional requirements driving the gene duplication in 12 Drosophila species
inferredcites →https://doi.org/10.1186/1471-2229-4-10openalex-snapshot
The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana
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Novel enzymes for the degradation of cellulose
inferredcites →https://doi.org/10.1186/1754-6834-6-41openalex-snapshot
Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes
inferredcites →https://doi.org/10.1186/gb-2008-9-1-r7openalex-snapshot
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
inferredcites →https://doi.org/10.1186/s12864-015-1344-4openalex-snapshot
CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts
inferredcites →https://doi.org/10.1186/s13068-015-0274-3openalex-snapshot
Substrate specificity and regioselectivity of fungal AA9 lytic polysaccharide monooxygenases secreted by Podospora anserina
inferredcites →https://doi.org/10.1371/journal.pcbi.1003998openalex-snapshot
Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies
inferredcites →https://doi.org/10.1371/journal.pgen.1006348openalex-snapshot
Metatranscriptomic Study of Common and Host-Specific Patterns of Gene Expression between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Genus Suillus
inferredcites →https://doi.org/10.1371/journal.pgen.1007742openalex-snapshot
Correction: Metatranscriptomic Study of Common and Host-Specific Patterns of Gene Expression between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Genus Suillus
inferredcites →https://doi.org/10.1371/journal.pone.0021800openalex-snapshot
REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms
inferredcites →https://doi.org/10.1371/journal.pone.0039597openalex-snapshot
The Irreversible Loss of a Decomposition Pathway Marks the Single Origin of an Ectomycorrhizal Symbiosis
inferredcites →https://doi.org/10.1371/journal.pone.0058294openalex-snapshot
Sequencing and Comparative Analysis of the Straw Mushroom (Volvariella volvacea) Genome
inferredcites →https://doi.org/10.1371/journal.pone.0086683openalex-snapshot
Systematic Identification and Evolutionary Analysis of Catalytically Versatile Cytochrome P450 Monooxygenase Families Enriched in Model Basidiomycete Fungi
inferredcites →https://doi.org/10.1371/journal.pone.0142100openalex-snapshot
Genome-Wide Annotation and Comparative Analysis of Cytochrome P450 Monooxygenases in Basidiomycete Biotrophic Plant Pathogens
inferredcites →https://doi.org/10.2174/138920211795564377openalex-snapshot
Multiple Multi-Copper Oxidase Gene Families in Basidiomycetes – What for?
inferredcites →https://doi.org/10.3389/fmicb.2015.01278openalex-snapshot
Comparative Analysis of Secretomes from Ectomycorrhizal Fungi with an Emphasis on Small-Secreted Proteins
inferredcites →https://doi.org/10.3852/11-056openalex-snapshot
Amanita thiersii is a saprotrophic fungus expanding its range in the United States
inferredcites →https://doi.org/10.3852/mycologia.98.6.982openalex-snapshot
Major clades of Agaricales: a multilocus phylogenetic overview
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Amanita inopinata, Its Ecology and Expansion in Europe

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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A fusarioid fungus forms mutualistic interactions with poplar trees that resemble ectomycorrhizal symbiosis
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Ecological genomics of saprotrophy to biotrophy transitions in the genus Clitopilus (Fr. ex Rabenh.) P. Kumm. (Agaricales, Entolomataceae)
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Ibotenic Acid Biosynthesis in the Fly Agaric Is Initiated by Glutamate Hydroxylation
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General Trends of Genomic Signatures of the Ectomycorrhizal Symbiosis in Fungi: A Comparison Across Multiple Lineages
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Genomic Comparisons of Two Armillaria Species with Different Ecological Behaviors and Their Associated Soil Microbial Communities
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Applying molecular and genetic methods to trees and their fungal communities
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Evolution of lignin decomposition systems in fungi
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Genome reduction and relaxed selection is associated with the transition to symbiosis in the basidiomycete genus Podaxis
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Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations
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Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits
inferred← citeshttps://doi.org/10.1093/femsre/fuab058openalex-snapshot
Fungi as mediators linking organisms and ecosystems
inferred← citeshttps://doi.org/10.1093/g3journal/jkad077openalex-snapshot
A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis
inferred← citeshttps://doi.org/10.1093/gbe/evaa193openalex-snapshot
De Novo Gene Birth, Horizontal Gene Transfer, and Gene Duplication as Sources of New Gene Families Associated with the Origin of Symbiosis inAmanita
inferred← citeshttps://doi.org/10.1093/gbe/evad136openalex-snapshot
Insights into the Ecological Diversification of the Hymenochaetales based on Comparative Genomics and Phylogenomics With an Emphasis onColtricia
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Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism
inferred← citeshttps://doi.org/10.1093/molbev/msad045openalex-snapshot
Speciation Underpinned by Unexpected Molecular Diversity in the Mycorrhizal Fungal GenusPisolithus
inferred← citeshttps://doi.org/10.1099/mgen.0.001218openalex-snapshot
Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly
inferred← citeshttps://doi.org/10.1101/2021.02.23.432530openalex-snapshot
Evolutionary priming and transition to the ectomycorrhizal habit in an iconic lineage of mushroom-forming fungi: is preadaptation a requirement?
inferred← citeshttps://doi.org/10.1111/1462-2920.14727openalex-snapshot
Laccaria bicolor MiSSP8 is a small‐secreted protein decisive for the establishment of the ectomycorrhizal symbiosis
inferred← citeshttps://doi.org/10.1111/nph.16545openalex-snapshot
In vitro evidence of root colonization suggests ecological versatility in the genus Mycena
inferred← citeshttps://doi.org/10.1111/nph.17160openalex-snapshot
Comparative genomics reveals dynamic genome evolution in host specialist ectomycorrhizal fungi
inferred← citeshttps://doi.org/10.1111/nph.17414openalex-snapshot
Symbiont switching and trophic mode shifts in Orchidaceae
inferred← citeshttps://doi.org/10.1111/nph.17858openalex-snapshot
Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales
inferred← citeshttps://doi.org/10.1111/nph.17892openalex-snapshot
Evolutionary transition to the ectomycorrhizal habit in the genomes of a hyperdiverse lineage of mushroom‐forming fungi
inferred← citeshttps://doi.org/10.1111/nph.18143openalex-snapshot
Comparative genomics reveals a dynamic genome evolution in the ectomycorrhizal milk‐cap (Lactarius) mushrooms
inferred← citeshttps://doi.org/10.1111/nph.20007openalex-snapshot
High rate of gene family evolution in proximity to the origin of ectomycorrhizal symbiosis in Inocybaceae
inferred← citeshttps://doi.org/10.1111/nph.70315openalex-snapshot
Elevated CO2 mediates ectomycorrhizal fungi species‐specific decreases of native soil carbon and causes negative priming under low nutrients
inferred← citeshttps://doi.org/10.1186/s12864-025-12103-wopenalex-snapshot
Characterization of the five Amanita complete mitochondrial genome and the phylogenetic relationship with other Amanita fungi
inferred← citeshttps://doi.org/10.1186/s12915-024-02031-8openalex-snapshot
The evolution of ectomycorrhizal symbiosis and host-plant switches are the main drivers for diversification of Amanitaceae (Agaricales, Basidiomycota)
inferred← citeshttps://doi.org/10.12688/f1000research.134814.1openalex-snapshot
Amanita thiersii and Amanita foetens are closely related but genetically and geographically distinct species, leaving the origins of A. thiersii and its range expansion enigmatic
inferred← citeshttps://doi.org/10.1371/journal.pone.0212769openalex-snapshot
Genome and secretome of Chondrostereum purpureum correspond to saprotrophic and phytopathogenic life styles
inferred← citeshttps://doi.org/10.33885/sf.2019.49.1247openalex-snapshot
La evolución de la simbiosis ectomicorrízica desde la perspectiva genómica
inferred← citeshttps://doi.org/10.3389/fmicb.2020.00455openalex-snapshot
Seeking the Roles for Fungal Small-Secreted Proteins in Affecting Saprophytic Lifestyles
inferred← citeshttps://doi.org/10.3389/fmicb.2020.01382openalex-snapshot
Comparative Mitogenome Analysis Reveals Mitochondrial Genome Differentiation in Ectomycorrhizal and Asymbiotic Amanita Species
inferred← citeshttps://doi.org/10.3389/fmicb.2021.732458openalex-snapshot
Whole-Genome and Transcriptome Sequencing of Phlebopus portentosus Reveals Its Associated Ectomycorrhizal Niche and Conserved Pathways Involved in Fruiting Body Development
inferred← citeshttps://doi.org/10.3389/fmicb.2023.1134228openalex-snapshot
Analysis of synonymous codon usage patterns in mitochondrial genomes of nine Amanita species
inferred← citeshttps://doi.org/10.5943/mycosphere/si/1f/1openalex-snapshot
On the evolution of ectomycorrhizal fungi
inferred← citeshttps://doi.org/10.70675/67774ec7za271z45ebzb84cz0d48d1d2f0efopenalex-snapshot
Caractéristiques génomiques du genre fongique Mucor et évolution adaptative liée à différents modes et conditions de vie au sein du genre
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