On the public citation graph

Lifestyle Transitions in Fusarioid Fungi are Frequent and Lack Clear Genomic Signatures

0 signed · 260 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.

Claim with ORCID

Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.

See reference health

What this work says

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

inferredcites →https://doi.org/10.1002/bies.950180811openalex-snapshot

The neutral theory is dead. The current significance and standing of neutral and nearly neutral theories

inferredcites →https://doi.org/10.1007/978-3-540-35306-5_10openalex-snapshot

SeqinR 1.0-2: A Contributed Package to the R Project for Statistical Computing Devoted to Biological Sequences Retrieval and Analysis

inferredcites →https://doi.org/10.1007/s00239-017-9801-0openalex-snapshot

The Distribution of Miniature Impala Elements and SIX Genes in the Fusarium Genus is Suggestive of Horizontal Gene Transfer

inferredcites →https://doi.org/10.1007/s10526-008-9181-xopenalex-snapshot

Biological control of Radopholus similis in banana by combined application of the mutualistic endophyte Fusarium oxysporum strain 162, the egg pathogen Paecilomyces lilacinus strain 251 and the antagonistic bacteria Bacillus firmus

inferredcites →https://doi.org/10.1007/s10658-013-0268-6openalex-snapshot

Fusarium oxysporum f.sp. cepae dynamics: in-plant multiplication and crop sequence simulations

inferredcites →https://doi.org/10.1007/s10886-009-9675-8openalex-snapshot

Comparative Toxicity of Mycotoxins to Navel Orangeworm (Amyelois transitella) and Corn Earworm (Helicoverpa zea)

inferredcites →https://doi.org/10.1007/s12600-016-0543-0openalex-snapshot

Invasive Asian Fusarium – Euwallacea ambrosia beetle mutualists pose a serious threat to forests, urban landscapes and the avocado industry

inferredcites →https://doi.org/10.1007/s13199-018-0545-4openalex-snapshot

Plant growth promoting endophytic fungi Asprgillus fumigatus TS1 and Fusarium proliferatum BRL1 produce gibberellins and regulates plant endogenous hormones

inferredcites →https://doi.org/10.1007/s13225-010-0024-6openalex-snapshot

Can leaf degrading enzymes provide evidence that endophytic fungi becoming saprobes?

inferredcites →https://doi.org/10.1016/j.cell.2016.02.028openalex-snapshot

Root Endophyte Colletotrichum tofieldiae Confers Plant Fitness Benefits that Are Phosphate Status Dependent

inferredcites →https://doi.org/10.1016/j.cell.2018.10.020openalex-snapshot

Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival

inferredcites →https://doi.org/10.1016/j.cub.2021.01.074openalex-snapshot

A genome-scale phylogeny of the kingdom Fungi

inferredcites →https://doi.org/10.1016/j.fbr.2007.06.002openalex-snapshot

Botryosphaeriaceae as endophytes and latent pathogens of woody plants: diversity, ecology and impact

inferredcites →https://doi.org/10.1016/j.fgb.2012.12.004openalex-snapshot

Phylogenetic analyses of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria

inferredcites →https://doi.org/10.1016/j.fgb.2013.04.004openalex-snapshot

An inordinate fondness for Fusarium: Phylogenetic diversity of fusaria cultivated by ambrosia beetles in the genus Euwallacea on avocado and other plant hosts

inferredcites →https://doi.org/10.1016/j.fgb.2014.08.007openalex-snapshot

Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment

inferredcites →https://doi.org/10.1016/j.fgb.2014.10.014openalex-snapshot

Discordant phylogenies suggest repeated host shifts in the Fusarium–Euwallacea ambrosia beetle mutualism

inferredcites →https://doi.org/10.1016/j.funbio.2015.10.002openalex-snapshot

The genome of Xylona heveae provides a window into fungal endophytism

inferredcites →https://doi.org/10.1016/j.funbio.2016.01.017openalex-snapshot

Fungal endophytes in germinated seeds of the common bean, Phaseolus vulgaris

inferredcites →https://doi.org/10.1016/j.funeco.2012.05.002openalex-snapshot

A fine line – endophytes or pathogens in Arabidopsis thaliana

inferredcites →https://doi.org/10.1016/j.funeco.2014.09.003openalex-snapshot

Endophytic association of the pine pathogen Fusarium circinatum with corn ( Zea mays )

inferredcites →https://doi.org/10.1016/j.ijfoodmicro.2007.07.024openalex-snapshot

Molecular biology of Fusarium mycotoxins

inferredcites →https://doi.org/10.1016/j.ijfoodmicro.2010.07.015openalex-snapshot

Mycotoxin production of selected Fusarium species at different culture conditions

inferredcites →https://doi.org/10.1016/j.myc.2018.09.002openalex-snapshot

A short LysM protein with high molecular diversity from an arbuscular mycorrhizal fungus, Rhizophagus irregularis

inferredcites →https://doi.org/10.1016/j.pbi.2011.03.005openalex-snapshot

How filamentous pathogens co-opt plants: the ins and outs of fungal effectors

inferredcites →https://doi.org/10.1016/j.pbi.2012.05.003openalex-snapshot

Challenges and progress towards understanding the role of effectors in plant–fungal interactions

inferredcites →https://doi.org/10.1016/j.pbi.2014.05.013openalex-snapshot

Broad compatibility in fungal root symbioses

inferredcites →https://doi.org/10.1016/j.pbi.2015.06.001openalex-snapshot

Reconsidering mutualistic plant–fungal interactions through the lens of effector biology

inferredcites →https://doi.org/10.1016/j.simyco.2014.12.002openalex-snapshot

Generic concepts in Nectriaceae

inferredcites →https://doi.org/10.1016/j.simyco.2021.100116openalex-snapshot

Fusarium: more than a node or a foot-shaped basal cell

inferredcites →https://doi.org/10.1016/j.tig.2003.12.003openalex-snapshot

Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision

inferredcites →https://doi.org/10.1016/j.tplants.2013.01.008openalex-snapshot

Evolution of the plant–microbe symbiotic ‘toolkit’

inferredcites →https://doi.org/10.1016/j.ympev.2014.04.024openalex-snapshot

Estimating the Phanerozoic history of the Ascomycota lineages: Combining fossil and molecular data

inferredcites →https://doi.org/10.1016/s0007-1536(78)80001-1openalex-snapshot

Do you believe in genera?

inferredcites →https://doi.org/10.1016/s0378-1119(02)00851-xopenalex-snapshot

Playing chicken ( Gallus gallus ): methodological inconsistencies of molecular divergence date estimates due to secondary calibration points

inferredcites →https://doi.org/10.1017/s095375620500273xopenalex-snapshot

The endophytic continuum

inferredcites →https://doi.org/10.1023/b:ejpp.0000032386.75915.a0openalex-snapshot

FUSARIUM-ID v. 1.0: A DNA Sequence Database for Identifying Fusarium

inferredcites →https://doi.org/10.1038/nature06107openalex-snapshot

Natural history and evolutionary principles of gene duplication in fungi

inferredcites →https://doi.org/10.1038/nature08850openalex-snapshot

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

inferredcites →https://doi.org/10.1038/nature08867openalex-snapshot

Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

inferredcites →https://doi.org/10.1038/ncomms11362openalex-snapshot

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

inferredcites →https://doi.org/10.1038/ncomms12662openalex-snapshot

Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum

inferredcites →https://doi.org/10.1038/ng.3223openalex-snapshot

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

inferredcites →https://doi.org/10.1038/nmeth.4285openalex-snapshot

ModelFinder: fast model selection for accurate phylogenetic estimates

inferredcites →https://doi.org/10.1038/s41467-018-07849-9openalex-snapshot

Contemporaneous radiations of fungi and plants linked to symbiosis

inferredcites →https://doi.org/10.1038/s41467-020-18795-wopenalex-snapshot

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

inferredcites →https://doi.org/10.1038/s41467-021-27479-yopenalex-snapshot

Genetic determinants of endophytism in the Arabidopsis root mycobiome

inferredcites →https://doi.org/10.1038/s41559-019-0834-1openalex-snapshot

Megaphylogeny resolves global patterns of mushroom evolution

inferredcites →https://doi.org/10.1038/s41598-018-19779-zopenalex-snapshot

The ‘forma specialis’ issue in Fusarium: A case study in Fusarium solani f. sp. pisi

inferredcites →https://doi.org/10.1038/s41598-018-24686-4openalex-snapshot

Comparative genomics provides insights into the lifestyle and reveals functional heterogeneity of dark septate endophytic fungi

inferredcites →https://doi.org/10.1038/s41598-018-30335-7openalex-snapshot

Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae

inferredcites →https://doi.org/10.1038/s41598-019-40965-0openalex-snapshot

Transposable elements contribute to fungal genes and impact fungal lifestyle

inferredcites →https://doi.org/10.1038/s42003-020-0770-2openalex-snapshot

The genome of opportunistic fungal pathogen Fusarium oxysporum carries a unique set of lineage-specific chromosomes

inferredcites →https://doi.org/10.1046/j.0028-646x.2001.00210.xopenalex-snapshot

Fungal symbiosis from mutualism to parasitism: who controls the outcome, host or invader?

inferredcites →https://doi.org/10.1073/pnas.0307827100openalex-snapshot

Codon usage between genomes is constrained by genome-wide mutational processes

inferredcites →https://doi.org/10.1073/pnas.2023575118openalex-snapshot

Weak selection on synonymous codons substantially inflates dN/dS estimates in bacteria

inferredcites →https://doi.org/10.1073/pnas.2111521118openalex-snapshot

Tryptophan metabolism and bacterial commensals prevent fungal dysbiosis in Arabidopsis roots

inferredcites →https://doi.org/10.1080/00275514.2019.1647074openalex-snapshot

Three novel Ambrosia Fusarium Clade species producing clavate macroconidia known (F. floridanum and F. obliquiseptatum) or predicted (F. tuaranense) to be farmed by Euwallacea spp. (Coleoptera: Scolytinae) on woody hosts

inferredcites →https://doi.org/10.1080/07060661.2011.536651openalex-snapshot

Characterization of Fusarium avenaceum from lupin in central Alberta: genetic diversity, mating type and aggressiveness

inferredcites →https://doi.org/10.1080/07060661.2020.1746695openalex-snapshot

Characterization of species ofFusariumcausing root rot of Soybean (Glycine maxL.) in South Dakota, USA

inferredcites →https://doi.org/10.1080/15572536.2006.11832614openalex-snapshot

Dating divergences in the Fungal Tree of Life: review and new analyses

inferredcites →https://doi.org/10.1089/cmb.2009.0179openalex-snapshot

How Many Bootstrap Replicates Are Necessary?

inferredcites →https://doi.org/10.1093/aob/mcp192openalex-snapshot

Calibrating the Tree of Life: fossils, molecules and evolutionary timescales

inferredcites →https://doi.org/10.1093/bioinformatics/bti079openalex-snapshot

HyPhy: hypothesis testing using phylogenies

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/btt086openalex-snapshot

QUAST: quality assessment tool for genome assemblies

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/bioinformatics/btw524openalex-snapshot

Multivariate Welch t -test on distances

inferredcites →https://doi.org/10.1093/bioinformatics/btz305openalex-snapshot

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

inferredcites →https://doi.org/10.1093/ee/nvv160openalex-snapshot

Larval Preference and Performance ofAmyelois transitella(Navel Orangeworm, Lepidoptera: Pyralidae) in Relation to the FungusAspergillus flavus

inferredcites →https://doi.org/10.1093/gbe/evab167openalex-snapshot

Positive Selection of Transcription Factors Is a Prominent Feature of the Evolution of a Plant Pathogenic Genus Originating in the Miocene

inferredcites →https://doi.org/10.1093/gbe/evw259openalex-snapshot

Comparative “Omics” of the Fusarium fujikuroi Species Complex Highlights Differences in Genetic Potential and Metabolite Synthesis

inferredcites →https://doi.org/10.1093/genetics/iyab066openalex-snapshot

An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely related Aspergillus fungi

inferredcites →https://doi.org/10.1093/jxb/erm230openalex-snapshot

Role of ethylene in the protection of tomato plants against soil-borne fungal pathogens conferred by an endophytic Fusarium solani strain

inferredcites →https://doi.org/10.1093/molbev/msaa015openalex-snapshot

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

inferredcites →https://doi.org/10.1093/molbev/msaa139openalex-snapshot

ASTRAL-Pro: Quartet-Based Species-Tree Inference despite Paralogy

inferredcites →https://doi.org/10.1093/molbev/msaa263openalex-snapshot

Contrast-FEL—A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches

inferredcites →https://doi.org/10.1093/molbev/msab309openalex-snapshot

A Mutation–Selection Model of Protein Evolution under Persistent Positive Selection

inferredcites →https://doi.org/10.1093/molbev/msj024openalex-snapshot

Bayesian Estimation of Species Divergence Times Under a Molecular Clock Using Multiple Fossil Calibrations with Soft Bounds

inferredcites →https://doi.org/10.1093/molbev/msm088openalex-snapshot

PAML 4: Phylogenetic Analysis by Maximum Likelihood

inferredcites →https://doi.org/10.1093/molbev/msr045openalex-snapshot

Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times

inferredcites →https://doi.org/10.1093/molbev/mst010openalex-snapshot

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

inferredcites →https://doi.org/10.1093/molbev/msv022openalex-snapshot

Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection

inferredcites →https://doi.org/10.1093/molbev/msv035openalex-snapshot

Gene-Wide Identification of Episodic Selection

inferredcites →https://doi.org/10.1093/molbev/msw079openalex-snapshot

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

inferredcites →https://doi.org/10.1093/molbev/msx281openalex-snapshot

UFBoot2: Improving the Ultrafast Bootstrap Approximation

inferredcites →https://doi.org/10.1093/molbev/msz014openalex-snapshot

A Machine Learning Method for Detecting Autocorrelation of Evolutionary Rates in Large Phylogenies

inferredcites →https://doi.org/10.1093/molbev/msz189openalex-snapshot

ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models

inferredcites →https://doi.org/10.1093/nar/15.3.1281openalex-snapshot

The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications

inferredcites →https://doi.org/10.1093/nar/gkh834openalex-snapshot

Solving the riddle of codon usage preferences: a test for translational selection

inferredcites →https://doi.org/10.1093/nar/gkn582openalex-snapshot

ExplorEnz: the primary source of the IUBMB enzyme list

inferredcites →https://doi.org/10.1093/nar/gky418openalex-snapshot

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

inferredcites →https://doi.org/10.1093/nar/gkz904openalex-snapshot

PHI-base: the pathogen–host interactions database

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a003851openalex-snapshot

A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach

inferredcites →https://doi.org/10.1093/sysbio/syp001openalex-snapshot

A Phylogenetic Estimation of Trophic Transition Networks for Ascomycetous Fungi: Are Lichens Cradles of Symbiotrophic Fungal Diversification?

inferredcites →https://doi.org/10.1093/sysbio/syr009openalex-snapshot

Evaluation of Bayesian Models of Substitution Rate Evolution—Parental Guidance versus Mutual Independence

inferredcites →https://doi.org/10.1093/sysbio/syr116openalex-snapshot

Testing the Impact of Calibration on Molecular Divergence Times Using a Fossil-Rich Group: The Case of Nothofagus (Fagales)

inferredcites →https://doi.org/10.1093/sysbio/syv033openalex-snapshot

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference

inferredcites →https://doi.org/10.1093/sysbio/syy001openalex-snapshot

Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case

inferredcites →https://doi.org/10.1094/mpmi-03-21-0063-ropenalex-snapshot

Metatranscriptomic Comparison of Endophytic and Pathogenic Fusarium –Arabidopsis Interactions Reveals Plant Transcriptional Plasticity

inferredcites →https://doi.org/10.1094/mpmi-05-12-0117-ropenalex-snapshot

Identification and Characterization of In planta–Expressed Secreted Effector Proteins fromMagnaporthe oryzaeThat Induce Cell Death in Rice

inferredcites →https://doi.org/10.1094/mpmi-06-14-0173-ropenalex-snapshot

The Genome of the Saprophytic Fungus Verticillium tricorpus Reveals a Complex Effector Repertoire Resembling That of Its Pathogenic Relatives

inferredcites →https://doi.org/10.1094/mpmi-06-17-0135-fiopenalex-snapshot

Accessories Make the Outfit: Accessory Chromosomes and Other Dispensable DNA Regions in Plant-Pathogenic Fungi

inferredcites →https://doi.org/10.1094/mpmi-08-21-0201-ropenalex-snapshot

EffectorP 3.0: Prediction of Apoplastic and Cytoplasmic Effectors in Fungi and Oomycetes

inferredcites →https://doi.org/10.1094/pd-74-0569openalex-snapshot

Additions to the Host Range of Fusarium oxysporum f. sp. radicis-lycopersici

inferredcites →https://doi.org/10.1094/pdis-01-13-0061-reopenalex-snapshot

Genetic Diversity and Aggressiveness of Fusarium spp. Isolated from Canola in Alberta, Canada

inferredcites →https://doi.org/10.1094/pdis-03-12-0276-pdnopenalex-snapshot

First Report of a Fusarium sp. and Its Vector Tea Shot Hole Borer (Euwallacea fornicatus) Causing Fusarium Dieback on Avocado in California

inferredcites →https://doi.org/10.1094/pdis-07-17-1042-reopenalex-snapshot

Two Novel Fungal Symbionts Fusarium kuroshium sp. nov. and Graphium kuroshium sp. nov. of Kuroshio Shot Hole Borer (Euwallacea sp. nr. fornicatus) Cause Fusarium Dieback on Woody Host Species in California

inferredcites →https://doi.org/10.1094/php-2005-1221-01-rvopenalex-snapshot

Panama Disease: An Old Nemesis Rears Its Ugly Head: Part 1. The Beginnings of the Banana Export Trades

inferredcites →https://doi.org/10.1094/phyto-08-20-0330-leopenalex-snapshot

Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a MonophyleticFusariumthat Includes theFusarium solaniSpecies Complex

inferredcites →https://doi.org/10.1098/rsbl.2008.0729openalex-snapshot

An examination of phylogenetic models of substitution rate variation among lineages

inferredcites →https://doi.org/10.1098/rstb.2015.0132openalex-snapshot

A mixed relaxed clock model

inferredcites →https://doi.org/10.1101/267914openalex-snapshot

STAG: Species Tree Inference from All Genes

inferredcites →https://doi.org/10.1101/gr.086512.108openalex-snapshot

The difficulty of avoiding false positives in genome scans for natural selection

inferredcites →https://doi.org/10.1101/gr.089532.108openalex-snapshot

ABySS: A parallel assembler for short read sequence data

inferredcites →https://doi.org/10.1101/gr.6743907openalex-snapshot

MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes

inferredcites →https://doi.org/10.1111/1462-2920.13445openalex-snapshot

Effector profiles distinguish formae speciales of Fusarium oxysporum

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

inferredcites →https://doi.org/10.1111/1462-2920.15095openalex-snapshot

Partial pathogenicity chromosomes in Fusarium oxysporum are sufficient to cause disease and can be horizontally transferred

inferredcites →https://doi.org/10.1111/2041-210x.12760openalex-snapshot

Intertwining phylogenetic trees and networks

inferredcites →https://doi.org/10.1111/j.1364-3703.2011.00783.xopenalex-snapshot

The Top 10 fungal pathogens in molecular plant pathology

inferredcites →https://doi.org/10.1111/j.1469-8137.2009.02773.xopenalex-snapshot

Fungal endophytes: diversity and functional roles

inferredcites →https://doi.org/10.1111/j.1469-8137.2012.04253.xopenalex-snapshot

Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops

inferredcites →https://doi.org/10.1111/j.1558-5646.2010.01055.xopenalex-snapshot

REPEATED EVOLUTION OF CROP THEFT IN FUNGUS-FARMING AMBROSIA BEETLES

inferredcites →https://doi.org/10.1111/j.1558-5646.2011.01558.xopenalex-snapshot

JOINT RECONSTRUCTION OF DIVERGENCE TIMES AND LIFE-HISTORY EVOLUTION IN PLACENTAL MAMMALS USING A PHYLOGENETIC COVARIANCE MODEL

inferredcites →https://doi.org/10.1111/mec.14585openalex-snapshot

Genomewide signatures of selection in Epichloë reveal candidate genes for host specialization

inferredcites →https://doi.org/10.1111/nph.13411openalex-snapshot

Mutualistic root endophytism is not associated with the reduction of saprotrophic traits and requires a noncompromised plant innate immunity

inferredcites →https://doi.org/10.1111/nph.14983openalex-snapshot

Time to re‐think fungal ecology? Fungal ecological niches are often prejudged

inferredcites →https://doi.org/10.1111/nph.17044openalex-snapshot

Desert truffle genomes reveal their reproductive modes and new insights into plant–fungal interaction and ectendomycorrhizal lifestyle

inferredcites →https://doi.org/10.1111/nph.17873openalex-snapshot

Ecological generalism drives hyperdiversity of secondary metabolite gene clusters in xylarialean endophytes

inferredcites →https://doi.org/10.1126/science.1136678openalex-snapshot

Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes

inferredcites →https://doi.org/10.1126/science.1194573openalex-snapshot

Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism

inferredcites →https://doi.org/10.1126/science.290.5494.1151openalex-snapshot

The Evolutionary Fate and Consequences of Duplicate Genes

inferredcites →https://doi.org/10.1126/science.abg0929openalex-snapshot

Lipid exchanges drove the evolution of mutualism during plant terrestrialization

inferredcites →https://doi.org/10.1128/aem.69.11.6418-6426.2003openalex-snapshot

Involvement of Two Cytosolic Enzymes and a Novel Intermediate, 5′-Oxoaverantin, in the Pathway from 5′-Hydroxyaverantin to Averufin in Aflatoxin Biosynthesis

inferredcites →https://doi.org/10.1128/mbio.00925-19openalex-snapshot

A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium

inferredcites →https://doi.org/10.1128/mbio.02391-19openalex-snapshot

Cause and Effectors: Whole-Genome Comparisons Reveal Shared but Rapidly Evolving Effector Sets among Host-Specific Plant-Castrating Fungi

inferredcites →https://doi.org/10.1128/mmbr.00050-14openalex-snapshot

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

inferredcites →https://doi.org/10.1128/msphere.00810-20openalex-snapshot

No to Neocosmospora : Phylogenomic and Practical Reasons for Continued Inclusion of the Fusarium solani Species Complex in the Genus Fusarium

inferredcites →https://doi.org/10.1146/annurev-arplant-043014-114623openalex-snapshot

Fungal Effectors and Plant Susceptibility

inferredcites →https://doi.org/10.1146/annurev-ecolsys-012021-114902openalex-snapshot

Evolution of the Mode of Nutrition in Symbiotic and Saprotrophic Fungi in Forest Ecosystems

inferredcites →https://doi.org/10.1146/annurev-ento-011019-024910openalex-snapshot

Ecology and Evolution of Insect–Fungus Mutualisms

inferredcites →https://doi.org/10.1146/annurev-micro-092412-155650openalex-snapshot

Fusarium Pathogenomics

inferredcites →https://doi.org/10.1146/annurev-phyto-082718-100204openalex-snapshot

Resolving Fusarium : Current Status of the Genus

inferredcites →https://doi.org/10.1146/annurev-phyto-102313-045831openalex-snapshot

Plant Cell Wall–Degrading Enzymes and Their Secretion in Plant-Pathogenic Fungi

inferredcites →https://doi.org/10.1146/annurev.ecolsys.36.102003.152626openalex-snapshot

The Evolution of Agriculture in Insects

inferredcites →https://doi.org/10.1146/annurev.genet.42.110807.091442openalex-snapshot

Selection on Codon Bias

inferredcites →https://doi.org/10.1146/annurev.phyto.112408.132637openalex-snapshot

Fungal Effector Proteins

inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot

BLAST+: architecture and applications

inferredcites →https://doi.org/10.1186/1471-2148-10-210openalex-snapshot

BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments

inferredcites →https://doi.org/10.1186/1471-2148-12-133openalex-snapshot

Molecular phylogeny of bark and ambrosia beetles reveals multiple origins of fungus farming during periods of global warming

inferredcites →https://doi.org/10.1186/1471-2164-14-274openalex-snapshot

Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

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-2011-12-10-r109openalex-snapshot

Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles

inferredcites →https://doi.org/10.1186/s12859-018-2129-yopenalex-snapshot

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

inferredcites →https://doi.org/10.1186/s12864-016-3044-0openalex-snapshot

Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest

inferredcites →https://doi.org/10.1186/s12864-021-07700-4openalex-snapshot

Historical genomics reveals the evolutionary mechanisms behind multiple outbreaks of the host-specific coffee wilt pathogen Fusarium xylarioides

inferredcites →https://doi.org/10.1186/s12864-021-08033-yopenalex-snapshot

Comparative transcriptomic analysis of races 1, 2, 5 and 6 of Fusarium oxysporum f.sp. pisi in a susceptible pea host identifies differential pathogenicity profiles

inferredcites →https://doi.org/10.1186/s12881-019-0909-5openalex-snapshot

Copy number variation is highly correlated with differential gene expression: a pan-cancer study

inferredcites →https://doi.org/10.1186/s13059-019-1832-yopenalex-snapshot

OrthoFinder: phylogenetic orthology inference for comparative genomics

inferredcites →https://doi.org/10.12688/f1000research.12232.1openalex-snapshot

BlobTools: Interrogation of genome assemblies

inferredcites →https://doi.org/10.1371/journal.pbio.3001007openalex-snapshot

ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference

inferredcites →https://doi.org/10.1371/journal.pbio.3001185openalex-snapshot

Signatures of optimal codon usage in metabolic genes inform budding yeast ecology

inferredcites →https://doi.org/10.1371/journal.pcbi.1007046openalex-snapshot

A new method for inferring timetrees from temporally sampled molecular sequences

inferredcites →https://doi.org/10.1371/journal.pgen.1000618openalex-snapshot

The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion

inferredcites →https://doi.org/10.1371/journal.pone.0016386openalex-snapshot

Light Converts Endosymbiotic Fungus to Pathogen, Influencing Seedling Survival and Niche-Space Filling of a Common Tropical Tree, Iriartea deltoidea

inferredcites →https://doi.org/10.1371/journal.pone.0112963openalex-snapshot

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

inferredcites →https://doi.org/10.1371/journal.pone.0148228openalex-snapshot

Consequences of Secondary Calibrations on Divergence Time Estimates

inferredcites →https://doi.org/10.1371/journal.pone.0175528openalex-snapshot

The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown

inferredcites →https://doi.org/10.1371/journal.pone.0197433openalex-snapshot

So many genes, so little time: A practical approach to divergence-time estimation in the genomic era

inferredcites →https://doi.org/10.1371/journal.pone.0201611openalex-snapshot

A population genomic characterization of copy number variation in the opportunistic fungal pathogen Aspergillus fumigatus

inferredcites →https://doi.org/10.1371/journal.ppat.1002608openalex-snapshot

The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

inferredcites →https://doi.org/10.1371/journal.ppat.1005197openalex-snapshot

Worse Comes to Worst: Bananas and Panama Disease—When Plant and Pathogen Clones Meet

inferredcites →https://doi.org/10.1534/genetics.104.037051openalex-snapshot

Rapid Subfunctionalization Accompanied by Prolonged and Substantial Neofunctionalization in Duplicate Gene Evolution

inferredcites →https://doi.org/10.21315/tlsr2018.29.2.14openalex-snapshot

Molecular Identification of Endophytic Fungi from Banana Leaves (Musa spp.)

inferredcites →https://doi.org/10.3114/sim.2011.68.05openalex-snapshot

A revision of Cyanonectria and Geejayessia gen. nov., and related species with Fusarium-like anamorphs

inferredcites →https://doi.org/10.32614/cran.package.nlmeopenalex-snapshot

nlme: Linear and Nonlinear Mixed Effects Models

inferredcites →https://doi.org/10.32614/cran.package.veganopenalex-snapshot

vegan: Community Ecology Package

inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot

R: A Language and Environment for Statistical Computing

inferredcites →https://doi.org/10.3389/fgene.2014.00138openalex-snapshot

Beyond fossil calibrations: realities of molecular clock practices in evolutionary biology

inferredcites →https://doi.org/10.3389/fgene.2020.00252openalex-snapshot

Quantifying the Error of Secondary vs. Distant Primary Calibrations in a Simulated Environment

inferredcites →https://doi.org/10.3389/fmicb.2018.00288openalex-snapshot

Copy Number Variation in Fungi and Its Implications for Wine Yeast Genetic Diversity and Adaptation

inferredcites →https://doi.org/10.3389/fmicb.2021.643731openalex-snapshot

Seed Banks as Incidental Fungi Banks: Fungal Endophyte Diversity in Stored Seeds of Banana Wild Relatives

inferredcites →https://doi.org/10.3389/fpls.2014.00299openalex-snapshot

Duplications and losses in gene families of rust pathogens highlight putative effectors

inferredcites →https://doi.org/10.3389/fpls.2016.00186openalex-snapshot

Kingdom-Wide Analysis of Fungal Small Secreted Proteins (SSPs) Reveals their Potential Role in Host Association

inferredcites →https://doi.org/10.3390/ijms22052508openalex-snapshot

Effector Profiles of Endophytic Fusarium Associated with Asymptomatic Banana (Musa sp.) Hosts

inferredcites →https://doi.org/10.3767/persoonia.2018.40.01openalex-snapshot

Symptomatic Citrus trees reveal a new pathogenic lineage in Fusarium and two new Neocosmospora species

inferredcites →https://doi.org/10.3767/persoonia.2019.43.04openalex-snapshot

Back to the roots: a reappraisal of Neocosmospora

inferredcites →https://doi.org/10.3767/persoonia.2021.47.06openalex-snapshot

Fungal Planet description sheets: 1284–1382

inferredcites →https://doi.org/10.3852/13-066openalex-snapshot

Fusarium euwallaceae sp. nov.—a symbiotic fungus of Euwallacea sp., an invasive ambrosia beetle in Israel and California

inferredcites →https://doi.org/10.3852/16-042openalex-snapshot

A phylum-level phylogenetic classification of zygomycete fungi based on genome-scale data

inferredcites →https://doi.org/10.4137/ebo.s6271openalex-snapshot

PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences

inferredcites →https://doi.org/10.5943/mycosphere/10/1/19openalex-snapshot

A worldwide list of endophytic fungi with notes on ecology and diversity

inferredcites →https://doi.org/10.7150/ijbs.1.24openalex-snapshot

Diversity of endophytic fungal community of cacao ( Theobroma cacao L.) and biological control of Crinipellis perniciosa, causal agent of Witches' Broom Disease

inferredcites →https://doi.org/10.7554/elife.22472openalex-snapshot

Codon optimization underpins generalist parasitism in fungi

inferredcites →https://doi.org/10.7717/peerj.1660openalex-snapshot

AMAS: a fast tool for alignment manipulation and computing of summary statistics

inferredcites →https://doi.org/10.7717/peerj.9341openalex-snapshot

Double lives: transfer of fungal endophytes from leaves to woody substrates

What points at this work

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

inferred← backgroundhttps://doi.org/10.5281/zenodo.6353640zenodo-depositor-declared

Data files for Hill et al. 2022 'Lifestyle transitions in fusarioid fungi are frequent and lack clear genomic signatures' doi:10.1093/molbev/msac085

inferred← citeshttps://doi.org/10.3897/imafungus.16.143240zenodo-depositor-declared

A fusarioid fungus forms mutualistic interactions with poplar trees that resemble ectomycorrhizal symbiosis

inferred← citeshttps://doi.org/10.3897/imafungus.17.192779zenodo-depositor-declared

Genomic and metabolic uniformity across diverse observed ecological contexts suggest that interactions of Pestalotiopsis formosana and P. neolitseae are context-dependent

inferred← citeshttps://doi.org/10.3897/imafungus.17.195303zenodo-depositor-declared

Genus-wide comparative genomics of Colletotrichum reveals evolutionary conservation and divergent ecological adaptations

inferred← extendshttps://doi.org/10.5281/zenodo.13829922zenodo-depositor-declared

inferred← citeshttps://doi.org/10.1002/tpg2.20539openalex-snapshot

Priority actions for Fusarium head blight resistance in durum wheat: Insights from the wheat initiative

inferred← citeshttps://doi.org/10.1007/s00253-023-12480-wopenalex-snapshot

Applying molecular and genetic methods to trees and their fungal communities

inferred← citeshttps://doi.org/10.1007/s10142-026-02005-9openalex-snapshot

Whole genome sequencing and annotation of a non-pathogenic Fusarium brachygibbosum TZ1MST22 strain isolated from Medicago sativa in Southern Tunisian oases

inferred← citeshttps://doi.org/10.1007/s11274-025-04375-xopenalex-snapshot

How genomics can help unravel the evolution of endophytic fungi

inferred← citeshttps://doi.org/10.1007/s11557-024-02025-4openalex-snapshot

Genomic features and evolution of lifestyles support the recognition of distinct genera among fusarioid fungi

inferred← citeshttps://doi.org/10.1007/s11557-026-02167-7openalex-snapshot

Alternaria atra from distinct ecological contexts share functional genomic repertoires

inferred← citeshttps://doi.org/10.1007/s13225-025-00550-5openalex-snapshot

Challenges and update on fungal endophytes: classification, definition, diversity, ecology, evolution and functions

inferred← citeshttps://doi.org/10.1007/s13225-025-00567-wopenalex-snapshot

Fusarium and allied genera from cropland in Xizang, China

inferred← citeshttps://doi.org/10.1007/s41348-026-01306-2openalex-snapshot

Fusarium isolates representing six species complexes from symptomatic scale-leaved conifers (Cupressaceae)

inferred← citeshttps://doi.org/10.1007/s42161-025-01987-yopenalex-snapshot

Antagonism of tomato endophytic fungi against grey mold disease

inferred← citeshttps://doi.org/10.1016/j.biotechadv.2024.108476openalex-snapshot

Fusarium as a promising fungal genus with potential application in bioremediation for pollutants mitigation: A review

inferred← citeshttps://doi.org/10.1016/j.funbio.2026.101847openalex-snapshot

Comparative genomics of Cadophora luteo-olivacea reveals a divergent lineage, conserved functional repertoires, and strain-level phenotypic variation

inferred← citeshttps://doi.org/10.1016/j.tim.2024.03.002openalex-snapshot

Cryptococcus neoformans: plant–microbe interactions and ecology

inferred← citeshttps://doi.org/10.1038/s41467-023-42142-4openalex-snapshot

Global diversity and biogeography of potential phytopathogenic fungi in a changing world

inferred← citeshttps://doi.org/10.1038/s41467-026-68330-6openalex-snapshot

Genomic and physiological signatures of adaptation in pathogenic fungi

inferred← citeshttps://doi.org/10.1038/s41598-025-26280-xopenalex-snapshot

Intergenerational and horizontal transmission of wheat endophytic fungi

inferred← citeshttps://doi.org/10.1038/s41598-026-40947-zopenalex-snapshot

The effect of biological control on mycotoxin concentrations and the mycobiome in durum wheat grain and stems

inferred← citeshttps://doi.org/10.1093/gbe/evad038openalex-snapshot

Tapping Culture Collections for Fungal Endophytes: First Genome Assemblies for Three Genera and Five Species in theAscomycota

inferred← citeshttps://doi.org/10.1094/pdis-07-23-1362-reopenalex-snapshot

Identification and Pathogenicity of Fusarium Species Associated with Young Vine Decline in California

inferred← citeshttps://doi.org/10.1094/phyto-02-26-0043-rvwopenalex-snapshot

Disease Is Optional: The Surprising Abundance of Facultative Fungal Plant Pathogens

inferred← citeshttps://doi.org/10.1094/phyto-07-25-0229-ropenalex-snapshot

Genomic and Transcriptomic Analyses Reveal Mechanisms Associated with Pathogenesis of Fusarium annulatum and F. commune in Nursery-Grown Conifer Seedlings

inferred← citeshttps://doi.org/10.1101/2025.03.12.642647openalex-snapshot

Leveraging existing data to maximise quality and consistency across gene model annotations: a Fusarium pan-annotation

inferred← citeshttps://doi.org/10.1101/2025.05.08.652889openalex-snapshot

Resources for molecular studies of unculturable obligate biotrophic fungal plant pathogens using their saprotrophic relatives

inferred← citeshttps://doi.org/10.1111/1755-0998.70045openalex-snapshot

Saprotrophic Arachnopeziza Species as New Resources to Study the Obligate Biotrophic Lifestyle of Powdery Mildew Fungi

inferred← citeshttps://doi.org/10.1111/jph.70379openalex-snapshot

Molecular Identification of Fusarium Species Associated With Coffee Plantations in Bolivia

inferred← citeshttps://doi.org/10.1111/mec.16909openalex-snapshot

Long‐term and rapid evolution in powdery mildew fungi

inferred← citeshttps://doi.org/10.1128/mmbr.00116-25openalex-snapshot

Lifestyle plasticity and the shared hypocrealean toolkit across Fusarium , Metarhizium , and Trichoderma

inferred← citeshttps://doi.org/10.1146/annurev-ento-121423-013411openalex-snapshot

Plant Pathogens Moonlighting as Beneficial Insect Symbionts

inferred← citeshttps://doi.org/10.1186/s12859-025-06164-7openalex-snapshot

FunFEA: an R package for fungal functional enrichment analysis

inferred← citeshttps://doi.org/10.1186/s12864-024-10200-wopenalex-snapshot

An evolutionary view of the Fusarium core genome

inferred← citeshttps://doi.org/10.1186/s12864-025-11432-0openalex-snapshot

Evolutionary genomics reveals variation in structure and genetic content implicated in virulence and lifestyle in the genus Gaeumannomyces

inferred← citeshttps://doi.org/10.1186/s13100-023-00305-6openalex-snapshot

Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen

inferred← citeshttps://doi.org/10.1186/s43008-024-00147-8openalex-snapshot

Phylogenomic approaches reveal a robust time-scale phylogeny of the Terminal Fusarium Clade

inferred← citeshttps://doi.org/10.1371/journal.ppat.1011497openalex-snapshot

Fusarium phytopathogens as insect mutualists

inferred← citeshttps://doi.org/10.1371/journal.ppat.1012769openalex-snapshot

A conserved fungal Knr4/Smi1 protein is crucial for maintaining cell wall stress tolerance and host plant pathogenesis

inferred← citeshttps://doi.org/10.14232/phd.11641openalex-snapshot

Comparative -omics analyses to understand wood decay strategies and evolution of pathogenicity in Armillaria spp.

inferred← citeshttps://doi.org/10.21203/rs.3.rs-9126008/v1openalex-snapshot

Two New Species of Pleosporales from Pteridophytes in China

inferred← citeshttps://doi.org/10.3114/fuse.2022.09.08openalex-snapshot

Fusariumand Allied Fusarioid Taxa (FUSA). 1

inferred← citeshttps://doi.org/10.3114/sim.2022.104.02openalex-snapshot

Fusarium diversity associated with diseased cereals in China, with an updated phylogenomic assessment of the genus

inferred← citeshttps://doi.org/10.3389/fmicb.2023.1268051openalex-snapshot

Chromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm

inferred← citeshttps://doi.org/10.3389/fmicb.2026.1841716openalex-snapshot

The endophyte Fusarium oxysporum 3RR genome analysis identifies bioactive compounds targeting biofilm formation

inferred← citeshttps://doi.org/10.3390/biology12030476openalex-snapshot

Intraspecific Comparative Analysis Reveals Genomic Variation of Didymella arachidicola and Pathogenicity Factors Potentially Related to Lesion Phenotype

inferred← citeshttps://doi.org/10.3390/biology12060809openalex-snapshot

Plant–Fungi Interactions: Where It Goes?

inferred← citeshttps://doi.org/10.3390/jof12100721openalex-snapshot

Biocontrol Potential of Bacillus velezensis xd3 in Alleviating Root Rot of Garlic (Allium sativum L.)

inferred← citeshttps://doi.org/10.3390/jof9070704openalex-snapshot

Genomic and Metabolomic Analysis of the Endophytic Fungus Fusarium sp. VM-40 Isolated from the Medicinal Plant Vinca minor

inferred← citeshttps://doi.org/10.48130/mycosphere-0026-0010openalex-snapshot

Taxonomic analysis of Amphisphaeriales in China: discovery of multiple novel taxa

inferred← citeshttps://doi.org/10.5943/mycosphere/14/1/25openalex-snapshot

Endophytic Fusarium and allied fungi from Rosa roxburghii in China

inferred← citeshttps://doi.org/10.6084/m9.figshare.24564179openalex-snapshot

Additional file 1 of Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen

inferred← citeshttps://doi.org/10.6084/m9.figshare.24564282openalex-snapshot

Additional file 2 of Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen

inferred← citeshttps://doi.org/10.6084/m9.figshare.26640169openalex-snapshot

Additional file 3 of Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen

inferred← citeshttps://doi.org/10.6084/m9.figshare.26640172openalex-snapshot

Additional file 4 of Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen

inferred← citeshttps://doi.org/10.6084/m9.figshare.26640175openalex-snapshot

Additional file 5 of Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen

inferred← citeshttps://doi.org/10.6084/m9.figshare.26640178openalex-snapshot

Additional file 6 of Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen

inferred← citeshttps://doi.org/10.6084/m9.figshare.26640181openalex-snapshot

Additional file 7 of Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen

inferred← citeshttps://doi.org/10.6084/m9.figshare.26640184openalex-snapshot

Additional file 8 of Long noncoding RNAs emerge from transposon-derived antisense sequences and may contribute to infection stage-specific transposon regulation in a fungal phytopathogen

inferred← citeshttps://doi.org/10.64898/2026.02.26.708203openalex-snapshot

Alternaria atra from distinct ecological roles share functional genomic repertoires

inferred← citeshttps://doi.org/10.64898/2026.03.13.711015openalex-snapshot

Transcriptional signatures underlying divergent lifestyles of endophytic and pathogenic fungi in early colonisation of wheat roots

inferred← citeshttps://doi.org/10.64898/2026.04.07.716880openalex-snapshot

Comparative genomics of Cadophora luteo-olivacea reveals a divergent lineage, conserved functional repertoires, and strain-level variation in pathogenicity

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.