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Evidence for host–microbiome co‐evolution in apple

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What this work says

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

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Vertical transmission of fungal endophytes is widespread in forbs

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The Apple Microbiome: Structure, Function, and Manipulation for Improved Plant Health

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Temperate Tree Fruits of North America: Malus Mill., Prunus L., Diospyros L., and Asimina Adans

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Plant–microbe interactions promoting plant growth and health: perspectives for controlled use of microorganisms in agriculture

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The vulnerability of US apple (Malus) genetic resources

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The Cucurbita pepo seed microbiome: genotype-specific composition and implications for breeding

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An accumulation of genetic variation and selection across the disease-related genes during apple domestication

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Effect of hybridization on endophytes: the endo-microbiome dynamics

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PCR protocols — A guide to methods and applications

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AMPLIFICATION AND DIRECT SEQUENCING OF FUNGAL RIBOSOMAL RNA GENES FOR PHYLOGENETICS

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Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley

inferredcites →https://doi.org/10.1016/j.csbj.2020.01.004openalex-snapshot

Nicotiana tabacum seed endophytic communities share a common core structure and genotype-specific signatures in diverging cultivars

inferredcites →https://doi.org/10.1016/j.jare.2020.12.008openalex-snapshot

Domestication affects the composition, diversity, and co-occurrence of the cereal seed microbiota

inferredcites →https://doi.org/10.1016/j.mib.2017.03.010openalex-snapshot

Ecological patterns of seed microbiome diversity, transmission, and assembly

inferredcites →https://doi.org/10.1016/j.postharvbio.2017.01.006openalex-snapshot

Composition of phenolic compounds in wild apple with multiple resistance mechanisms against postharvest blue mold decay

inferredcites →https://doi.org/10.1016/j.postharvbio.2018.05.005openalex-snapshot

Compositional shifts in the surface fungal communities of apple fruits during cold storage

inferredcites →https://doi.org/10.1016/j.tig.2013.10.002openalex-snapshot

The domestication and evolutionary ecology of apples

inferredcites →https://doi.org/10.1016/j.tree.2020.01.006openalex-snapshot

Agriculture and the Disruption of Plant–Microbial Symbiosis

inferredcites →https://doi.org/10.1038/hortres.2016.47openalex-snapshot

Spatial and compositional variation in the fungal communities of organic and conventionally grown apple fruit at the consumer point-of-purchase

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Influence of resistance breeding in common bean on rhizosphere microbiome composition and function

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Bayesian community-wide culture-independent microbial source tracking

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Differential abundance analysis for microbial marker-gene surveys

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DADA2: High-resolution sample inference from Illumina amplicon data

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Temporal and spatial dynamics in the apple flower microbiome in the presence of the phytopathogen Erwinia amylovora

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Maize germplasm chronosequence shows crop breeding history impacts recruitment of the rhizosphere microbiome

inferredcites →https://doi.org/10.1038/s41396-021-00993-zopenalex-snapshot

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

inferredcites →https://doi.org/10.1038/s41467-017-00262-8openalex-snapshot

Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence

inferredcites →https://doi.org/10.1038/s41467-017-00336-7openalex-snapshot

Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement

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Bacterial seed endophyte shapes disease resistance in rice

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Emerging strategies for precision microbiome management in diverse agroecosystems

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Eco-evolutionary interaction between microbiome presence and rapid biofilm evolution determines plant host fitness

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Detecting macroecological patterns in bacterial communities across independent studies of global soils

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Microbiome innovations for a sustainable future

inferredcites →https://doi.org/10.1038/s41587-019-0209-9openalex-snapshot

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

inferredcites →https://doi.org/10.1038/s41598-020-69175-9openalex-snapshot

Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat

inferredcites →https://doi.org/10.1046/j.1469-8137.2002.00397.xopenalex-snapshot

Coevolution of roots and mycorrhizas of land plants

inferredcites →https://doi.org/10.1073/pnas.1302837110openalex-snapshot

Diversity and heritability of the maize rhizosphere microbiome under field conditions

inferredcites →https://doi.org/10.1073/pnas.1321597111openalex-snapshot

Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives

inferredcites →https://doi.org/10.1080/01621459.1952.10483441openalex-snapshot

Use of Ranks in One-Criterion Variance Analysis

inferredcites →https://doi.org/10.1093/aob/mcz010openalex-snapshot

Resource allocation trade-offs and the loss of chemical defences during apple domestication

inferredcites →https://doi.org/10.1093/bioinformatics/btq706openalex-snapshot

phangorn: phylogenetic analysis in R

inferredcites →https://doi.org/10.1093/femsec/fiaa119openalex-snapshot

Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables

inferredcites →https://doi.org/10.1093/nar/gks1219openalex-snapshot

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040454openalex-snapshot

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

inferredcites →https://doi.org/10.1094/pbiomes-06-18-0029-ropenalex-snapshot

Tomato Seeds Preferably Transmit Plant Beneficial Endophytes

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The persistence of vertically transmitted fungi in grass metapopulations

inferredcites →https://doi.org/10.1098/rspb.2007.1187openalex-snapshot

Human selection and the relaxation of legume defences against ineffective rhizobia

inferredcites →https://doi.org/10.1111/1462-2920.12442openalex-snapshot

Root microbiome relates to plant host evolution in maize and other P oaceae

inferredcites →https://doi.org/10.1111/1462-2920.12686openalex-snapshot

Bacterial networks and co‐occurrence relationships in the lettuce root microbiota

inferredcites →https://doi.org/10.1111/1462-2920.15392openalex-snapshot

Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root

inferredcites →https://doi.org/10.1111/1462-2920.15469openalex-snapshot

Global analysis of the apple fruit microbiome: are all apples the same?

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Diversity and specificity of Rhizobium leguminosarum biovar viciae on wild and cultivated legumes

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Fungal endophytes in a 400‐million‐yr‐old land plant: infection pathways, spatial distribution, and host responses

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The UNITE database for molecular identification of fungi – recent updates and future perspectives

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Ongoing coevolution in mycorrhizal interactions

inferredcites →https://doi.org/10.1111/j.1600-0706.2011.19299.xopenalex-snapshot

Incorporating the process of vertical transmission into understanding of host–symbiont dynamics

inferredcites →https://doi.org/10.1111/j.2041-210x.2012.00224.xopenalex-snapshot

betapart: an R package for the study of beta diversity

inferredcites →https://doi.org/10.1111/mec.13510openalex-snapshot

Host associations and beta diversity of fungal endophyte communities in New Guinea rainforest trees

inferredcites →https://doi.org/10.1111/nph.13697openalex-snapshot

Plant compartment and biogeography affect microbiome composition in cultivated and native Agave species

inferredcites →https://doi.org/10.1111/nph.14323openalex-snapshot

Plant domestication and the assembly of bacterial and fungal communities associated with strains of the common sunflower, Helianthus annuus

inferredcites →https://doi.org/10.1111/nph.16867openalex-snapshot

Targeted plant hologenome editing for plant trait enhancement

inferredcites →https://doi.org/10.1111/nph.17622openalex-snapshot

Prioritizing host phenotype to understand microbiome heritability in plants

inferredcites →https://doi.org/10.1111/tpj.14170openalex-snapshot

Genome‐wide association studies on the phyllosphere microbiome: Embracing complexity in host–microbe interactions

inferredcites →https://doi.org/10.1126/science.1240659openalex-snapshot

The Hologenomic Basis of Speciation: Gut Bacteria Cause Hybrid Lethality in the Genus Nasonia

inferredcites →https://doi.org/10.1126/science.aba6605openalex-snapshot

Plant evolution driven by interactions with symbiotic and pathogenic microbes

inferredcites →https://doi.org/10.1128/aem.01543-13openalex-snapshot

Shared Metabolic Pathways in a Coevolved Insect-Bacterial Symbiosis

inferredcites →https://doi.org/10.1128/mbio.00602-12openalex-snapshot

Unexpected Diversity during Community Succession in the Apple Flower Microbiome

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/msystems.00028-16openalex-snapshot

Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes

inferredcites →https://doi.org/10.1128/msystems.00097-18openalex-snapshot

Is Host Filtering the Main Driver of Phylosymbiosis across the Tree of Life?

inferredcites →https://doi.org/10.1186/s40168-018-0403-xopenalex-snapshot

Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence

inferredcites →https://doi.org/10.1186/s40168-018-0519-zopenalex-snapshot

The wild side of plant microbiomes

inferredcites →https://doi.org/10.1186/s40168-018-0570-9openalex-snapshot

The response of dominant and rare taxa for fungal diversity within different root environments to the cultivation of Bt and conventional cotton varieties

inferredcites →https://doi.org/10.1186/s40168-020-00805-0openalex-snapshot

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inferredcites →https://doi.org/10.1186/s40168-020-00875-0openalex-snapshot

Microbiome definition re-visited: old concepts and new challenges

inferredcites →https://doi.org/10.1371/journal.pbio.2000225openalex-snapshot

Phylosymbiosis: Relationships and Functional Effects of Microbial Communities across Host Evolutionary History

inferredcites →https://doi.org/10.1371/journal.pgen.1002703openalex-snapshot

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inferredcites →https://doi.org/10.1371/journal.pone.0024452openalex-snapshot

Desert Farming Benefits from Microbial Potential in Arid Soils and Promotes Diversity and Plant Health

inferredcites →https://doi.org/10.1371/journal.pone.0061217openalex-snapshot

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

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An Ordination of the Upland Forest Communities of Southern Wisconsin

inferredcites →https://doi.org/10.3389/fmicb.2019.01629openalex-snapshot

An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples?

inferredcites →https://doi.org/10.3389/fmicb.2019.02502openalex-snapshot

Microbiome Response to Hot Water Treatment and Potential Synergy With Biological Control on Stored Apples

inferredcites →https://doi.org/10.3389/fpls.2017.01981openalex-snapshot

Transcriptomic Response of Resistant (PI613981–Malus sieversii) and Susceptible (“Royal Gala”) Genotypes of Apple to Blue Mold (Penicillium expansum) Infection

inferredcites →https://doi.org/10.3389/fpls.2018.00024openalex-snapshot

What Is There in Seeds? Vertically Transmitted Endophytic Resources for Sustainable Improvement in Plant Growth

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Microbiome-Assisted Breeding to Understand Cultivar-Dependent Assembly in Cucurbita pepo

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Special Issue: Coevolution of Hosts and Their Microbiome

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Effect of Washing, Waxing and Low-Temperature Storage on the Postharvest Microbiome of Apple

What points at this work

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

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Host signature as major driver of root and rhizosphere core microbiomes that differently affect plant functional traits

inferred← citeshttps://doi.org/10.1111/1365-2435.14278openalex-snapshot

Phenotypic evolution of agricultural crops

inferred← citeshttps://doi.org/10.1111/1751-7915.14077openalex-snapshot

The Brassica napus seed microbiota is cultivar‐specific and transmitted via paternal breeding lines

inferred← citeshttps://doi.org/10.1111/1758-2229.13301openalex-snapshot

Seed or soil: Tracing back the plant mycobiota primary sources

inferred← citeshttps://doi.org/10.1111/mec.17769openalex-snapshot

Evolutionary History and Rhizosphere Microbial Community Composition in Domesticated Hops ( Humulus lupulus L . )

inferred← citeshttps://doi.org/10.1111/nph.18187openalex-snapshot

Impact of global change on the plant microbiome

inferred← citeshttps://doi.org/10.1111/nph.70698openalex-snapshot

Fruit function beyond dispersal: effect of fruit decomposition on the plant microbiome assembly

inferred← citeshttps://doi.org/10.1111/pce.15350openalex-snapshot

Microbial Biotic Associations Dominated Adaptability Differences of Dioecious Poplar Under Salt Stress

inferred← citeshttps://doi.org/10.1111/ppl.71016openalex-snapshot

Leaf Fungal Microbiome Is Modulated by Interspecific Hybridization Events Between Coffea Species

inferred← citeshttps://doi.org/10.1128/aem.00299-24openalex-snapshot

Bacterial-fungal crosstalk is defined by a fungal lactone mycotoxin and its degradation by a bacterial lactonase

inferred← citeshttps://doi.org/10.1128/msphere.00607-23openalex-snapshot

Taxonomic and functional assembly cues enrich the endophytic tobacco microbiota across epiphytic compartments

inferred← citeshttps://doi.org/10.1146/annurev-phyto-121823-025820openalex-snapshot

Biological Control of Postharvest Diseases: The Evolution of New Concepts and Perspectives

inferred← citeshttps://doi.org/10.1186/s12866-024-03574-0openalex-snapshot

Unravelling the microbiome of wild flowering plants: a comparative study of leaves and flowers in alpine ecosystems

inferred← citeshttps://doi.org/10.1186/s12870-025-06935-7openalex-snapshot

Phyllosphere synthetic microbial communities: a new frontier in plant protection

inferred← citeshttps://doi.org/10.1186/s40793-022-00402-8openalex-snapshot

The microbiome and resistome of apple fruits alter in the post-harvest period

inferred← citeshttps://doi.org/10.1186/s40793-023-00501-0openalex-snapshot

The microbiome of Riccia liverworts is an important reservoir for microbial diversity in temporary agricultural crusts

inferred← citeshttps://doi.org/10.1186/s40793-026-00880-0openalex-snapshot

Phenotypic resistance profiles and resistome variations between endophytic and epiphytic bacteria in apple fruits

inferred← citeshttps://doi.org/10.15252/embr.202357455openalex-snapshot

Co‐evolution within the plant holobiont drives host performance

inferred← citeshttps://doi.org/10.17352/ojeb.000046openalex-snapshot

The Seed Microbiome: Microbial Hashes for Plant Wellbeing

inferred← citeshttps://doi.org/10.17660/actahortic.2026.1458.57openalex-snapshot

Pre- and post-storage dynamics of apple surface microbial communities across different cultivars

inferred← citeshttps://doi.org/10.21203/rs.3.rs-3773072/v1openalex-snapshot

Phylosymbiosis drives the distribution of pathogen-protective bacteria in Appalachian salamanders

inferred← citeshttps://doi.org/10.21203/rs.3.rs-4011955/v1openalex-snapshot

Disentangling the impact of soil type, geographical location, altitude, and family identity on the flower and leaf microbiome in alpine plants

inferred← citeshttps://doi.org/10.21203/rs.3.rs-9344661/v1openalex-snapshot

Regional and Management-driven Variation in Apple Microbiome and Resistome

inferred← citeshttps://doi.org/10.31676/0235-2591-2025-6-15-20openalex-snapshot

Patterns of endophytic bacteria prevalence in flowers of the Debryansk black currant cultivar and its parental forms

inferred← citeshttps://doi.org/10.31676/2073-4948-2026-84-15-30openalex-snapshot

Research into the phylogenetic structure of phytomicrobiome for use in plant breeding

inferred← citeshttps://doi.org/10.3389/fmicb.2022.1075399openalex-snapshot

Plant genotype influence the structure of cereal seed fungal microbiome

inferred← citeshttps://doi.org/10.3389/fmicb.2023.1065302openalex-snapshot

Environmental factors and host genotype control foliar epiphytic microbial community of wild soybeans across China

inferred← citeshttps://doi.org/10.3389/fmicb.2024.1342407openalex-snapshot

The effects of chemical fungicides and salicylic acid on the apple microbiome and fungal disease incidence under changing environmental conditions

inferred← citeshttps://doi.org/10.3389/fmicb.2024.1399406openalex-snapshot

The functional identification and evaluation of endophytic bacteria sourced from the roots of tolerant Achyranthes bidentata to overcome monoculture problems of Rehmannia glutinosa

inferred← citeshttps://doi.org/10.3389/fpls.2022.891155openalex-snapshot

Bacterial Microbiome in the Phyllo-Endosphere of Highly Specialized Rock Spleenwort

inferred← citeshttps://doi.org/10.3389/fpls.2023.1141692openalex-snapshot

Comparative transcriptome profiling provides insights into the growth promotion activity of Pseudomonas fluorescens strain SLU99 in tomato and potato plants

inferred← citeshttps://doi.org/10.3389/fpls.2025.1652366openalex-snapshot

Aureobasidium pullulans: a microbiome-based perspective from global biomes to edible plant tissues

inferred← citeshttps://doi.org/10.3390/biology12020143openalex-snapshot

The Co-Association of Enterobacteriaceae and Pseudomonas with Specific Resistant Cucumber against Fusarium Wilt Disease

inferred← citeshttps://doi.org/10.3390/horticulturae11050536openalex-snapshot

The Role of Root Endophyte Pseudomonas putida A32 in the Protection of Two Pepper Genotypes from Pseudomonas syringae pv. aptata

inferred← citeshttps://doi.org/10.3390/ijms26051922openalex-snapshot

Unraveling the Mechanism of the Endophytic Bacterial Strain Pseudomonas oryzihabitans GDW1 in Enhancing Tomato Plant Growth Through Modulation of the Host Transcriptome and Bacteriome

inferred← citeshttps://doi.org/10.3390/microorganisms10091777openalex-snapshot

Endophytes: Improving Plant Performance

inferred← citeshttps://doi.org/10.3390/microorganisms13071614openalex-snapshot

Shifts in Fungal Communities and Potential Functions Under Masson Pine Forest-to-Tea Plantation Conversion in Subtropical China

inferred← citeshttps://doi.org/10.3390/plants14101511openalex-snapshot

Metagenomic Analysis of Wild Apple (Malus sieversii) Trees from Natural Habitats of Kazakhstan

inferred← citeshttps://doi.org/10.37828/em.2026.100.15openalex-snapshot

Microbiota-mediated trade-off in oligophagous insects: balancing dietary specialization and adaptive plasticity

inferred← citeshttps://doi.org/10.48130/sse-2023-0010openalex-snapshot

Different microbial assembly between cultivated and wild tomatoes under P stress

inferred← citeshttps://doi.org/10.5423/ppj.oa.03.2023.0038openalex-snapshot

Variations in Kiwifruit Microbiota across Cultivars and Tissues during Developmental Stages

inferred← citeshttps://doi.org/10.6084/m9.figshare.23280996openalex-snapshot

Additional file 1 of The microbiome of Riccia liverworts is an important reservoir for microbial diversity in temporary agricultural crusts

inferred← citeshttps://doi.org/10.7717/peerj.18811openalex-snapshot

Anthropogenic reverberations on the gut microbiome of dwarf chameleons (Bradypodion)

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