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Choices on sampling, sequencing, and analyzing DNA influence the estimation of community composition of plant fungal symbionts

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What this work says

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

inferredcites →https://doi.org/10.1002/aps3.11449openalex-snapshot

Choices on sampling, sequencing, and analyzing DNA influence the estimation of community composition of plant fungal symbionts

inferredcites →https://doi.org/10.1002/cpmb.59openalex-snapshot

Overview of Next‐Generation Sequencing Technologies

inferredcites →https://doi.org/10.1007/s00442-003-1311-7openalex-snapshot

Community assembly: when should history matter?

inferredcites →https://doi.org/10.1016/b978-0-12-370526-6.x5001-6openalex-snapshot

Mycorrhizal Symbiosis

inferredcites →https://doi.org/10.1016/j.fbr.2013.09.001openalex-snapshot

Lineages of ectomycorrhizal fungi revisited: Foraging strategies and novel lineages revealed by sequences from belowground

inferredcites →https://doi.org/10.1016/j.funeco.2015.06.006openalex-snapshot

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

inferredcites →https://doi.org/10.1016/j.funeco.2019.03.005openalex-snapshot

Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline

inferredcites →https://doi.org/10.1016/j.soilbio.2014.09.010openalex-snapshot

The role of stochasticity differs in the assembly of soil- and root-associated fungal communities

inferredcites →https://doi.org/10.1038/ismej.2013.10openalex-snapshot

Robust estimation of microbial diversity in theory and in practice

inferredcites →https://doi.org/10.1038/nmeth.2604openalex-snapshot

UPARSE: highly accurate OTU sequences from microbial amplicon reads

inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot

QIIME allows analysis of high-throughput community sequencing data

inferredcites →https://doi.org/10.1038/s41579-018-0116-yopenalex-snapshot

Mycobiome diversity: high-throughput sequencing and identification of fungi

inferredcites →https://doi.org/10.1038/srep31439openalex-snapshot

Divergent habitat filtering of root and soil fungal communities in temperate beech forests

inferredcites →https://doi.org/10.1093/bioinformatics/btq461openalex-snapshot

Search and clustering orders of magnitude faster than BLAST

inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1098/rstb.2011.0063openalex-snapshot

Disentangling the importance of ecological niches from stochastic processes across scales

inferredcites →https://doi.org/10.1111/1365-2745.13312openalex-snapshot

Symbiotic interactions above treeline of long‐lived pines: Mycorrhizal advantage of limber pine (Pinus flexilis) over Great Basin bristlecone pine (Pinus longaeva) at the seedling stage

inferredcites →https://doi.org/10.1111/2041-210x.12073openalex-snapshot

Improved software detection and extraction of ITS1 and ITS 2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

inferredcites →https://doi.org/10.1111/j.1365-294x.1993.tb00005.xopenalex-snapshot

ITS primers with enhanced specificity for basidiomycetes ‐ application to the identification of mycorrhizae and rusts

inferredcites →https://doi.org/10.1111/mec.15674openalex-snapshot

Effects of soil preservation for biodiversity monitoring using environmental DNA

inferredcites →https://doi.org/10.1111/nph.14195openalex-snapshot

Change in soil fungal community structure driven by a decline in ectomycorrhizal fungi following a mountain pine beetle (Dendroctonus ponderosae) outbreak

inferredcites →https://doi.org/10.1126/science.1231923openalex-snapshot

Roots and Associated Fungi Drive Long-Term Carbon Sequestration in Boreal Forest

inferredcites →https://doi.org/10.1126/science.1256688openalex-snapshot

Global diversity and geography of soil fungi

inferredcites →https://doi.org/10.1186/1471-2180-10-189openalex-snapshot

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1371/journal.pcbi.1003531openalex-snapshot

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

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

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

inferredcites →https://doi.org/10.1371/journal.pone.0078295openalex-snapshot

Fungi at a Small Scale: Spatial Zonation of Fungal Assemblages around Single Trees

inferredcites →https://doi.org/10.1371/journal.pone.0206428openalex-snapshot

Evaluation of the ribosomal DNA internal transcribed spacer (ITS), specifically ITS1 and ITS2, for the analysis of fungal diversity by deep sequencing

inferredcites →https://doi.org/10.18637/jss.v067.i01openalex-snapshot

Fitting Linear Mixed-Effects Models Using lme4

inferredcites →https://doi.org/10.1890/08-1291.1openalex-snapshot

Root tip competition among ectomycorrhizal fungi: Are priority effects a rule or an exception?

inferredcites →https://doi.org/10.1890/10-1345.1openalex-snapshot

A novel statistical method for classifying habitat generalists and specialists

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/fpls.2019.00214openalex-snapshot

Root-Associated Fungal Communities From Two Phenologically Contrasting Silver Fir (Abies alba Mill.) Groups of Trees

inferredcites →https://doi.org/10.3897/mbmg.4.58365openalex-snapshot

Soil stabilisation for DNA metabarcoding of plants and fungi. Implications for sampling at remote locations or via third-parties

inferredcites →https://doi.org/10.7717/peerj.545openalex-snapshot

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

inferredcites →https://doi.org/10.7717/peerj.6895openalex-snapshot

Large-scale insect outbreak homogenizes the spatial structure of ectomycorrhizal fungal communities

What points at this work

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

inferred← citeshttps://doi.org/10.3897/bdj.14.e198617zenodo-depositor-declared

MycorrhizaTracer: A bioinformatic pipeline for fungi and plant classification of Sanger DNA sequences

inferred← citeshttps://doi.org/10.1007/s00572-024-01147-7openalex-snapshot

Distinct orchid mycorrhizal fungal communities among co-occurring Vanilla species in Costa Rica: root substrate and population-based segregation

inferred← citeshttps://doi.org/10.1016/j.foodcont.2023.110086openalex-snapshot

Tracking adulteration of nectar honey varieties using a high-resolution melting qPCR technique validated with melissopalinology

inferred← citeshttps://doi.org/10.1016/j.foreco.2025.122786openalex-snapshot

Does topography affect the ectomycorrhizal fungal community structure of Scots Pine (Pinus sylvestris L.) grown on the sand coastal dunes in Poland and Lithuania

inferred← citeshttps://doi.org/10.21203/rs.3.rs-1838768/v1openalex-snapshot

Biodiversity and antimicrobial activity of intestinal fungi from three species of coral reef fishes

inferred← citeshttps://doi.org/10.3389/fmicb.2022.1007935openalex-snapshot

Abiotic environmental factors drive the diversity, compositional dynamics and habitat preference of ectomycorrhizal fungi in Pannonian forest types

inferred← citeshttps://doi.org/10.3390/jof9060613openalex-snapshot

Diversity and Antimicrobial Activity of Intestinal Fungi from Three Species of Coral Reef Fish

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