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Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce

https://doi.org/10.1128/msystems.00884-20

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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/bimj.200810425openalex-snapshot

Simultaneous Inference in General Parametric Models

inferredcites →https://doi.org/10.1007/978-0-387-98141-3openalex-snapshot

ggplot2: Elegant Graphics for Data Analysis

inferredcites →https://doi.org/10.1007/978-3-642-57219-7_16openalex-snapshot

Fungal Diversity in Ectomycorrhizal Communities of Norway Spruce [Picea abies (L.) Karst.] and Beech (Fagus sylvatica L.) Along North-South Transects in Europe

inferredcites →https://doi.org/10.1007/978-3-642-75168-4openalex-snapshot

Nitrogen in Terrestrial Ecosystems

inferredcites →https://doi.org/10.1007/978-981-10-4059-7openalex-snapshot

Probiotics in Agroecosystem

inferredcites →https://doi.org/10.1007/978-981-10-4059-7_13openalex-snapshot

Exploring the Plant Microbiome Through Multi-omics Approaches

inferredcites →https://doi.org/10.1007/s10709-014-9783-4openalex-snapshot

Technical challenges in metatranscriptomic studies applied to the bacterial communities of freshwater ecosystems

inferredcites →https://doi.org/10.1007/s12064-012-0162-3openalex-snapshot

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

inferredcites →https://doi.org/10.1007/s13199-015-0350-2openalex-snapshot

Functions, mechanisms and regulation of endophytic and epiphytic microbial communities of plants

inferredcites →https://doi.org/10.1016/j.cpc.2010.04.018openalex-snapshot

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

inferredcites →https://doi.org/10.1016/j.fbr.2007.09.003openalex-snapshot

Degradation and transformation of humic substances by saprotrophic fungi: processes and mechanisms

inferredcites →https://doi.org/10.1016/j.funeco.2010.09.008openalex-snapshot

Conservation of ectomycorrhizal fungi: exploring the linkages between functional and taxonomic responses to anthropogenic N deposition

inferredcites →https://doi.org/10.1016/j.funeco.2014.12.005openalex-snapshot

Prospects and challenges for fungal metatranscriptomics of complex communities

inferredcites →https://doi.org/10.1016/j.mimet.2012.09.036openalex-snapshot

Application of peptide nucleic acid (PNA)-PCR clamping technique to investigate the community structures of rhizobacteria associated with plant roots

inferredcites →https://doi.org/10.1016/j.soilbio.2018.07.005openalex-snapshot

Microbial community response to growing season and plant nutrient optimisation in a boreal Norway spruce forest

inferredcites →https://doi.org/10.1016/j.soilbio.2019.107570openalex-snapshot

Why does nitrogen addition to forest soils inhibit decomposition?

inferredcites →https://doi.org/10.1016/s0378-1127(98)00509-xopenalex-snapshot

The effect of water and nutrient availability on the productivity of Norway spruce in northern and southern Sweden

inferredcites →https://doi.org/10.1038/ismej.2011.95openalex-snapshot

Active and total microbial communities in forest soil are largely different and highly stratified during decomposition

inferredcites →https://doi.org/10.1038/ismej.2016.184openalex-snapshot

Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands

inferredcites →https://doi.org/10.1038/ismej.2016.42openalex-snapshot

Consortia of low-abundance bacteria drive sulfate reduction-dependent degradation of fermentation products in peat soil microcosms

inferredcites →https://doi.org/10.1038/nature11237openalex-snapshot

Defining the core Arabidopsis thaliana root microbiome

inferredcites →https://doi.org/10.1038/nature11336openalex-snapshot

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

inferredcites →https://doi.org/10.1038/nbt.1883openalex-snapshot

Full-length transcriptome assembly from RNA-Seq data without a reference genome

inferredcites →https://doi.org/10.1038/nmeth.1517openalex-snapshot

De novo assembly and analysis of RNA-seq data

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot

Fast and sensitive protein alignment using DIAMOND

inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot

DADA2: High-resolution sample inference from Illumina amplicon data

inferredcites →https://doi.org/10.1038/nmicrobiol.2016.242openalex-snapshot

Relic DNA is abundant in soil and obscures estimates of soil microbial diversity

inferredcites →https://doi.org/10.1038/s41396-018-0342-3openalex-snapshot

Dual RNA-seq reveals large-scale non-conserved genotype × genotype-specific genetic reprograming and molecular crosstalk in the mycorrhizal 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/s41522-017-0046-xopenalex-snapshot

Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities

inferredcites →https://doi.org/10.1038/s41564-017-0089-zopenalex-snapshot

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

inferredcites →https://doi.org/10.1038/srep15407openalex-snapshot

Revealing crosstalk of plant and fungi in the symbiotic roots of sewage-cleaning Eichhornia crassipes using direct de novo metatranscriptomic analysis

inferredcites →https://doi.org/10.1038/srep26447openalex-snapshot

MetaTrans: an open-source pipeline for metatranscriptomics

inferredcites →https://doi.org/10.1073/pnas.1117018109openalex-snapshot

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

inferredcites →https://doi.org/10.1093/bioinformatics/btt656openalex-snapshot

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

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

Trimmomatic: a flexible trimmer for Illumina sequence data

inferredcites →https://doi.org/10.1093/bioinformatics/btu719openalex-snapshot

deML: robust demultiplexing of Illumina sequences using a likelihood-based approach

inferredcites →https://doi.org/10.1093/bioinformatics/btv033openalex-snapshot

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

inferredcites →https://doi.org/10.1093/bioinformatics/btw354openalex-snapshot

MultiQC: summarize analysis results for multiple tools and samples in a single report

inferredcites →https://doi.org/10.1093/femsre/fuw017openalex-snapshot

Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes

inferredcites →https://doi.org/10.1093/molbev/msx148openalex-snapshot

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

inferredcites →https://doi.org/10.1093/nar/gkl200openalex-snapshot

AUGUSTUS: ab initio prediction of alternative transcripts

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/nar/gkt1183openalex-snapshot

MycoCosm portal: gearing up for 1000 fungal genomes

inferredcites →https://doi.org/10.1093/nar/gku169openalex-snapshot

MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences

inferredcites →https://doi.org/10.1093/nar/gkv1070openalex-snapshot

KEGG as a reference resource for gene and protein annotation

inferredcites →https://doi.org/10.1093/nar/gkv227openalex-snapshot

Identification of protein coding regions in RNA transcripts

inferredcites →https://doi.org/10.1093/nar/gky1085openalex-snapshot

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

inferredcites →https://doi.org/10.1101/081026openalex-snapshot

Gist – an ensemble approach to the taxonomic classification of metatranscriptomic sequence data

inferredcites →https://doi.org/10.1109/mcse.2007.55openalex-snapshot

Matplotlib: A 2D Graphics Environment

inferredcites →https://doi.org/10.1111/1462-2920.13026openalex-snapshot

Microbial activity in forest soil reflects the changes in ecosystem properties between summer and winter

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.1365-2486.2007.01420.xopenalex-snapshot

Carbon allocation in forest ecosystems

inferredcites →https://doi.org/10.1111/j.1469-8137.2004.01159.xopenalex-snapshot

A meta‐analysis of mycorrhizal responses to nitrogen, phosphorus, and atmospheric CO 2 in field studies

inferredcites →https://doi.org/10.1111/j.1469-8137.2005.01376.xopenalex-snapshot

UNITE: a database providing web‐based methods for the molecular identification of ectomycorrhizal fungi

inferredcites →https://doi.org/10.1111/j.1469-8137.2009.03160.xopenalex-snapshot

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

inferredcites →https://doi.org/10.1111/j.1654-1103.2003.tb02228.xopenalex-snapshot

VEGAN, a package of R functions for community ecology

inferredcites →https://doi.org/10.1111/nph.12791openalex-snapshot

Ectomycorrhizal C ortinarius species participate in enzymatic oxidation of humus in northern forest ecosystems

inferredcites →https://doi.org/10.1111/nph.13557openalex-snapshot

The Plant Genome Integrative Explorer Resource: PlantGen IE .org

inferredcites →https://doi.org/10.1126/science.1146689openalex-snapshot

Microbial Population Structures in the Deep Marine Biosphere

inferredcites →https://doi.org/10.1128/jb.186.9.2629-2635.2004openalex-snapshot

Divergence and Redundancy of 16S rRNA Sequences in Genomes with Multiple rrn Operons

inferredcites →https://doi.org/10.1139/b04-123openalex-snapshot

Mycorrhizal fungi as drivers of ecosystem processes in heathland and boreal forest biomes

inferredcites →https://doi.org/10.1139/x06-035openalex-snapshot

Influence of long-term nutrient optimization on biomass, carbon, and nitrogen acquisition and allocation in Norway spruce

inferredcites →https://doi.org/10.1186/1471-2105-12-35openalex-snapshot

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

inferredcites →https://doi.org/10.1186/s12859-018-2189-zopenalex-snapshot

SAMSA2: a standalone metatranscriptome analysis pipeline

inferredcites →https://doi.org/10.1186/s12864-017-4168-6openalex-snapshot

TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms

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/10.1186/s13059-016-1116-8openalex-snapshot

IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses

inferredcites →https://doi.org/10.1186/s40168-018-0432-5openalex-snapshot

Trees, fungi and bacteria: tripartite metatranscriptomics of a root microbiome responding to soil contamination

inferredcites →https://doi.org/10.1186/s40168-018-0469-5openalex-snapshot

Low-abundant bacteria drive compositional changes in the gut microbiota after dietary alteration

inferredcites →https://doi.org/10.1371/journal.pone.0052249openalex-snapshot

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

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.0139080openalex-snapshot

Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies)

inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot

Cutadapt removes adapter sequences from high-throughput sequencing reads

inferredcites →https://doi.org/10.3233/978-1-61499-649-1-87openalex-snapshot

Jupyter Notebooks – a publishing format for reproducible computational workflows

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

pheatmap: Pretty Heatmaps

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

R: A Language and Environment for Statistical Computing

inferredcites →https://doi.org/10.3389/fgene.2019.00904openalex-snapshot

Advances and Challenges in Metatranscriptomic Analysis

inferredcites →https://doi.org/10.3389/fmicb.2015.00337openalex-snapshot

Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests

inferredcites →https://doi.org/10.3389/fmicb.2017.00975openalex-snapshot

A Small Number of Low-abundance Bacteria Dominate Plant Species-specific Responses during Rhizosphere Colonization

inferredcites →https://doi.org/10.3389/fmicb.2017.01294openalex-snapshot

Unraveling Core Functional Microbiota in Traditional Solid-State Fermentation by High-Throughput Amplicons and Metatranscriptomics Sequencing

inferredcites →https://doi.org/10.3389/fmicb.2018.00388openalex-snapshot

Metatranscriptomics and Amplicon Sequencing Reveal Mutualisms in Seagrass Microbiomes

inferredcites →https://doi.org/10.3897/mycokeys.10.4852openalex-snapshot

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

inferredcites →https://doi.org/10.4137/bbi.s34610openalex-snapshot

Use of Metatranscriptomics in Microbiome Research

inferredcites →https://doi.org/10.48550/arxiv.1201.0490openalex-snapshot

Scikit-learn: Machine Learning in Python

inferredcites →https://doi.org/10.7717/peerj.1420openalex-snapshot

Swarm v2: highly-scalable and high-resolution amplicon clustering

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

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inferred← citeshttps://doi.org/10.1007/978-981-92-0339-0_7openalex-snapshot

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inferred← citeshttps://doi.org/10.1007/s11104-023-06364-1openalex-snapshot

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inferred← citeshttps://doi.org/10.1007/s11356-022-20317-8openalex-snapshot

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inferred← citeshttps://doi.org/10.1007/s11557-022-01859-0openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.apsoil.2026.107050openalex-snapshot

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inferred← citeshttps://doi.org/10.1016/j.cpb.2026.100672openalex-snapshot

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inferred← citeshttps://doi.org/10.1080/17429145.2026.2649126openalex-snapshot

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inferred← citeshttps://doi.org/10.1111/nph.19471openalex-snapshot

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