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Multiomic analisys reveals that viroid infection induces a temporal reprograming of plant-defence mechanisms at multiple regulatory levels
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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/wrna.1570openalex-snapshot
Current overview on viroid–host interactions
inferredcites →https://doi.org/10.1007/s00018-008-8027-0openalex-snapshot
The post-transcriptional steps of eukaryotic ribosome biogenesis
inferredcites →https://doi.org/10.1007/s00299-019-02414-0openalex-snapshot
Epigenetics in the plant–virus interaction
inferredcites →https://doi.org/10.1007/s10327-003-0083-6openalex-snapshot
Accumulation of short interfering RNAs characteristic of RNA silencing precedes recovery of tomato plants from severe symptoms of Potato spindle tuber viroid infection
inferredcites →https://doi.org/10.1007/s10327-014-0566-7openalex-snapshot
Changes in relative expression levels of viroid-specific small RNAs and microRNAs in tomato plants infected with severe and mild symptom-inducing isolates of Potato spindle tuber viroid
inferredcites →https://doi.org/10.1007/s11033-019-05084-zopenalex-snapshot
Small RNA sequencing identifies cucumber miRNA roles in waterlogging-triggered adventitious root primordia formation
inferredcites →https://doi.org/10.1016/0042-6822(71)90342-4openalex-snapshot
Potato spindle tuber “virus”
inferredcites →https://doi.org/10.1016/0092-8674(94)90119-8openalex-snapshot
RNA-directed de novo methylation of genomic sequences in plants
inferredcites →https://doi.org/10.1016/j.cj.2020.07.007openalex-snapshot
Roles of miR319-regulated TCPs in plant development and response to abiotic stress
inferredcites →https://doi.org/10.1016/j.devcel.2007.04.012openalex-snapshot
Sequence and Expression Differences Underlie Functional Specialization of Arabidopsis MicroRNAs miR159 and miR319
inferredcites →https://doi.org/10.1016/j.devcel.2014.06.017openalex-snapshot
Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis
inferredcites →https://doi.org/10.1016/j.gene.2015.03.076openalex-snapshot
In silico prediction and validation of potential gene targets for pospiviroid-derived small RNAs during tomato infection
inferredcites →https://doi.org/10.1016/j.scienta.2020.109845openalex-snapshot
MicroRNA expression dynamics reshape the cultivar-specific response of pepper (Capsicum annuum L.) to potato spindle tuber viroid (PSTVd) infection
inferredcites →https://doi.org/10.1016/j.tplants.2009.03.002openalex-snapshot
Interplay between viroid-induced pathogenesis and RNA silencing pathways
inferredcites →https://doi.org/10.1016/j.virol.2007.05.011openalex-snapshot
Characterization of small RNAs derived from Citrus exocortis viroid (CEVd) in infected tomato plants
inferredcites →https://doi.org/10.1016/j.virol.2011.01.021openalex-snapshot
Accumulation of Potato spindle tuber viroid-specific small RNAs is accompanied by specific changes in gene expression in two tomato cultivars
inferredcites →https://doi.org/10.1016/j.virusres.2015.08.018openalex-snapshot
Viroids, infectious long non-coding RNAs with autonomous replication
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/s41438-021-00480-8openalex-snapshot
sRNAanno—a database repository of uniformly annotated small RNAs in plants
inferredcites →https://doi.org/10.1038/s41598-017-08823-zopenalex-snapshot
Potato spindle tuber viroid infection triggers degradation of chloride channel protein CLC-b-like and Ribosomal protein S3a-like mRNAs in tomato plants
inferredcites →https://doi.org/10.1055/s-0040-1714414openalex-snapshot
Advances in Transcriptomics in the Response to Stress in Plants
inferredcites →https://doi.org/10.1073/pnas.0400104101openalex-snapshot
On the role of RNA silencing in the pathogenicity and evolution of viroids and viral satellites
inferredcites →https://doi.org/10.1080/15476286.2018.1462653openalex-snapshot
Alterations of the viroid regions that interact with the host defense genes attenuate viroid infection in host plant
inferredcites →https://doi.org/10.1080/15476286.2019.1697487openalex-snapshot
Dynamic architecture and regulatory implications of the miRNA network underlying the response to stress in melon
inferredcites →https://doi.org/10.1093/bioinformatics/bti310openalex-snapshot
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btp616openalex-snapshot
edgeR : a Bioconductor package for differential expression analysis of digital gene expression data
inferredcites →https://doi.org/10.1093/bioinformatics/btq033openalex-snapshot
BEDTools: a flexible suite of utilities for comparing genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btr167openalex-snapshot
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btu638openalex-snapshot
HTSeq—a Python framework to work with high-throughput sequencing data
inferredcites →https://doi.org/10.1093/jxb/erw353openalex-snapshot
Changes in the DNA methylation pattern of the host male gametophyte of viroid-infected cucumber plants
inferredcites →https://doi.org/10.1093/molbev/msaa091openalex-snapshot
Viral Fitness Determines the Magnitude of Transcriptomic and Epigenomic Reprograming of Defense Responses in Plants
inferredcites →https://doi.org/10.1093/nar/29.11.2395openalex-snapshot
Replicating potato spindle tuber viroid RNA is accompanied by short RNA fragments that are characteristic of post-transcriptional gene silencing
inferredcites →https://doi.org/10.1093/nar/gkt968openalex-snapshot
A pathogenic non-coding RNA induces changes in dynamic DNA methylation of ribosomal RNA genes in host plants
inferredcites →https://doi.org/10.1093/nar/gky1034openalex-snapshot
RNAcentral: a hub of information for non-coding RNA sequences
inferredcites →https://doi.org/10.1093/nar/gky316openalex-snapshot
psRNATarget: a plant small RNA target analysis server (2017 release)
inferredcites →https://doi.org/10.1093/nar/gky602openalex-snapshot
DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts
inferredcites →https://doi.org/10.1093/nar/gky944openalex-snapshot
Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops
inferredcites →https://doi.org/10.1093/nar/gkz121openalex-snapshot
Does co-transcriptional regulation of alternative splicing mediate plant stress responses?
inferredcites →https://doi.org/10.1093/nar/gkz679openalex-snapshot
Citrus exocortis viroid causes ribosomal stress in tomato plants
inferredcites →https://doi.org/10.1094/mpmi-03-17-0071-ropenalex-snapshot
Hop stunt viroid: Effect on Host (Humulus lupulus) Transcriptome and Its Interactions With Hop Powdery Mildew (Podospheara macularis)
inferredcites →https://doi.org/10.1094/mpmi-08-15-0194-fiopenalex-snapshot
Epigenetic Mechanisms: An Emerging Player in Plant-Microbe Interactions
inferredcites →https://doi.org/10.1094/mpmi-09-11-0258openalex-snapshot
Global Analysis of Tomato Gene Expression During Potato spindle tuber viroid Infection Reveals a Complex Array of Changes Affecting Hormone Signaling
inferredcites →https://doi.org/10.1094/mpmi.2001.14.11.1332openalex-snapshot
Potato spindle tuber viroid as Inducer of RNA Silencing in Infected Tomato
inferredcites →https://doi.org/10.1094/mpmi.2002.15.10.990openalex-snapshot
Potato spindle tuber viroid Strains of Different Pathogenicity Induces and Suppresses Expression of Common and Unique Genes in Infected Tomato
inferredcites →https://doi.org/10.1099/0022-1317-82-4-953openalex-snapshot
The molecular characterization of 16 new sequence variants of Hop stunt viroid reveals the existence of invariable regions and a conserved hammerhead-like structure on the viroid molecule
inferredcites →https://doi.org/10.1101/cshperspect.a019471openalex-snapshot
Epigenetic Regulation in Plant Responses to the Environment
inferredcites →https://doi.org/10.1101/gad.1914110openalex-snapshot
Mechanisms of HDA6-mediated rRNA gene silencing: suppression of intergenic Pol II transcription and differential effects on maintenance versus siRNA-directed cytosine methylation
inferredcites →https://doi.org/10.1101/gr.133744.111openalex-snapshot
Detecting differential usage of exons from RNA-seq data
inferredcites →https://doi.org/10.1105/tpc.114.133991openalex-snapshot
Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in Brachypodium distachyon
inferredcites →https://doi.org/10.1105/tpc.15.00523openalex-snapshot
Small RNA Derived from the Virulence Modulating Region of the Potato spindle tuber viroid Silences callose synthase Genes of Tomato Plants
inferredcites →https://doi.org/10.1105/tpc.16.00158openalex-snapshot
EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments
inferredcites →https://doi.org/10.1111/j.1364-3703.2009.00608.xopenalex-snapshot
High‐throughput sequencing of Hop stunt viroid ‐derived small RNAs from cucumber leaves and phloem
inferredcites →https://doi.org/10.1111/j.1364-3703.2012.00794.xopenalex-snapshot
Microarray analysis of Etrog citron ( Citrus medica L.) reveals changes in chloroplast, cell wall, peroxidase and symporter activities in response to viroid infection
inferredcites →https://doi.org/10.1111/j.1365-313x.2007.03203.xopenalex-snapshot
Mature monomeric forms of Hop stunt viroid resist RNA silencing in transgenic plants
inferredcites →https://doi.org/10.1111/j.1365-313x.2012.04940.xopenalex-snapshot
Small RNAs containing the pathogenic determinant of a chloroplast‐replicating viroid guide the degradation of a host mRNA as predicted by RNA silencing
inferredcites →https://doi.org/10.1111/mpp.12721openalex-snapshot
Viroid‐derived small RNA induces early flowering in tomato plants by RNA silencing
inferredcites →https://doi.org/10.1111/mpp.13022openalex-snapshot
Hop stunt viroid: A polyphagous pathogenic RNA that has shed light on viroid–host interactions
inferredcites →https://doi.org/10.1111/nph.12196openalex-snapshot
Viroids: a light in the darkness of the lnc RNA ‐directed regulatory networks in plants
inferredcites →https://doi.org/10.1111/nph.14001openalex-snapshot
A pathogenic long noncoding RNA redesigns the epigenetic landscape of the infected cells by subverting host Histone Deacetylase 6 activity
inferredcites →https://doi.org/10.1111/ppa.12358openalex-snapshot
Alterations in host DNA methylation in response to constitutive expression of Hop stunt viroid RNA in Nicotiana benthamiana plants
inferredcites →https://doi.org/10.1111/ppl.12662openalex-snapshot
Stress response regulation by epigenetic mechanisms: changing of the guards
inferredcites →https://doi.org/10.1111/tpj.13414openalex-snapshot
Natural variation for gene expression responses to abiotic stress in maize
inferredcites →https://doi.org/10.1128/jvi.00247-17openalex-snapshot
Comprehensive Transcriptome Analyses Reveal that Potato Spindle Tuber Viroid Triggers Genome-Wide Changes in Alternative Splicing, Inducible trans -Acting Activity of Phased Secondary Small Interfering RNAs, and Immune Responses
inferredcites →https://doi.org/10.1128/jvi.02339-06openalex-snapshot
A Structured Viroid RNA Serves as a Substrate for Dicer-Like Cleavage To Produce Biologically Active Small RNAs but Is Resistant to RNA-Induced Silencing Complex-Mediated Degradation
inferredcites →https://doi.org/10.1128/jvi.76.24.13094-13096.2002openalex-snapshot
Two Chloroplastic Viroids Induce the Accumulation of Small RNAs Associated with Posttranscriptional Gene Silencing
inferredcites →https://doi.org/10.1146/annurev-phyto-080508-081927openalex-snapshot
The Biology of Viroid-Host Interactions
inferredcites →https://doi.org/10.1146/annurev-phyto-080615-100308openalex-snapshot
DNA Methylation and Demethylation in Plant Immunity
inferredcites →https://doi.org/10.1146/annurev-virology-091919-092331openalex-snapshot
Advances in Viroid-Host Interactions
inferredcites →https://doi.org/10.1177/0748730414553029openalex-snapshot
Detecting Rhythms in Time Series with RAIN
inferredcites →https://doi.org/10.1186/1743-422x-10-164openalex-snapshot
A remarkable synergistic effect at the transcriptomic level in peach fruits doubly infected by prunus necrotic ringspot virus and peach latent mosaic viroid
inferredcites →https://doi.org/10.1186/1746-4811-10-23openalex-snapshot
GrainScan: a low cost, fast method for grain size and colour measurements
inferredcites →https://doi.org/10.1186/s12864-017-3665-yopenalex-snapshot
Genome-wide analysis of microRNA targeting impacted by SNPs in cucumber genome
inferredcites →https://doi.org/10.1186/s12870-019-1679-0openalex-snapshot
Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon
inferredcites →https://doi.org/10.1186/s13007-019-0470-4openalex-snapshot
Highly efficient construction of infectious viroid-derived clones
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.pone.0007539openalex-snapshot
Deep Sequencing of the Small RNAs Derived from Two Symptomatic Variants of a Chloroplastic Viroid: Implications for Their Genesis and for Pathogenesis
inferredcites →https://doi.org/10.1371/journal.pone.0007686openalex-snapshot
Deep Sequencing of Viroid-Derived Small RNAs from Grapevine Provides New Insights on the Role of RNA Silencing in Plant-Viroid Interaction
inferredcites →https://doi.org/10.1371/journal.pone.0150711openalex-snapshot
Insight on Genes Affecting Tuber Development in Potato upon Potato spindle tuber viroid (PSTVd) Infection
inferredcites →https://doi.org/10.1371/journal.ppat.1003007openalex-snapshot
Epigenetics of Host–Pathogen Interactions: The Road Ahead and the Road Behind
inferredcites →https://doi.org/10.1371/journal.ppat.1008110openalex-snapshot
Silencing of transcription factor encoding gene StTCP23 by small RNAs derived from the virulence modulating region of potato spindle tuber viroid is associated with symptom development in potato
inferredcites →https://doi.org/10.14806/ej.17.1.200openalex-snapshot
Cutadapt removes adapter sequences from high-throughput sequencing reads
inferredcites →https://doi.org/10.1515/bc.2010.148openalex-snapshot
Characterization of plant miRNAs and small RNAs derived from potato spindle tuber viroid (PSTVd) in infected tomato
inferredcites →https://doi.org/10.18637/jss.v061.i06openalex-snapshot
NbClust : An R Package for Determining the Relevant Number of Clusters in a Data Set
inferredcites →https://doi.org/10.2183/pjab.97.020openalex-snapshot
Progress in 50 years of viroid research—Molecular structure, pathogenicity, and host adaptation
inferredcites →https://doi.org/10.3389/fgene.2020.00246openalex-snapshot
Identification of MicroRNAs and Their Targets That Respond to Powdery Mildew Infection in Cucumber by Small RNA and Degradome Sequencing
inferredcites →https://doi.org/10.3389/fmicb.2017.02427openalex-snapshot
Global Transcriptomic Changes Induced by Infection of Cucumber (Cucumis sativus L.) with Mild and Severe Variants of Hop Stunt Viroid
inferredcites →https://doi.org/10.3389/fmicb.2021.646273openalex-snapshot
Next-Generation Sequencing Identification and Characterization of MicroRNAs in Dwarfed Citrus Trees Infected With Citrus Dwarfing Viroid in High-Density Plantings
inferredcites →https://doi.org/10.3389/fpls.2017.01983openalex-snapshot
Editorial: Epigenetic Modifications Associated with Abiotic and Biotic Stresses in Plants: An Implication for Understanding Plant Evolution
inferredcites →https://doi.org/10.3390/cells10051187openalex-snapshot
Viroids as a Tool to Study RNA-Directed DNA Methylation in Plants
inferredcites →https://doi.org/10.3390/ijms18020432openalex-snapshot
Alternative Splicing in Plant Genes: A Means of Regulating the Environmental Fitness of Plants
inferredcites →https://doi.org/10.3390/ijms20133154openalex-snapshot
Evaluation of Disease Severity and Global Transcriptome Response Induced by Citrus bark cracking viroid, Hop latent viroid, and Their Co-Infection in Hop (Humulus lupulus L.)
inferredcites →https://doi.org/10.3390/ijms21197383openalex-snapshot
Effects of Host-Adaptive Mutations on Hop Stunt Viroid Pathogenicity and Small RNA Biogenesis
inferredcites →https://doi.org/10.3390/ijms22073725openalex-snapshot
Degradome Analysis of Tomato and Nicotiana benthamiana Plants Infected with Potato Spindle Tuber Viroid
inferredcites →https://doi.org/10.3390/v1020241openalex-snapshot
Evolutionary Constraints to Viroid Evolution
inferredcites →https://doi.org/10.3390/v11110992openalex-snapshot
Root Transcriptomic Analysis Reveals Global Changes Induced by Systemic Infection of Solanum lycopersicum with Mild and Severe Variants of Potato Spindle Tuber Viroid
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1016/b978-0-323-99688-4.00009-2openalex-snapshot
Viroid infection and host epigenetic alterations
inferred← citeshttps://doi.org/10.1101/2022.02.02.478822openalex-snapshot
An integrative approach: using transcriptomic data and network analysis of transcriptional reprogramming in tomato response to PSTVd variants
inferred← citeshttps://doi.org/10.3390/biology12020172openalex-snapshot
Viroids: Non-Coding Circular RNAs Able to Autonomously Replicate and Infect Higher Plants
inferred← citeshttps://doi.org/10.4995/thesis/10251/192635openalex-snapshot
Heterologous expression of circular RNAs in Escherichia coli for analyzing the ligation process of chloroplastic viroids and producing double-stranded RNAs with insecticidal activity
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