4.7 Article

Integrative time-scale and multi-omics analysis of host responses to viroid infection

Related references

Note: Only part of the references are listed.
Article Virology

Role of RNA silencing in plant-viroid interactions and in viroid pathogenesis

Francesco Di Serio et al.

Summary: Viroids, small non-protein coding circular RNAs, can infect host plants independently of helper viruses. This review focuses on the role of post-transcriptional RNA silencing in the interaction between viroids and plants, specifically in plant antiviroid defense and viroid pathogenesis. The review also pays tribute to Dr. Ricardo Flores, who made significant contributions to elucidate molecular mechanisms involved in plant-viroid interactions.

VIRUS RESEARCH (2023)

Article Biochemistry & Molecular Biology

Interpretation of network-based integration from multi-omics longitudinal data

Antoine Bodein et al.

Summary: Multi-omics integration is crucial for understanding complex biological processes, but the challenge lies in interpretation. A generic approach is proposed to build hybrid multi-omics networks for predicting regulatory mechanisms and functional modules.

NUCLEIC ACIDS RESEARCH (2022)

Article Biochemistry & Molecular Biology

Insights into the Transcriptional Reprogramming in Tomato Response to PSTVd Variants Using Network Approaches

Katia Avina-Padilla et al.

Summary: This study used a network approach to analyze the transcription factors and differentially expressed target genes in tomato infected with mild and severe variants of PSTVd. The results identified specific transcription factors that regulate genes involved in critical signaling pathways. Functional enrichment analysis showed that these transcription factors are associated with metabolism, plant defense, signaling, and hormone-related processes. The study also found other transcription factors that are associated with symptom development.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

Article Cell Biology

Cytosine Methylation in Genomic DNA and Characterization of DNA Methylases and Demethylases and Their Expression Profiles in Viroid-Infected Hop Plants (Humulus lupulus Var. 'Celeia')

Andrej Secnik et al.

Summary: Abiotic and biotic stresses can induce changes in DNA methylation in host plants, especially when infected with viroids. The study focused on determining the levels of 5-methylcytosine in hop plants infected with various viroids, finding different methylation levels among the infected plants. Additionally, new genes related to DNA methylation were identified in the hop plant's genome.

CELLS (2022)

Article Plant Sciences

Hop stunt viroid: A polyphagous pathogenic RNA that has shed light on viroid-host interactions

Joan Marquez-Molins et al.

Summary: Taxonomy Hop stunt viroid belongs to the family Pospiviroidae, replicates through an asymmetric rolling-circle model, consists of a single-stranded circular RNA, distributed worldwide, infects a wide range of hosts causing five different diseases.

MOLECULAR PLANT PATHOLOGY (2021)

Article Plant Sciences

Multi-omics network-based functional annotation of unknown Arabidopsis genes

Thomas Depuydt et al.

Summary: This study introduces a novel automated function prediction method that leverages complementary information from gene co-expression networks to successfully predict biological process annotations for Arabidopsis thaliana genes. Using experimental data validation, high-confidence functional annotations were obtained for unknown genes and genes with computational annotations, shedding light on a variety of developmental processes and molecular responses in Arabidopsis.

PLANT JOURNAL (2021)

Article Horticulture

MicroRNA expression dynamics reshape the cultivar-specific response of pepper (Capsicum annuum L.) to potato spindle tuber viroid (PSTVd) infection

E. Apostolova et al.

Summary: PSTVd is a small pathogenic RNA infecting plants, with its pathogenicity influenced by the viroid strain's characteristics, host genomic traits, and interactions in a dynamic environment. Research on pepper cultivars shows specific miRNA expression differences upon PSTVd infection, advancing our understanding of the role of miRNAs in the PSTVd-pepper pathosystem.

SCIENTIA HORTICULTURAE (2021)

Article Plant Sciences

sRNAanno-a database repository of uniformly annotated small RNAs in plants

Chengjie Chen et al.

Summary: This study comprehensively annotated small RNAs in 143 plant species with fully sequenced genomes and publicly available sRNA data, providing a valuable resource for genomic and genetic research on plant small RNAs. The sRNAanno database offers more complete and reliable miRNA annotations compared to other public plant sRNA databases, as well as genomic information on PHAS loci and hc-siRNA loci from these plant species.

HORTICULTURE RESEARCH (2021)

Review Plant Sciences

Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value

Tinashe Zenda et al.

Summary: Innovative crop improvement methods, such as utilizing genetic variation from crop wild relatives and underutilized species, are essential for breeding climate-resilient crops. Omics technologies play a crucial role in revealing key genes and metabolic pathways, aiding marker-assisted breeding in major crop species.

FRONTIERS IN PLANT SCIENCE (2021)

Article Biochemistry & Molecular Biology

Degradome Analysis of Tomato and Nicotiana benthamiana Plants Infected with Potato Spindle Tuber Viroid

Beatriz Navarro et al.

Summary: Through high-throughput sequencing and analysis, it was found that only a few mRNAs were targeted by vd-sRNAs and led to downregulation of protein expression in tomato and Nicotiana benthamiana plants infected with Potato Spindle Tuber Viroid (PSTVd). However, despite similar symptoms in both plants, different response pathways may be involved.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Microbiology

Next-Generation Sequencing Identification and Characterization of MicroRNAs in Dwarfed Citrus Trees Infected With Citrus Dwarfing Viroid in High-Density Plantings

Tyler Dang et al.

Summary: CDVd infection leads to dwarfing of citrus trees, with distinct miRNAs identified in different tissues and some significantly downregulated in infected trees. These CDVd-responsive miRNAs may play crucial roles in regulating important citrus growth and developmental processes.

FRONTIERS IN MICROBIOLOGY (2021)

Review Cell Biology

Viroids as a Tool to Study RNA-Directed DNA Methylation in Plants

Michael Wassenegger et al.

Summary: The review discusses the role of Pospiviroidae in the discovery of RdDM, the gradual elucidation of mechanistic details over the years, and proposes a revised RdDM model based on evidence from viroid and non-viroid systems.

CELLS (2021)

Review Plant Sciences

Applications of Multi-Omics Technologies for Crop Improvement

Yaodong Yang et al.

Summary: Omics approaches, including genomics, transcriptomics, proteomics, metabolomics, ionomics, and phenomics, have been instrumental in understanding key biological processes in crops such as growth, yield, and stress responses. These techniques have been applied to important crops like wheat, soybean, tomato, barley, maize, millet, cotton, and rice.

FRONTIERS IN PLANT SCIENCE (2021)

Article Microbiology

Advances in Viroid-Host Interactions

Beatriz Navarro et al.

Summary: Viroids are small, single-stranded, circular RNAs that infect plants, representing the lowest complexity level for infectious agents. Despite their small size, they contain RNA structural elements necessary for interacting with host factors during the infectious cycle and serve as models for studying RNA structure-function relationships. Replication occurs through rolling-circle mechanisms in the nuclei or chloroplasts, and viroids can move locally and systemically, eliciting symptoms in infected plants through pathogenic pathways linked to RNA silencing and plant defense responses.

ANNUAL REVIEW OF VIROLOGY, VOL 8 (2021)

Review Cell Biology

Current overview on viroid-host interactions

Charith Raj Adkar-Purushothama et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2020)

Article Biochemistry & Molecular Biology

Dynamic architecture and regulatory implications of the miRNA network underlying the response to stress in melon

Alejandro Sanz-Carbonell et al.

RNA BIOLOGY (2020)

Review Plant Sciences

Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology

Ili Nadhirah Jamil et al.

FRONTIERS IN PLANT SCIENCE (2020)

Review Genetics & Heredity

Advances in Transcriptomics in the Response to Stress in Plants

Xiaojuan Wang et al.

GLOBAL MEDICAL GENETICS (2020)

Article Plant Sciences

Inferring the regulatory network of the miRNA-mediated response to biotic and abiotic stress in melon

Alejandro Sanz-Carbonell et al.

BMC PLANT BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Does co-transcriptional regulation of alternative splicing mediate plant stress responses?

Ibtissam Jabre et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Plant Sciences

Epigenetics in the plant-virus interaction

Chenguang Wang et al.

PLANT CELL REPORTS (2019)

Article Biochemical Research Methods

Highly efficient construction of infectious viroid-derived clones

Joan Marquez-Molins et al.

PLANT METHODS (2019)

Article Biochemistry & Molecular Biology

Small RNA sequencing identifies cucumber miRNA roles in waterlogging-triggered adventitious root primordia formation

Xuewen Xu et al.

MOLECULAR BIOLOGY REPORTS (2019)

Article Biochemistry & Molecular Biology

RNAcentral: a hub of information for non-coding RNA sequences

Blake A. Sweeney et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

Cucurbit Genomics Database (CuGenDB): a central portal for comparative and functional genomics of cucurbit crops

Yi Zheng et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Plant Sciences

Stress response regulation by epigenetic mechanisms: changing of the guards

Maria Luz Annacondia et al.

PHYSIOLOGIA PLANTARUM (2018)

Review Biochemistry & Molecular Biology

Alternative Splicing in Plant Genes: A Means of Regulating the Environmental Fitness of Plants

Xudong Shang et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2017)

Article Biochemistry & Molecular Biology

Hop stunt viroid: Effect on Host (Humulus lupulus) Transcriptome and Its Interactions With Hop Powdery Mildew (Podospheara macularis)

Madhu Kappagantu et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2017)

Article Plant Sciences

Natural variation for gene expression responses to abiotic stress in maize

Amanda J. Waters et al.

PLANT JOURNAL (2017)

Article Biotechnology & Applied Microbiology

Genome-wide analysis of microRNA targeting impacted by SNPs in cucumber genome

Jian Ling et al.

BMC GENOMICS (2017)

Review Plant Sciences

DNA Methylation and Demethylation in Plant Immunity

A. Deleris et al.

ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 54 (2016)

Article Plant Sciences

Changes in the DNA methylation pattern of the host male gametophyte of viroid-infected cucumber plants

Mayte Castellano et al.

JOURNAL OF EXPERIMENTAL BOTANY (2016)

Review Biochemistry & Molecular Biology

Epigenetic Mechanisms: An Emerging Player in Plant-Microbe Interactions

Qian-Hao Zhu et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2016)

Article Virology

Viroids, infectious long non-coding RNAs with autonomous replication

Selma Gago-Zachert

VIRUS RESEARCH (2016)

Article Biochemical Research Methods

HTSeq-a Python framework to work with high-throughput sequencing data

Simon Anders et al.

BIOINFORMATICS (2015)

Article Statistics & Probability

NbClust: AnRPackage for Determining the Relevant Number of Clusters in a Data Set

Malika Charrad et al.

Journal of Statistical Software (2015)

Article Biochemical Research Methods

Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger et al.

BIOINFORMATICS (2014)

Article Biochemistry & Molecular Biology

A pathogenic non-coding RNA induces changes in dynamic DNA methylation of ribosomal RNA genes in host plants

German Martinez et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Cell Biology

Epigenetic Regulation in Plant Responses to the Environment

David C. Baulcombe et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2014)

Article Biotechnology & Applied Microbiology

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

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemistry & Molecular Biology

Detecting differential usage of exons from RNA-seq data

Simon Anders et al.

GENOME RESEARCH (2012)

Review Microbiology

Epigenetics of Host-Pathogen Interactions: The Road Ahead and the Road Behind

Elena Gomez-Diaz et al.

PLOS PATHOGENS (2012)

Article Biochemical Research Methods

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

Felix Krueger et al.

BIOINFORMATICS (2011)

Article Biotechnology & Applied Microbiology

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

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Article Statistics & Probability

ggplot2

Hadley Wickham

WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL STATISTICS (2011)

Article Biochemical Research Methods

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

Mark D. Robinson et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Characterization of plant miRNAs and small RNAs derived from potato spindle tuber viroid (PSTVd) in infected tomato

Natalie Diermann et al.

BIOLOGICAL CHEMISTRY (2010)

Article Plant Sciences

High-throughput sequencing of Hop stunt viroid-derived small RNAs from cucumber leaves and phloem

German Martinez et al.

MOLECULAR PLANT PATHOLOGY (2010)

Article Plant Sciences

The Biology of Viroid-Host Interactions

Biao Ding

Annual Review of Phytopathology (2009)

Review Virology

Evolutionary Constraints to Viroid Evolution

Santiago F. Elena et al.

VIRUSES-BASEL (2009)

Review Biochemistry & Molecular Biology

The post-transcriptional steps of eukaryotic ribosome biogenesis

A. K. Henras et al.

CELLULAR AND MOLECULAR LIFE SCIENCES (2008)

Article Biochemical Research Methods

GMAP: a genomic mapping and alignment program for mRNA and EST sequences

TD Wu et al.

BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

Potato spindle tuber viroid as inducer of RNA silencing in infected tomato

A Itaya et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2001)

Article Biochemistry & Molecular Biology

Identification of an in vitro ribonucleoprotein complex between a viroid RNA and a phloem protein from cucumber plants

G Gómez et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2001)