The Emerging Role of Omics-Based Approaches in Plant Virology
Abstract
1. Introduction
1.1. Plant–Virus Interactions
1.2. Introduction to Omics: Basics
2. Application of Genomics in Plant Virus Disease Control
3. Application of Transcriptomics in Plant Virus Disease Control
4. Application of Proteomics in Plant Virus Disease Control
5. Application of Metabolomics in Plant Virus Disease Control
6. Challenges and Pitfalls of Individual Omics Technologies
7. Multi-Omics
8. Future Directions
8.1. Single-Cell and Spatial Omics
8.2. Artificial Intelligence and Machine Learning
8.3. Experimental Verification
8.4. Localisation Studies: Relocalisation, Retention, Sequestration—New Omics?
8.5. Biological Pitfalls
- Some additional biological aspects should be considered when planning omics related research on plant–virus interactions.
- Effect of viral tropism. Plant viral tropism refers to the bias a virus has for infecting and replicating within specific cell types or tissues [183]. Certain viruses may preferentially invade reproductive organs, meristems, and seeds, overcoming antiviral barriers to establish persistent infections [183]. In contrast, other viruses may be strictly limited to specific tissues, e.g., the phloem, the plant′s vascular tissue responsible for transporting organic nutrients [184]. It is also well known that viral replication sites vary depending on the virus type. Most RNA viruses replicate in the cytoplasm, while many DNA viruses replicate in the nucleus [185]. Some viruses, regardless of their genome type, establish specialised compartments within the cell to facilitate their replication [19,185]. These compartments may concentrate viral proteins and RNA to spatially organise the replication events.
- Mixed infections. In the field, mixed infections consist of two or more plant viruses, which often culminate in very complex multifaceted interactions between the host and viruses which may differentially modulate plant responses to environmental conditions, virus loads, virus tissue tropisms and light period [186]. Mixed infections very commonly occur and therefore omics-based research should recognise the complexities of mixed infections so that important knowledge can be obtained for effective control of plant viruses.
9. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
PAMP | Pathogen-associated molecular pattern |
PTI | PAMP-triggered immunity |
ETI | Effector-triggered immunity |
PRRs | Pattern recognition receptors |
ROS | Reactive oxygen species |
SA | Salicylic acid |
SAR | Systemic acquired resistance |
RNAi | RNA interference |
TGS | Transcriptional gene silencing |
PTGS | Post-transcriptional gene silencing |
siRNAs | Small interfering RNAs |
NGS | Next generation sequencing |
RNAseq | RNA sequencing |
MS | Mass spectrometry |
NMR | Nuclear magnetic resonance |
SNPs | Single nucleotide polymorphisms |
GWAS | Genome-wide association studies |
lncRNAs | Long non-coding RNAs |
smRNAs | Small RNAs |
DEGs | Differentially expressed genes |
vsiRNAs | Viral small interfering RNAs |
MTC | Methionine cycle |
PARylation | Poly ADP-ribosylation |
mROS | Mitochondrial reactive oxidative species |
AI | Artificial intelligence |
ML | Machine learning |
SG | Stress granules |
PB | Processing bodies |
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Virus/Genus (RNA or DNA) | Plant | Examples of Modulated Pathways | References |
---|---|---|---|
Transcriptomics | |||
TYLCV/Begomovirus (DNA) | Tomato | Gibberellin-mediated antiviral defence | [28] |
RBSDV/Reovirus (RNA) | Rice | m6A methylation | [29] |
RSV/Tennuivirus (RNA) | Rice | m6A methylation | [29] |
CGMMV/Tobamovirus (RNA) | Watermelon | m6A methylation | [30] |
PVY/Potyvirus (RNA) | Potato | Photosynthesis, carbohydrate synthesis | [31] |
TYLCV/Begomovirus (DNA) | Tomato | Defence response, ubiquitination | [32] |
PVY/Potyvirus (RNA) | Potato | Resistance, susceptibility, photosynthesis | [33] |
RSV/Tennuivirus (RNA) | Rice | Photosynthesis, flowering, stress/defence responses | [34] |
CaLCuV/Begomovirus (DNA) | Arabidopsis thaliana | Translation machinery | [35] |
TuMV/Potyvirus (RNA) | |||
CMV/Cucumovirus (RNA) | Arabidopsis halleri | Plant–pathogen interaction | [36] |
BrYV/Polerovirus (RNA) | |||
SVBV/Caulimovirus (DNA) | Strawberry | Pigment metabolism, plant–pathogen interactions | [37] |
TMV/Tobamovirus (RNA) | Tobacco | Reprogramming auxin-regulated gene expression | [38] |
CMV/Cucumovirus (RNA) | Tobacco | Photosynthesis and chlorophyll metabolism | [39] |
CCYV/Crinivirus (RNA) | Cucumber | Phenylpropanoid synthesis, phenylalanine metabolism | [40] |
MIMV/Nucleorhabdovirus (RNA) | Maize | Immune receptor signalling, RNA silencing, developmental processes | [41] |
CBSV/Ipomovirus (RNA) | Cassava | [42] | |
TYLCV/Begomovirus (DNA) | Tomato | Long non-coding and circular RNAs | [43] |
CMV/Cucumovirus (RNA) | Capsicum annuum | Response to stress, defence response | [44] |
BCTV/Geminivirus (DNA) | Sugar beet | Primary metabolic processes, volatile compounds | [45] |
SLCCNV/Begomovirus (DNA) | Zucchini | Photosynthesis, plant–pathogen interactions | [46] |
PVY/Potyvirus (RNA) | Potato | Poly(ADP)-ribosylation, methionine cycle | [47] |
Proteomics | |||
CWMV/Furovirus (RNA) | Nicotiana benthamiana | Abscisic acid-mediated antiviral defence | [48] |
ORMV/Tobamovirus (RNA) | N. benthamiana | Jasmonic and abscisic acid signalling, intracellular | [49] |
MNSV/Gammacarmovirus (RNA) | Melon | Processes controlling redox balance and cell death | [50] |
RSV/Tennuivirus (RNA) | Rice | Chlorophyll biosynthesis and cell death processes | [51] |
TMV/Tobamovirus (RNA) | Tobacco | Photosynthesis | [52] |
TYLCCNV/Begomovirus (DNA) | Tobacco | Stress defence, energy production, photosynthesis | [53] |
CSMV/Comovirus (RNA) | Vigna unguiculata | Redox homeostasis, protein synthesis, defence, stress | [54] |
PSbMV/Potyvirus (RNA) | Pisum sativum | Plant–pathogen response, lipid metabolism | [55] |
SRBSDV/Fijivirus (RNA) | Rice | Defence superoxide dismutase and catalase activities | [56] |
CPSMV/Comovirus (RNA) | V. unguiculata | Photosynthesis, stress response, and oxidative burst | [57] |
TSWV/Orthotospovirus (RNA) | Tobacco | Cell death, host defence, metabolism | [58] |
PVY/Potyvirus (RNA) | Potato | Methionine cycle | [59] |
Metabolomics | |||
TRV/Tobravirus (RNA) | A. thaliana | Lipid and fatty acid metabolism | [60] |
RBSDV/Reovirus (RNA) | Maize | Lipid and fatty acid metabolism | [61] |
CCYV/Crinivirus (RNA) | Cucumber | Lipid metabolism | [62] |
SCMV/Potyvirus (RNA) | Maize | Phenylpropanoid pathway | [63] |
GLRaV-3/Ampelovirus (RNA) | Grapevine | Phenylalanine metabolism, salicylic acid pathway | [64] |
HpMV/Carlavirus (RNA) | |||
ApMV/Ilarvirus (RNA) | Hop | Accumulation of monoterpenes hydrocarbons | [65] |
HLVd (viroid) | |||
CMV/Cucumovirus (RNA) | Passion fruit | Levels of secondary metabolites and antioxidants | [66] |
SaLV/Potyvirus (RNA) | Saffron | Composition of picrocrocin, safranal, and kaempferols | [67] |
HgYMV/Begomovirus (DNA) | Horsegram | Accumulation of sugars, alkanes, and carboxylic acids | [68] |
Transcriptomics and Proteomics | |||
MYMIV/Begomovirus (DNA) | Soybean | Cell cycle, cell-wall biogenesis, hormone assimilation | [69] |
PVY/Potyvirus (RNA) | Potato | Plant immunity regulation | [70,71] |
SCMV/Potyvirus (RNA) | Sugarcane | Photosynthesis | [72] |
SCMV/Potyvirus (RNA) | Sugarcane | Sugar metabolism | [73] |
TuMV/Potyvirus (RNA) | Cabbage | Calcium signalling pathways, heat shock responses | [74] |
GFLV/Nepovirus (RNA) | N. benthamiana | Chitinase activity and hypersensitive response | [75] |
Transcriptomics and Metabolomics | |||
PVY/Potyvirus (RNA) | Potato | Phenylpropanoids and antioxidant pathways | [76] |
GRBaV/Grablovirus (DNA) | Grapevine | Abscisic acid, ethylene, and auxin pathways | [77] |
GRBaV/Grablovirus (DNA) | Grapevine | Auxin-mediated pathways and photosynthesis | [78] |
TuMV/Potyvirus (RNA) | Brassica rapa | Volatile organic compounds | [79] |
TSWV/Orthotospovirus (RNA) | Tomato | Plant hormone signalling and flavonoid pathway | [80] |
Proteomics and Metabolomics | |||
SLCMV/Begomovirus (DNA) | Cassava | Plant–pathogen interaction, hormone signalling | [81] |
Interactomics | |||
TSWV/Orthotospovirus (RNA) | N. benthamiana | TSWV NSs-interacting proteins | [82] |
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Samarskaya, V.; Spechenkova, N.; Kalinina, N.O.; Love, A.J.; Taliansky, M. The Emerging Role of Omics-Based Approaches in Plant Virology. Viruses 2025, 17, 986. https://doi.org/10.3390/v17070986
Samarskaya V, Spechenkova N, Kalinina NO, Love AJ, Taliansky M. The Emerging Role of Omics-Based Approaches in Plant Virology. Viruses. 2025; 17(7):986. https://doi.org/10.3390/v17070986
Chicago/Turabian StyleSamarskaya, Viktoriya, Nadezhda Spechenkova, Natalia O. Kalinina, Andrew J. Love, and Michael Taliansky. 2025. "The Emerging Role of Omics-Based Approaches in Plant Virology" Viruses 17, no. 7: 986. https://doi.org/10.3390/v17070986
APA StyleSamarskaya, V., Spechenkova, N., Kalinina, N. O., Love, A. J., & Taliansky, M. (2025). The Emerging Role of Omics-Based Approaches in Plant Virology. Viruses, 17(7), 986. https://doi.org/10.3390/v17070986