Plant Virology Research Articles

Diverse roles of phytohormonal signaling in modulating plant-virus interaction.

Virus infection brings about changes in the transcriptome, proteome and metabolome status of the infected plant wherein substantial alterations in the abundance of phytohormones and associated components involved in their signaling pathways have been observed. In the recent years, extensive research in the field of plant virology has showcased the undisputable significance of phytohormone signaling during plant-virus interactions. Apart from acting as growth regulators, phytohormones elicit robust immune response, which restricts the viral multiplication within the plant as well as its propagation by vector. Interestingly, these pathways have been shown to not only act as isolated mechanisms but as complex intertwined regulatory cascades where, the cross-talk among different phytohormones and with other antiviral pathways takes place during plant-virus interplay. Viruses cleverly disrupt phytohormone homeostasis via their multifunctional effectors that seems to be smart approach adopted by viruses to circumvent phytohormone-mediated plant immune responses. In this review, we summarize the current understanding of role of phytohormone signaling pathways during plant-virus interaction in activating antiviral immune responses of plant and also, how viruses exploit these signaling pathways favoring their pathogenesis.

Enhanced antiviral defense against begomoviral infection in Nicotiana benthamiana through strategic utilization of fluorescent carbon quantum dots to activate plant immunity.

Owing to their unique physiochemical properties, low toxicity, antipathogenic effects and tunability, fluorescent carbon quantum dots (CQDs) represent a new generation of carbon-based nanomaterials. Despite the mounting research on the efficacy of CQDs against resilient plant pathogens, their potential ability to mitigate viral pathogens and the underlying molecular mechanism(s) remain understudied. In this study, we optimized the CQDs to maximize their antiviral effects against a highly pathogenic Begomovirus (cotton leaf curl Multan virus, CLCuMuV) and elucidated the mechanistic pathways associated with CQDs-mediated viral inhibition. To fine-tune the CQDs-induced antiviral effects against CLCuMuV and investigate the underlying molecular mechanisms,we used HR-TEM, XRD, FT-IR, XPS, and UV‒Vis spectrophotometry to characterize the CQDs. SPAD and FluorCam were used for physiological and photosynthetic performance analysis. Transcriptome, RT‒qPCR, integrated bioinformatics and molecular biology were employed to investigate gene expression, viral quantification and data validation. The application of fluorescent, hexagonal crystalline, UV-absorptive and water-soluble CQDs (0.01mg/ml) significantly reduced the CLCuMuV titer and mitigated viral symptoms in N. benthamiana at the early (5 dpi) and late (20 dpi) stages of infection. CQDs significantly increased the morphophysiological properties, relative chlorophyll contents and photosynthetic (Fv/Fm, QY_max, NPQ and Rfd) performance of the CLCuMuV-infected plants. While CLCuMuV infection disrupted plant immunity, the CQDs improved the antiviral defense response by regulating important immunity-related genes involved in endocytosis/necroptosis, Tam3-transposase, the ABC transporter/sphingolipid signaling pathway and serine/threonine protein kinase activities. CQDs potentially triggered TSS and TTS alternative splicing events in CLCuMuV-infected plants. Overall, these findings underscore the antiviral potential of CQDs, their impact on plant resilience, and their ability to modulate gene expression in response to viral stress. This study's molecular insights provide a foundation for further research on nanomaterial applications in plant virology and crop protection, emphasizing the promising role of CQDs in enhancing plant health and combating viral infections.

Emerging strategies in plant virus disease control: insights from the 56th meeting of the DPG working group “Viruskrankheiten der Pflanzen”

Transforming agriculture into a sustainable system includes innovative, safe, and sustainable management of virus diseases. Advances in cutting-edge biotechnological tools, such as CRISPR/Cas9 genome editing (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9), environmental RNA interference (RNAi), and the application of natural antiviral compounds, present promising new strategies for effective virus control. Highly sensitive and validated diagnostic tools allow early detection and targeted management strategies. The 56th meeting of the Deutsche Phytomedizinische Gesellschaft (DPG) working group on "Viruskrankheiten der Pflanzen" tackled the latest developments and challenges in the field of plant virology in Germany, covering topics on genomic technologies, diagnostics and quarantine regulations, virus–host interaction, virus diversity, plant immunity, and more. A special emphasis lay on the applied side of plant virology, as here, pressing agricultural challenges have to be met. In this perspectives paper, we give a summary on the conference’s findings and highlight possibilities to derive novel strategies for disease control.

Overview of transcriptome changes and phenomic profile of sanitized artichoke vis-à-vis non-sanitized plants.

Plant tissue in vitro culture is increasingly used in agriculture to improve crop production, nutritional quality, and commercial value. In plant virology, the technique is used as sanitation protocol to produce virus-free plants. Sanitized (S) artichokes show increased vigour compared to their non-sanitized (NS) counterparts, because viral infections lead to a decline of growth and development. To investigate mechanisms that control the complex traits related to morphology, growth, and yield in S artichokes compared to NS plants, RNAseq analysis and phenotyping by imaging were used. The role of peroxidases (POD) was also investigated to understand their involvement in sanitized plant development. Results showed that virus infection affected regulation of cell cycle, gene expression and signal transduction modulating cellular response to stimulus/stress. Moreover, primary metabolism and photosynthesis were also influenced, contributing to explain the main morphological differences observed between S and NS artichokes. Sanitized artichokes are also characterized by higher POD activity, probably associated with increased plant growth, rather than strengthening of cell walls. Overall, results show that the differences in development of S artichokes may be derived from the in vitro culture stressor, as well as through pathogen elimination, which, in turn, improve qualitative and quantitative artichoke production.

High-throughput sequencing for plant virology diagnostics and its potential in plant health certification

High-throughput sequencing (HTS) technologies have revolutionized plant virology through simultaneous detection of mixed viral infections. HTS advances have uncovered and improved understanding of virus biology, ecology, and evolution which is vital for viral disease management. Plant viruses continue to threaten global agricultural productivity and strict quarantine measures are essential to prevent the introduction and spread of virulent viruses around the world. The gradual decrease in HTS operational costs, including improved computational systems and automation through robotics, has facilitated the adoption of this tool for plant diagnostics, including its use in surveillance and quarantine programs. However, the speed of technology advancements and distinct HTS chemistries, laboratory procedures, data management, and bioinformatic analyses have proven challenging. In addition, the lack of viral species reference sequences, compared with the estimated number of distinct viral taxa, makes classification and identification of novel viruses difficult. There is a need for standardized HTS testing, especially within plant health programs. In this review, we consider the application of HTS in plant virology, explore the technical challenges faced and the opportunities for HTS in plant health certification. We propose standards for overcoming current barriers and for ensuring reliable and reproducible results. These efforts will impact global plant health by reducing the risk of introduction and the spread of damaging novel viruses.

Molecular characterization of cotton leaf curl Multan beta-satellite occurance on chili plants in Multan, Pakistan

The prevalence of cotton leaf curl disease (CLCuD) has significantly hampered chili (Capsicum spp.) production, presenting a formidable challenge in Pakistan. During a chili field survey in 2018, distinct symptoms, including stunted growth, yellowing, and severe leaf curling, were observed on several plants. Subsequently, a comprehensive sampling effort was undertaken, collecting a total of 39 symptomatic samples from diverse locations across Multan, Punjab. The DNA extraction from these samples was conducted at the plant virology laboratory at Bahauddin Zakariya University, Multan, marking a crucial step in the investigation of this debilitating disease and its impact on chili production in the region. Molecular analysis with PCR using Av/Ac Core, Beta 01/02, and CLCuMuBF11/R33 primers confirmed begomovirus infection in chili plants. Positive amplification demonstrated a 71.79% infection rate, with 579 bp, 1.4 kb, and 481 bp amplicons for Av/Ac Core, Beta 01/02, and CLCuMuBF11/R33, respectively. Sequencing identified cotton leaf curl Multan beta-satellite (MT668934) infecting the chili plant. Effectively managing these begomoviruses is crucial to curbing their multiplication and protecting vital crops like chili. Addressing the distributions of beta-satellites in agricultural fields, particularly chili, is imperative to prevent further viral spread.

Genome organization of satellite DNA beta molecule associated with Mungbean yellow mosaic India virus Gujarat, India

Recent advancements in genomics have unveiled fascinating insights into the intricate world of plant pathogens. The discovery of an intriguing association between the DNA beta and MYMIV-[IN:Ana: CpMBKA25:04], a strain containing 1367 base pairs of nucleotides, has sparked a wave of scientific curiosity. Through sequence identity matrix analysis, it was revealed that this strain shares a striking 96% similarity with the Potato apical leaf curl virus, closely followed by the Tomato leaf curl beta satellite virus [Accession No. AY230138] at 95.3%. In contrast, its relationship with the beta satellite Bhendi yellow vein beta satellite [Accession No. AJ308425] stood at a comparative 45.7% when compared against seventeen other DNA beta isolates infecting various crops. Noteworthy features of the beta satellite sequences include a distinctive putative stem-loop structure TAATATT/AC in the common region and a recurring GCTACGC repeat sequence. An A-rich region spanning from nucleotides 910 to 1120 further adds to the genetic complexity of this novel strain. Intriguingly, an analysis of the amino acid sequence unveiled additional residues V, C, and N at the carboxyl end of the βC1 protein, setting it apart from its counterparts. The identity matrix analysis established a 95.9% similarity between βC1 and the beta satellite associated with Tomato leaf curl Karnataka virus and Potato apical leaf curl virus, phylogenetic analysis placed the beta satellite linked with MYMIV-[IN:Ana: CpMBKA25:04] in a distinct category within the Papaya leaf curl virus family, shedding light on its unique evolutionary lineage and biological significance in the realm of plant virology.

Viroids, Satellite RNAs and Prions: Folding of Nucleic Acids and Misfolding of Proteins.

Theodor ("Ted") Otto Diener (* 28 February 1921 in Zürich, Switzerland; † 28 March 2023 in Beltsville, MD, USA) pioneered research on viroids while working at the Plant Virology Laboratory, Agricultural Research Service, USDA, in Beltsville. He coined the name viroid and defined viroids' important features like the infectivity of naked single-stranded RNA without protein-coding capacity. During scientific meetings in the 1970s and 1980s, viroids were often discussed at conferences together with other "subviral pathogens". This term includes what are now called satellite RNAs and prions. Satellite RNAs depend on a helper virus and have linear or, in the case of virusoids, circular RNA genomes. Prions, proteinaceous infectious particles, are the agents of scrapie, kuru and some other diseases. Many satellite RNAs, like viroids, are non-coding and exert their function by thermodynamically or kinetically controlled folding, while prions are solely host-encoded proteins that cause disease by misfolding, aggregation and transmission of their conformations into infectious prion isoforms. In this memorial, we will recall the work of Ted Diener on subviral pathogens.

Effective plant virus enrichment using carbon nanotubes and microfluidics

Plant virus detection and identification in crops is a pillar for disease management, import of crop material, production of clean stock plants and basic plant virology studies. In this report, we present a platform for the enrichment and isolation of known or unknown viruses. This platform is based on carbon nanotube arrays inside a microfluidic device that can be a solution for the identification of low titer viruses from plants. Using our microfluidic devices, we achieved enrichment of two economically important viruses, the orthotospovirus, tomato spotted wilt orthotospovirus (TSWV) and the potyvirus, zucchini yellow mosaic virus (ZYMV). The carbon nanotube arrays integrated in these microfluidic devices are capable of trapping viruses discriminated by their size; the virus rich arrays can be then analyzed by common downstream techniques including immunoassays, PCR, HTS and electron microscopy. This procedure offers a simple to operate and portable sample preparation device capable of trapping viruses from raw plant extracts while reducing the host contamination.

First Report of Melon Chlorotic Spot Virus in Cultivated Sorrel (Rumex acetosa) in Belgium

In 2020, symptoms of putative viral origin were observed on 7% of tomatoes in an organic vegetable farm in Belgium (deformed uneven ripened fruits, vein clearing, mosaic and purple leaves, stunted plants). The leaves of twenty symptomatic plants were collected, pooled and screened for viruses using high throughput sequencing technologies (HTS) on Illumina NextSeq500 following a virion-associated nucleic acid (VANA) protocol (Temple et al., 2021, Be_SL1). In total, 3,665,498 reads (PE150) were generated. Bioinformatic analyses (denovo assembly, tblastx search on NCBI and mapping) using Geneious Prime® 2020.1.2 revealed the presence of three viruses known to infect tomatoes: Physostegia chlorotic mottle virus (PhCMoV), 547,142 reads map on NC_055466, potato virus Y (PVY), 4056 reads map on MW595184, and melon chlorotic spot virus (MeCSV), 55 reads mapped to six out of the eight different MeCSV segments (NC_040448-55). Tomato plants have already been artificially inoculated by MeCSV (Lecoq et al., 2019) but this detection (confirmed by independent RT-PCR on the pooled sample) is the first one in natural condition on farm. The high prevalence of symptoms triggered the research of alternative perennial hosts that can serve as a reservoir during inter-cropping season. One plant of Rumex acetosa showing vein clearing (CT-122) was collected in the same greenhouse the year after. Total RNA was extracted, followed by ribodepletion, and Illumina HTS using the protocol described in Temple et al., (2021) for Be_GP1. In total, 4,549,721 PE150 reads were obtained and bioinformatic analyses confirmed the presence of MeCSV (8,816 reads mapped on eight RNA segments NC_040448-55 with an average 96,52% coverage of the reference sequences, supplementary table 1) and suggested the presence of an unclassified partitivirus. Consensus sequences were extracted for each segment of MeCSV (OQ818038-45) and showed between 83% and 87% of nucleotide identity with the reference sequences NC_040448-55. RNA1 segment was used to design MeCSV-specific RT-PCR primers for detection (MeCSV-125F 5’-TTTAAGGCCAGATCCAGAGGTTC-3’/ MeCSV-498R 5’-TGGATGTGACAACCTGGTAGTAC-3’). Thereafter, in July 2022, 42 R. acetosa plants were collected in the same greenhouse. Among them, seven plants showed vein clearing, two showed yellowing with necrosis, two exhibited yellowing and vein clearing (Supplementary figure 1), and one showed mosaic. The 42 plants were subjected to RNA extraction and RT-PCR for MeCSV (Supplementary figure 2) and PhCMoV detection. MeCSV was detected in 13 plants (two asymptomatic plants and all the symptomatic plants except the one exhibiting mosaic where PhCMoV was detected). PhCMoV was also detected in three plants with vein clearing, one with yellowing and one of the two asymptomatic plants infected by MeCSV. Our results report the first detection of MeCSV in R. acetosa and the first detection of MeCSV in Belgium. In addition, according to the hierarchical approach for assessing causal relationships in plant virology (Fox et al., 2020), a preliminary association was observed between symptoms and MeCSV detection [6% prevalence on asymptomatic plants and 92% prevalence on diseased plants (from which seven symptomatic samples were not co-infected by PhCMoV)]. Symptom causality should be further investigated but this results are important for disease management because they suggested that cultivated perennial R. acetosa may serve as a reservoir for two emergent plant viruses (PhCMoV and MeCSV) (Lecoq et al., 2019, Temple et al., 2021).

Plant virology in the 21st century in China: Recent advances and future directions.

Plant viruses are a group of intracellular pathogens that persistently threaten global food security. Significant advances in plant virology have been achieved by Chinese scientists over the last 20 years, including basic research and technologies for preventing and controlling plant viral diseases. Here, we review these milestones and advances, including the identification of new crop-infecting viruses, dissection of pathogenic mechanisms of multiple viruses, examination of multilayered interactions among viruses, their host plants, and virus-transmitting arthropod vectors, and in-depth interrogation of plant-encoded resistance and susceptibility determinants. Notably, various plant virus-based vectors have also been successfully developed for gene function studies and target gene expression in plants. We also recommend future plant virology studies in China.

Effects of meteorological variables on potato leaf roll virus and potato virus y infections on different potato varieties under natural and mulched conditions

After rice and wheat, potatoes are the third most important staple crop in Pakistan, but due to various virus diseases attacks, yield remains very low. Among viral pathogens, potato leaf roll virus (PLRV) and potato virus Y (PVY) are the most destructive viruses present in all potato-growing areas. A field experiment was conducted at the Research Farm of Plant Virology Section, Ayub Agricultural Research Institute, Faisalabad, to evaluate the effects of meteorological variables on the development of virus infections (PLRV and PVY) on different potato varieties under natural and mulched conditions. Results indicated that the development of infections of PVY and PLRV was delayed in different potato varieties under mulched conditions. The potato variety Simply Red had the highest PLRV and PVY disease incidences under unmulched and mulched circumstances, while Sahiwal Red and Ruby had the lowest infection rates. The least PVY disease incidence was noted under mulched conditions on FD-81-1. Mulched conditions were better in the reduction of diseases than unmulched conditions. The average high temperature (HT) ranged from 21.9 ◦C to 27 ◦C was most favorable for the development of PLRV and PVY on all six tested potato varieties in both conditions. The average low temperature (LT) ranged from 8 ◦C to 15 ◦C was favorable for the progression of PLRV and PVY diseases in both conditions. The relative humidity (RH) range of 50-60% was conducive for the development of PLRV and PVY diseases. It is concluded that mulching application is an essential tool to enhance the yield of potato crops by reducing their specific diseases.

Plant virology: an RNA treasure trove.

Key principles pertaining to RNA biology not infrequently have their origins in plant virology. Examples have arisen from studies on viral RNA-intrinsic properties and the infection process from gene expression, replication, movement, and defense evasion to biotechnological applications. Since RNA is at the core of the central dogma in molecular biology, how plant virology assisted in the reinforcement or adaptations of this concept, while at other instances shook up elements of the doctrine, is discussed. Moreover, despite the negative effects of viral diseases in agriculture worldwide, plant viruses can be considered a scientific treasure trove. Today they remain tools of discovery for biotechnology, studying evolution, cell biology, and host-microbe interactions.

Effect of Cucumber mosaic virus (CMV) on the Content of Some Cucumber Genotypes of Nitrogen, Protein, Phenols, and Flavonoids

This study was carried out to secreen the response of ten cucumber genotypes (AH-38، HA-37،HA-2160 ،HA2114 ، HA-2122 ،HA-12 ،HA-16 ،HA-41 ،CU-O719 , and CU-2102) against Cucumber mosaic virus (CMV) and to know the effect of infection on some of the plant contents of nitrogen, protein, phenols, and flavonoids. This study was carried out in the laboratory of Plant Virology and plastic houses of the College of Agriculture, University of Kerbala. The results showed that all cucumber genotypes tested in this study are susceptibe to CMV with severity infection ranged from 15-100%. It was also proved that the viral infection had a clear effect on reducing the content of the plant of nitrogen and protein in the genotypes and the most affected genotype was HA-2122 that was a significantly different from the content of nitrogen and protein in the non-infected plants. CMV was also found to have an effect in increasing the plant content of phenols and flavonoids in all genotypes infected with the virus (CMV) and the most affected genotypes were HA-37 and HA-41 (2.51 and 2.42 mg g-1 dry weight, respectively) and significantly different from the content of the same non-infected genotypes that gave rates of 1.66, 1.78 and 1.71 mg g-1 dry weight, respectively.

Effect of Cucumber mosaic virus on the Content of Some Melon Genotypes of Some Mineral Elements and Plant Hormones

This study was conducted to determine the effect of cucumber mosaic virus (CMV) infection on the levels of some mineral elements and plant hormones in some melon genotypes. All experiments mentioned in this research were conducted in the Laboratory of plant virology and Greenhouses belonging to the Plant Protection Department/ College of the Agriculture/ University of Kerbala. PCR amplification using the complementary DNA (cDNA), synthesized from RNA isolated from an infected plant, produced a 650bp PCR product. A BLAST search using the nucleotide sequence of the PCR product demonstrated that this CMV isolate was previously registered at the National Centre for Biotechnology Information (NCBI) with a similarity of 100% with some CMV isolates identified in Hungary (AJ517802), Australia (U22821), and Slovenia (OL142046). It was also found that all melon genotypes evaluated in this study were susceptible to CMV, and the genotypes HA-144 and HA-609 were the most susceptible to CMV among the other tested genotypes. Results also showed that the CMV infection significantly reduced the levels of some minerals (calcium, magnesium, and manganese), and the genotypes HA-144, GM-3034, and GA-1534 were the most affected by the virus.; whereas the mineral elements sodium and potassium were significantly increased in their levels in infected plants, especially in the genotype HA-609. The CMV infection also clearly reduced the level of the hormone gibberellin in genotypes and the GA-1534 genotype was the most impacted and significantly different from their levels in the uninfected plants. However, the CMVinfected genotypes showed a significant increase in the level of the hormones cytokinin.

Charting the course of plant virology: innovations in diagnostics and beyond—reports from the DPG meeting

Plant viruses pose a significant threat to global agriculture, resulting in economic losses and threatening food security. High-throughput sequencing and molecular techniques are advancing our understanding of these viruses, allowing for their detection, characterization, and control. The 55th meeting of the DPG Working Group “Viruskrankheiten der Pflanzen” showcased these advancements, encouraging international collaboration and idea exchange to tackle plant virus challenges. The perspectives paper we present summarizes this conference’s findings, highlighting the potential of these technologies in revolutionizing plant virus research.

Plant Virus Sensor for the Rapid Detection of Bean Pod Mottle Virus Using Virus-Specific Nanocavities.

This study presents a miniaturized sensor for rapid, selective, and sensitive detection of bean pod mottle virus (BPMV) in soybean plants. The sensor employs molecularly imprinted polymer technology to generate BPMV-specific nanocavities in porous polypyrrole. Leveraging the porous structure, high surface reactivity, and electron transfer properties of polypyrrole, the sensor achieves a sensitivity of 143 μA ng-1 mL cm-2, a concentration range of 0.01-100,000 ng/mL, a detection time of less than 2 min, and a detection limit of 41 pg/mL. These capabilities outperform those of conventional methods, such as enzyme-linked immunosorbent assays and reverse transcription polymerase chain reactions. The sensor possesses the ability to distinguish BPMV-infected soybean plants from noninfected ones while rapidly quantifying virus levels. Moreover, it can reveal the spatial distribution of virus concentration across distinct leaves, a capability not previously attained by cost-effective sensors for such detailed viral data within a plant. The BPMV-specific nanocavities can also be easily restored and reactivated for multiple uses through a simple wash with acetic acid. While MIP-based sensors for plant virus detection have been relatively understudied, our findings demonstrate their potential as portable, on-site diagnostic tools that avoid complex and time-consuming sample preparation procedures. This advancement addresses a critical need in plant virology, enhancing the detection and management of plant viral diseases.

Diversity and Pathobiology of an Ilarvirus Unexpectedly Detected in Diverse Plants and Global Sequencing Data.

High-throughput sequencing (HTS) and sequence mining tools revolutionized virus detection and discovery in recent years, and implementing them with classical plant virology techniques results in a powerful approach to characterize viruses. An example of a virus discovered through HTS is Solanum nigrum ilarvirus 1 (SnIV1) (Bromoviridae), which was recently reported in various solanaceous plants from France, Slovenia, Greece, and South Africa. It was likewise detected in grapevines (Vitaceae) and several Fabaceae and Rosaceae plant species. Such a diverse set of source organisms is atypical for ilarviruses, thus warranting further investigation. In this study, modern and classical virological tools were combined to accelerate the characterization of SnIV1. Through HTS-based virome surveys, mining of sequence read archive datasets, and a literature search, SnIV1 was further identified from diverse plant and non-plant sources globally. SnIV1 isolates showed relatively low variability compared with other phylogenetically related ilarviruses. Phylogenetic analyses showed a distinct basal clade of isolates from Europe, whereas the rest formed clades of mixed geographic origin. Furthermore, systemic infection of SnIV1 in Solanum villosum and its mechanical and graft transmissibility to solanaceous species were demonstrated. Near-identical SnIV1 genomes from the inoculum (S. villosum) and inoculated Nicotiana benthamiana were sequenced, thus partially fulfilling Koch's postulates. SnIV1 was shown to be seed-transmitted and potentially pollen-borne, has spherical virions, and possibly induces histopathological changes in infected N. benthamiana leaf tissues. Overall, this study provides information to better understand the diversity, global presence, and pathobiology of SnIV1; however, its possible emergence as a destructive pathogen remains uncertain.

Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies.

Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area. For this purpose, HTS has greatly facilitated the sequencing of new genomes of detected viruses and their comparison. However, bioinformatics analyses allowing reconstruction of genome sequences and detection of single nucleotide polymorphisms (SNPs) can potentially create bias and has not been widely addressed so far. Therefore, more knowledge is required on the limitations of predicting SNPs based on HTS-generated sequence samples. To address this issue, we compared the ability of 14 plant virology laboratories, each employing a different bioinformatics pipeline, to detect 21 variants of pepino mosaic virus (PepMV) in three samples through large-scale performance testing (PT) using three artificially designed datasets. To evaluate the impact of bioinformatics analyses, they were divided into three key steps: reads pre-processing, virus-isolate identification, and variant calling. Each step was evaluated independently through an original, PT design including discussion and validation between participants at each step. Overall, this work underlines key parameters influencing SNPs detection and proposes recommendations for reliable variant calling for plant viruses. The identification of the closest reference, mapping parameters and manual validation of the detection were recognized as the most impactful analysis steps for the success of the SNPs detections. Strategies to improve the prediction of SNPs are also discussed.

Tobamoviruses: old and new threats to tomato cultivation

AbstractMosaic diseases caused by tobamoviruses have posed significant threats to tomato production. In this review, we overview studies of tomato mosaic diseases published over the past century, which have led to several important discoveries in plant virology, such as the application of attenuated strains. A resistance breeding program established in the 1970s successfully controlled tomato mosaic virus for over 40 years; however, newly emerging tobamoviruses are posing serious challenges in current tomato production. We introduce recent biotechnological attempts to engineer tobamovirus-resistant tomato plants, which offer promising technologies for eradicating the current outbreak.