Plant-virus Interactions Research Articles

Metabolic profiles of Sri Lankan cassava mosaic virus-infected and healthy cassava (Manihot esculenta Crantz) cultivars with tolerance and susceptibility phenotypes

BackgroundCassava mosaic disease (CMD) of cassava (Manihot esculenta Crantz) has expanded across many continents. Sri Lankan cassava mosaic virus (SLCMV; family Geminiviridae), which is the predominant cause of CMD in Thailand, has caused agricultural and economic damage in many Southeast Asia countries such as Vietnam, Loas, and Cambodia. The recent SLCMV epidemic in Thailand was commonly found in cassava plantations. Current understanding of plant–virus interactions for SLCMV and cassava is limited. Accordingly, this study explored the metabolic profiles of SLCMV-infected and healthy groups of tolerant (TME3 and KU50) and susceptible (R11) cultivars of cassava. Findings from the study may help to improve cassava breeding, particularly when combined with future transcriptomic and proteomic research.ResultsSLCMV-infected and healthy leaves were subjected to metabolite extraction followed by ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS/MS). The resulting data were analyzed using Compound Discoverer software, the mzCloud, mzVault, and ChemSpider databases, and published literature. Of the 85 differential compounds (SLCMV-infected vs healthy groups), 54 were differential compounds in all three cultivars. These compounds were analyzed using principal component analysis (PCA), hierarchical clustering dendrogram analysis, heatmap analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation. Chlorogenic acid, DL-carnitine, neochlorogenic acid, (E)-aconitic acid, and ascorbyl glucoside were differentially expressed only in TME3 and KU50, with chlorogenic acid, (E)-aconitic acid, and neochlorogenic acid being downregulated in both SLCMV-infected TME3 and KU50, DL-carnitine being upregulated in both SLCMV-infected TME3 and KU50, and ascorbyl glucoside being downregulated in SLCMV-infected TME3 but upregulated in SLCMV-infected KU50. Furthermore, 7-hydroxycoumarine was differentially expressed only in TME3 and R11, while quercitrin, guanine, N-acetylornithine, uridine, vorinostat, sucrose, and lotaustralin were differentially expressed only in KU50 and R11.ConclusionsMetabolic profiling of three cassava landrace cultivars (TME3, KU50, and R11) was performed after SLCMV infection and the profiles were compared with those of healthy samples. Certain differential compounds (SLCMV-infected vs healthy groups) in different cultivars of cassava may be involved in plant–virus interactions and could underlie the tolerance and susceptible responses in this important crop.

Small Talk: On the Possible Role of Trans-Kingdom Small RNAs during Plant-Virus-Vector Tritrophic Communication.

Small RNAs (sRNAs) are the hallmark and main effectors of RNA silencing and therefore are involved in major biological processes in plants, such as regulation of gene expression, antiviral defense, and plant genome integrity. The mechanisms of sRNA amplification as well as their mobile nature and rapid generation suggest sRNAs as potential key modulators of intercellular and interspecies communication in plant-pathogen-pest interactions. Plant endogenous sRNAs can act in cis to regulate plant innate immunity against pathogens, or in trans to silence pathogens' messenger RNAs (mRNAs) and impair virulence. Likewise, pathogen-derived sRNAs can act in cis to regulate expression of their own genes and increase virulence towards a plant host, or in trans to silence plant mRNAs and interfere with host defense. In plant viral diseases, virus infection alters the composition and abundance of sRNAs in plant cells, not only by triggering and interfering with the plant RNA silencing antiviral response, which accumulates virus-derived small interfering RNAs (vsiRNAs), but also by modulating plant endogenous sRNAs. Here, we review the current knowledge on the nature and activity of virus-responsive sRNAs during virus-plant interactions and discuss their role in trans-kingdom modulation of virus vectors for the benefit of virus dissemination.

Long-Term Anthropogenic Management and Associated Loss of Plant Diversity Deeply Impact Virome Richness and Composition of Poaceae Communities.

Modern agriculture has influenced plant virus emergence through ecosystem simplification, introduction of new host species, and reduction in crop genetic diversity. Therefore, it is crucial to better understand virus distributions across cultivated and uncultivated communities in agro-ecological interfaces, as well as virus exchange among them. Here, we advance fundamental understanding in this area by characterizing the virome of three co-occurring replicated Poaceae community types that represent a gradient of grass species richness and management intensity, from highly managed crop monocultures to little-managed, species-rich grasslands. We performed a large-scale study on 950 wild and cultivated Poaceae over 2 years, combining untargeted virome analysis down to the virus species level with targeted detection of three plant viruses. Deep sequencing revealed (i) a diversified and largely unknown Poaceae virome (at least 51 virus species or taxa), with an abundance of so-called persistent viruses; (ii) an increase of virome richness with grass species richness within the community; (iii) stability of virome richness over time but a large viral intraspecific variability; and (iv) contrasting patterns of virus prevalence, coinfections, and spatial distribution among plant communities and species. Our findings highlight the complex structure of plant virus communities in nature and suggest the influence of anthropogenic management on viral distribution and prevalence. IMPORTANCE Because viruses have been mostly studied in cultivated plants, little is known about virus diversity and ecology in less-managed vegetation or about the influence of human management and agriculture on virome composition. Poaceae (grass family)-dominated communities provide invaluable opportunities to examine these ecological issues, as they are distributed worldwide across agro-ecological gradients, are essential for food security and conservation, and can be infected by numerous viruses. Here, we used multiple levels of analysis that considered plant communities, individual plants, virus species, and haplotypes to broaden understanding of the Poaceae virome and to evaluate host-parasite richness relationships within agro-ecological landscapes in our study area. We emphasized the influence of grass diversity and land use on the composition of viral communities and their life history strategies, and we demonstrated the complexity of plant-virus interactions in less-managed grass communities, such as the higher virus prevalence and overrepresentation of mixed virus infection compared to theoretical predictions.

Substâncias naturais de plantas: relação com a defesa em infecções virais e aplicação na agricultura sustentável

During evolution, plants developed a complex set of morphological, biochemical and molecular, preformed and inducible defense mechanisms that allowed them to live in stressful conditions. In addition, the ability of plants to synthesize organic compounds (primary and secondary metabolites and plant hormones) has ensure success in colonizing challenging environments. With the practice of intensive monoculture, aiming to feed an increasingly numerous population, the incidence of plant viruses has increased almost in the same proportion. Thus, aggressive control practices to the environment and human health such as the use of pesticides began to be recommended in an uncontrolled way, which has encouraged the search for a more sustainable agriculture. Therefore, understanding the mechanisms used by viroses to interfere with metabolism in compatible and incompatible interactions, as well as those used by plants to overcome or not the infection, is fundamental and can help to clarify important points in plant-virus interactions, enabling the recommendation and use of ecologically friendly crop management. In this review, the molecular aspects of plant-virus interactions, the metabolic changes induced by the viruses, the use of natural products to control plant viruses and the application of these compounds in sustainable agriculture will be addressed.

Pathogen-triggered metabolic adjustments to potato virus Y infection in potato.

Potato (Solanum tuberosum L) is affected by several viral pathogens with the most economically damaging being potato virus Y (PVY). At least nine biologically distinct variants of PVY are known to attack potato, with necrotic types named PVYNTN and PVYN-Wi being the most recent additions to the list. So far, the molecular plant-virus interactions underlying this pathogenicity are not fully understood. In this study, gas chromatography coupled with mass spectroscopy (GC-MS) was used for an untargeted investigation of the changes in leaf metabolomes of PVY-resistant cultivar Premier Russet, and a susceptible cultivar, Russet Burbank, following inoculation with three PVY strains, PVYNTN, PVYN-Wi, and PVYO. Analysis of the resulting GC-MS spectra with the online software Metaboanalyst (version 5.0) uncovered several common and strain-specific metabolites that are induced by PVY inoculation. In Premier Russet, the major overlap in differential accumulation was found between PVYN-Wi and PVYO. However, the 14 significant pathways occurred solely due to PVYN-Wi. In contrast, the main overlap in differential metabolite profiles and pathways in Russet Burbank was between PVYNTN and PVYO. Overall, limited overlap was observed between PVYNTN and PVYN-Wi. As a result, PVYN-Wi-induced necrosis may be mechanistically distinguishable from that of PVYNTN. Furthermore, 10 common and seven cultivar-specific metabolites as potential indicators of PVY infection and susceptibility/resistance were identified by using PLS-DA and ANOVA. In Russet Burbank, glucose-6-phosphate and fructose-6-phosphate were particularly affected by strain-time interaction. This highlights the relevance of the regulation of carbohydrate metabolism for defense against PVY. Some strain- and cultivar-dependent metabolite changes were also observed, reflecting the known genetic resistance-susceptibility dichotomy between the two cultivars. Consequently, engineering broad-spectrum resistance may be the most effective breeding strategy for managing these necrotic strains of PVY.

ADP-Ribosylation and Antiviral Resistance in Plants

ADP-ribosylation (ADPRylation) is a versatile posttranslational modification in eukaryotic cells which is involved in the regulation of a wide range of key biological processes, including DNA repair, cell signalling, programmed cell death, growth and development and responses to biotic and abiotic stresses. Members of the poly(ADP-ribosyl) polymerase (PARP) family play a central role in the process of ADPRylation. Protein targets can be modified by adding either a single ADP-ribose moiety (mono(ADP-ribosyl)ation; MARylation), which is catalysed by mono(ADP-ribosyl) transferases (MARTs or PARP "monoenzymes"), or targets may be decorated with chains of multiple ADP-ribose moieties (PARylation), via the activities of PARP "polyenzymes". Studies have revealed crosstalk between PARylation (and to a lesser extent, MARylation) processes in plants and plant-virus interactions, suggesting that these tight links may represent a novel factor regulating plant antiviral immunity. From this perspective, we go through the literature linking PARylation-associated processes with other plant regulation pathways controlling virus resistance. Once unraveled, these links may serve as the basis of innovative strategies to improve crop resistance to viruses under challenging environmental conditions which could mitigate yield losses.

Viral strain-dependent impact of plant developmental stages on the nestedness and modularity of plant-virus interaction matrices.

This study examines the specificity of adaptation of lineages of turnip mosaic virus that were experimentally evolved from naïve and preadapted strains to Arabidopsis thaliana plants at various plant developmental stages. We conducted a cross-infection experiment involving three plant developmental stages and assessed the progression of disease and symptoms. We found a significative interaction between the host developmental stage where the virus evolved and the host developmental stage in which the virus was tested. The analysis of the resulting interaction matrices revealed significant nestedness for viruses evolved from the naïve strain, but not for those originating from the preadapted one. Furthermore, there was an absence of modularity across all matrices. Our findings suggest that the past adaptation history of the ancestral strain influences its future evolution, and each plant developmental stage imposes unique selective constraints. The study highlights the complexity of host-parasite interactions and the potential influence of the host's developmental stage on viral adaptation.

Cucumber Mosaic Virus-Induced Systemic Necrosis in Arabidopsis thaliana: Determinants and Role in Plant Defense.

Effector-triggered immunity (ETI) is one of the most studied mechanisms of plant resistance to viruses. During ETI, viral proteins are recognized by specific plant R proteins, which most often trigger a hypersensitive response (HR) involving programmed cell death (PCD) and a restriction of infection in the initially infected sites. However, in some plant-virus interactions, ETI leads to a response in which PCD and virus multiplication are not restricted to the entry sites and spread throughout the plant, leading to systemic necrosis. The host and virus genetic determinants, and the consequences of this response in plant-virus coevolution, are still poorly understood. Here, we identified an allelic version of RCY1-an R protein-as the host genetic determinant of broad-spectrum systemic necrosis induced by cucumber mosaic virus (CMV) infection in the Arabidopsis thaliana Co-1 ecotype. Systemic necrosis reduced virus fitness by shortening the infectious period and limiting virus multiplication; thus, this phenotype could be adaptive for the plant population as a defense against CMV. However, the low frequency (less than 1%) of this phenotype in A. thaliana wild populations argues against this hypothesis. These results expand current knowledge on the resistance mechanisms to virus infections associated with ETI in plants.

Resistance genes on the verge of plant-virus interaction.

Viruses are acellular pathogens that cause severe infections in plants, resulting in worldwide crop losses every year. The lack of chemical agents to control viral diseases exacerbates the situation. Thus, to devise proper management strategies, it is important that the defense mechanisms of plants against viruses are understood. Resistance (R) genes regulate plant defense against invading pathogens by eliciting a hypersensitive response (HR). Compatible interaction between plant R gene and viral avirulence (Avr) protein activates the necrotic cell death response at the site of infection, resulting in the cessation of disease. Here, we review different aspects of R gene-mediated dominant resistance against plant viruses in dicotyledonous plants and possible ways for developing crops with better disease resistance.

Nicotiana benthamiana Kunitz peptidase inhibitor-like protein involved in chloroplast-to-nucleus regulatory pathway in plant-virus interaction.

Plant viruses use a variety of strategies to infect their host. During infection, viruses cause symptoms of varying severity, which are often associated with altered leaf pigmentation due to structural and functional damage to chloroplasts that are affected by viral proteins. Here we demonstrate that Nicotiana benthamiana Kunitz peptidase inhibitor-like protein (KPILP) gene is induced in response to potato virus X (PVX) infection. Using reverse genetic approach, we have demonstrated that KPILP downregulates expression of LHCB1 and LHCB2 genes of antenna light-harvesting complex proteins, HEMA1 gene encoding glutamyl-tRNA reductase, which participates in tetrapyrrole biosynthesis, and RBCS1A gene encoding RuBisCO small subunit isoform involved in the antiviral immune response. Thus, KPILP is a regulator of chloroplast retrograde signaling system during developing PVX infection. Moreover, KPILP was demonstrated to affect carbon partitioning: reduced glucose levels during PVX infection were associated with KPILP upregulation. Another KPILP function is associated with plasmodesmata permeability control. Its ability to stimulate intercellular transport of reporter 2xGFP molecules indicates that KPILP is a positive plasmodesmata regulator. Moreover, natural KPILP glycosylation is indispensable for manifestation of this function. During PVX infection KPILP increased expression leads to the reduction of plasmodesmata callose deposition. These results could indicate that KPILP affects plasmodesmata permeability via callose-dependent mechanism. Thus, virus entering a cell and starting reproduction triggers KPILP expression, which leads to downregulation of nuclear-encoded chloroplast genes associated with retrograde signaling, reduction in photoassimilates accumulation and increase in intercellular transport, creating favorable conditions for reproduction and spread of viral infection.

Exploiting Virus Infection to Protect Plants from Abiotic Stresses: Tomato Protection by a Begomovirus.

Tomato cultivation is threatened by environmental stresses (e.g., heat, drought) and by viral infection (mainly viruses belonging to the tomato yellow leaf curl virus family-TYLCVs). Unlike many RNA viruses, TYLCV infection does not induce a hypersensitive response and cell death in tomato plants. To ensure a successful infection, TYLCV preserves a suitable cellular environment where it can reproduce. Infected plants experience a mild stress, undergo adaptation and become partially "ready" to exposure to other environmental stresses. Plant wilting and cessation of growth caused by heat and drought is suppressed by TYLCV infection, mainly by down-regulating the heat shock transcription factors, HSFA1, HSFA2, HSFB1 and consequently, the expression of HSF-regulated stress genes. In particular, TYLCV captures HSFA2 by inducing protein complexes and aggregates, thus attenuating an acute stress response, which otherwise causes plant death. Viral infection mitigates the increase in stress-induced metabolites, such as carbohydrates and amino acids, and leads to their reallocation from shoots to roots. Under high temperatures and water deficit, TYLCV induces plant cellular homeostasis, promoting host survival. Thus, this virus-plant interaction is beneficial for both partners.

Identification of viral genes involved in pepper mottle virus replication and symptom development in Nicotiana benthamiana.

Pepper mottle virus (PepMoV) infects primarily Capsicum species, including pepper and bell pepper which are important vegetable and spice crops in Korea. We have previously collected 13 PepMoV isolates from nine regions comprising five provinces, causing different symptoms on inoculated indicator host plants in Korea. To further identify the responsible symptom determinant(s) and explore viral protein functions of PepMoV, two out of 13 isolates, including 134 and 205136, were used in this study. Isolate 134 causes necrosis and yellowing, while 205136 causes severe mottle and yellowing symptoms on Nicotiana benthamiana. All chimeric and site-directed mutants contain the PepMoV 134 genome as a backbone with specific regions switched for those from counterparts of PepMoV 205136. Effects of all mutants compared with 134 after inoculation onto N. benthamiana by agroinfiltration. Results from our study provide direct evidence that the helper component-proteinase (HC-Pro) and the nuclear inclusion protein b (NIb)-coat protein (CP) regions are involved in virus accumulation and symptom determinants. In addition, we mapped to amino acid residues tyrosine, glycine, and leucine at position 360, 385, and 527, respectively, in the HC-Pro region participate in faster viral accumulation or movement in the plant. The residue valine at position 2773 of NIb plays an essential role in isolate 134 symptom development. As part of this study, we seek to gain insight into viral factors involved in the PepMoV infection cycle and a better understanding of plant-virus interactions. These findings complement the insufficiency of the gene function study of the PepMoV virus and provide a novel perspective for the protein function study of the Potyvirus.

Comparative transcriptome analysis of Citrus macrophylla tree infected with Citrus tristeza virus stem pitting mutants provides new insight into the role of phloem regeneration in stem pitting disease.

Stem pitting is a complex and economically important virus-associated disease of perennial woody plants. Molecular mechanisms and pathways occurring during virus-plant interaction that result in this phenomenon are still obscure. Previous studies indicated that different Citrus tristeza virus (CTV) mutants induce defined stem pitting phenotypes ranging from mild (CTVΔp13) to severe (CTVΔp33) in Citrus macrophylla trees. In this study, we conducted comparative transcriptome analyses of C. macrophylla trees infected with CTV mutants (CTVΔp13 and CTVΔp33) and a full-length virus in comparison to healthy plants as control. The mild CTV stem pitting mutant had very few differentially expressed genes (DEGs) related to plant defense mechanism and plant growth and development. In contrast, substantial gene expression changes were observed in plants infected with the severe mutant and the full-length virus, indicating that both the p13 and p33 proteins of CTV acted as a regulator of symptom production by activating and modulating plant responses, respectively. The analysis of transcriptome data for CTVΔp33 and the full-length virus suggested that xylem specification has been blocked by detecting several genes encoding xylem, cell wall and lignin degradation, and cell wall loosening enzymes. Furthermore, stem pitting was accompanied by downregulation of transcription factors involved in regulation of xylem differentiation and downregulation of some genes involved in lignin biosynthesis, showing that the xylem differentiation and specification program has been shut off. Upregulation of genes encoding transcription factors associated with phloem and cambium development indicated the activation of this program in stem pitting disease. Furthermore, we detected the induction of several DEGs encoding proteins associated with cell cycle re-entry such as chromatin remodeling factors and cyclin, and histone modification. This kind of expression pattern of genes related to xylem differentiation and specification, phloem and cambium development, and cell cycle re-entry is demonstrated during secondary vascular tissue (SVT) regeneration. The microscopy analysis confirmed that the regeneration of new phloem is associated with stem pitting phenotypes. The findings of this study, thus, provide evidence for the association between stem pitting phenotypes and SVT regeneration, suggesting that the expression of these genes might play important roles in development of stem pitting symptoms. Overall, our findings suggest that phloem regeneration contributes to development of stem pitting symptoms.

Genetics of novel leaf curl virus disease resistant pepper genotypes and antioxidative profile analysis of their progenies

Pepper/Chilli leaf curl virus disease (PepLCVD/ChiLCVD) is the most destructive disease of pepper that seriously reduced pepper production. The LCVD is transmitted by vector whitefly (Bemisia tabaci) so efficiently that even single whitefly is able to transmit the virus. The effective way to manage the LCVD in pepper is to introduce LCVD resistance into agronomically desired cultivars, but the lack of resistant sources is a major hurdle in this technique. So with this objective, we identified new resistant sources against LCVD using astringent artificial screening techniques. The genetics of these new sources was confirmed using artificial inoculation methods on parental lines and their progenies that developed by using susceptible bell pepper genotype PAU SM-1. The progenies of crosses S-343 and SL 475 with susceptible genotype reveal monogenic dominant control of LCVD resistance while progenies of crosses SL 492 and JL 282 reveal monogenic recessive gene control for LCVD resistance. Moreover, antioxidative and biochemical parameter analysis demonstrate high levels of peroxidase (PO), polyphenol oxidase (PPO), ascorbate peroxidase (APX), phenylalanine ammonia-lyase (PAL), tyrosine ammonia lyase (TAL) and superoxide dismutase (SOD) and phenolic compounds in leaves of resistant plants than susceptible plants. Furthermore, all the studied traits and treatments were subjected to principal component analysis (PCA), correlation, and clustering analysis. The first three PCA components describe 70.55% variation for both studied traits and treatments. Hence, the newly identified sources could be further used for resistant breeding programs, and their antioxidative profile data could be used as biochemical markers for studying further plant-virus interactions.

(Z)-3-hexenol primes callose deposition against whitefly-mediated begomovirus infection in tomato.

Rapid callose accumulation has been shown to mediate defense in certain plant-virus interactions. Exposure to the green leaf volatile (Z)-3-hexenol (Z-3-HOL) can prime tomato (Solanum lycopersicum) for an enhanced defense against subsequent infection by whitefly-transmitted Tomato yellow leaf curl virus (TYLCV). However, the molecular mechanisms affecting Z-3-HOL-induced resistance are poorly understood. Here, we explored the mechanisms underlying Z-3-HOL-induced resistance against whitefly-transmitted TYLCV infection and the role of callose accumulation during this process. Tomato plants pre-treated with Z-3-HOL displayed callose priming upon whitefly infestation. The callose inhibitor 2-deoxy-d-glucose abolished Z-3-HOL-induced resistance, confirming the importance of callose in this induced resistance. We also found that Z-3-HOL pre-treatment enhanced salicylic acid levels and activated sugar signaling in tomato upon whitefly infestation, which increased the expression of the cell wall invertase gene Lin6 to trigger augmented callose deposition against TYLCV infection resulting from whitefly transmission. Using virus-induced gene silencing, we demonstrated the Lin6 expression is relevant for sugar accumulation mediated callose priming in restricting whitefly-transmitted TYLCV infection in plants that have been pre-treated with Z-3-HOL. Moreover, Lin6 induced the expression of the callose synthase gene Cals12, which is also required for Z-3-HOL-induced resistance of tomato against whitefly-transmitted TYLCV infection. These findings highlight the importance of sugar signaling in the priming of callose as a defense mechanism in Z-3-HOL-induced resistance of tomato against whitefly-transmitted TYLCV infection. The results will also increase our understanding of defense priming can be useful for the biological control of viral diseases.

Sugarcane Streak Mosaic Virus P1 Attenuates Plant Antiviral Immunity and Enhances Potato Virus X Infection in Nicotiana benthamiana.

The sugarcane streak mosaic virus (SCSMV) is the most important disease in sugarcane produced in southern China. The SCSMV encoded protein 1 (P1SCSMV) is important in disease development, but little is known about its detailed functions in plant–virus interactions. Here, the differential accumulated proteins (DAPs) were identified in the heterologous expression of P1SCSMV via a potato virus X (PVX)-based expression system, using a newly developed four-dimensional proteomics approach. The data were evaluated for credibility and reliability using qRT-RCR and Western blot analyses. The physiological response caused by host factors that directly interacted with the PVX-encoded proteins was more pronounced for enhancing the PVX accumulation and pathogenesis in Nicotiana benthamiana. P1SCSMV reduced photosynthesis by damaging the photosystem II (PSII). Overall, P1SCSMV promotes changes in the physiological status of its host by up- or downregulating the expression of host factors that directly interact with the viral proteins. This creates optimal conditions for PVX replication and movement, thereby enhancing its accumulation levels and pathogenesis. Our investigation is the first to supply detailed evidence of the pathogenesis-enhancing role of P1SCSMV, which provides a deeper understanding of the mechanisms behind virus–host interactions.

Studies on plant–virus interactions for development of multiple resistance to plant viruses

Studies on plant–virus interactions for development of multiple resistance to plant viruses

Expanding the environmental virome: Infection profile in a native rainforest tree species.

Agroforestry systems (AFS) for cocoa production combine traditional land-use practices with local biodiversity conservation, resulting in both ecological and agricultural benefits. The cacao-cabruca AFS model is widely implemented in regions of the Brazilian Atlantic Forest. Carpotroche brasiliensis (Raddi) A. Gray (Achariaceae) is a tree found in cabruca landscapes that is often used for reforestation and biotechnological applications. Despite its importance, we still lack information about viruses circulating in C. brasiliensis, particularly considering the possibility of spillover that could affect cocoa production. In our study, we analyzed the Carpotroche brasiliensis virome from Atlantic Forest and cacao-cabruca AFS regions using metatranscriptomics from several vegetative and reproductive organs. Our results revealed a diverse virome detecting near-complete or partial coding sequences of single- and double-stranded DNA and RNA viruses classified into at least six families (Botourmiaviridae, Bromoviridae, Caulimoviridae, Genomoviridae, Mitoviridae, and Rhabdoviridae) plus unclassified elements. We described with high confidence the near-complete and the partial genomes of two tentative novel viruses: Carpotroche-associated ilarvirus and Carpotroche-associated genomovirus, respectively. Interestingly, we also described sequences likely derived from a rhabdovirus, which could represent a novel member of the genus Gammanucleorhabdovirus. We observed higher viral diversity in cacao-cabruca AFS and reproductive organs of C. brasiliensis with preferential tropism to fruits, which could directly affect production. Altogether, our results provide data to better understand the virome in this unexplored agroecological interface, such as cacao-cabruca AFS and forest ecosystem, providing information on the aspects of virus–plant interactions.

ABA INSENSITIVE 5 confers geminivirus resistance via suppression of the viral promoter activity in plants

Geminiviruses are a large group of plant viruses that have been a serious threat to worldwide agriculture. Transcription of the virus-encoded genes is necessary for geminiviruses to complete their life cycle, but the host proteins which directly target geminivirus promoters for suppression of viral gene transcription remain to be identified. Using Beet severe curly top virus (BSCTV) which causes severe plant symptoms as a system, we performed a yeast one-hybrid screening and identified ABA INSENSITIVE 5 (ABI5), a critical transcription factor in Abscisic acid (ABA) signaling transduction, as an interactor with the viral promoter. Further data showed that an ABA-responsive element in the viral promoter is necessary for its interaction with ABI5 and symptom development. Overexpression of ABI5 suppresses the transcription activity of the viral promoter and BSCTV infection in Nicotiana benthamiana and Arabidopsis; whilst depletion of ABI5 enhances the infection of BSCTV in Arabidopsis. Taken together, our study uncovered the function of ABI5 in the plant-virus interaction and will provide us with a new strategy to protect crops from geminivirus infection.

Unveiling the nature's fruit basket to computationally identify Citrus sinensis csi-mir169–3p as a probable plant miRNA against Reference and Omicron SARS-CoV-2 genome

The fundamental role of microRNAs (miRNAs) has long been associated with regulation of gene expression during transcription and post transcription of mRNA's 3′UTR by the RNA interference mechanism. Also, the process of how miRNAs tend to induce mRNA degradation has been predominantly studied in many infectious diseases. In this article, we would like to discuss the interaction of dietary plant miRNAs derived from fresh fruits against the viral genome of the causative agent of COVID-19, specifically targeting the 3′UTR of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) genome. Expanding the analysis, we have also identified plant miRNAs that interact against the Omicron (B.1.1.529) variant of SARS-CoV-2 across 37 countries/territories throughout the world. This cross-species virus-plant interaction led us to identify the alignment of dietary plant miRNAs found in fruits like Citrus sinensis (Orange), Prunus persica (Peaches), Vitis vinifera (Grapes) and Malus domestica (Apple) onto the viral genomes. In particular, the interaction of C. sinensis miRNA - csi-miR169–3p and SARS-CoV-2 is noteworthy, as the targeted 3′UTR region “CTGCCT” is found conserved amongst all curated 772 Omicron variants across the globe. Hence this site “CTGCCT” and miRNA csi-miR169–3p may become promising therapeutic candidates to induce viral genome silencing. Thereby, this study reveals the mechanistic way of how fruits tend to enact a fight against viruses like SARS-CoV-2 and aid in maintaining a strong immune system of an individual.