Mitoviruses are simple RNA viruses typically associated with fungal mitochondria, although recent studies suggest their presence in plant transcriptomes. In this study, we report the identification and molecular characterization of a novel mitovirus from Colocasia esculenta using high-throughput sequencing (HTS). Analysis of symptomatic leaf tissues revealed a 2,644 nucleotide-long viral genome encoding a single open reading frame (ORF) for an RNA-dependent RNA polymerase (RdRp) of 544 amino acids. The viral sequence, tentatively named Colocasia esculenta associated mitovirus 2 (CeaMV2), showed 60.76% amino acid identity with known mitoviruses, supporting its classification as a novel species within the family Mitoviridae. Phylogenetic analysis showed that CeaMV2 clustered within the family Mitoviridae, grouped with other plant-associated mitoviruses, supporting its placement within the family Mitoviridae. The conserved domain searches confirmed the presence of the mitovirus-specific RdRp domain (Pfam: PF05919). RT-PCR and Sanger sequencing further validated the presence of CeaMV2 in C. esculenta leaf samples. The relatively short RdRp and its expression in plant transcriptome suggest possible association with plant mitochondria. Furthermore, in-silico analysis identified several plant-derived mature miRNAs, such as sbi-miR6231-3p, with high binding affinity to the CeaMV2 RdRp gene, suggesting a potential role for RNA interference in the host-virus interaction. This finding expands the known diversity of mitoviruses and highlights the utility of HTS in uncovering cryptic viral infections and potential RNAi-based defense mechanisms in economically important crops.

Citrus yellow vein clearing virus (CYVCV) is a positive-sense, single-stranded RNA virus belonging to the family Alphaflexiviridae that poses a major threat to citrus production worldwide and is widespread in Kinnow mandarin orchards. Despite its prevalence, seasonal fluctuations in CYVCV infection remain poorly understood. This study examined the year-long (2024) temporal-dynamics of CYVCV in Kinnow plants confirmed to be singly-infected and free from other viruses, using symptom monitoring, high-throughput sequencing (HTS), and RT-qPCR. Leaves were collected quarterly (February, May, August, and November) from CYVCV-infected plants maintained at IARI, New Delhi. HTS confirmed CYVCV in symptomatic samples revealed clear seasonal trends and viral abundance, with sequencing depth and FPKM values peaking in February and November, while the virus was nearly undetectable in May and August months. Single nucleotide variant (SNV) analysis further highlighted genetic variability in viral populations across seasons. RT-qPCR analysis corroborated HTS results and revealed clear seasonal variation in viral load, with higher accumulation during cooler months and minimal detection during warmer periods. A strong association between viral load and symptom expression was observed. Additionally, a sensitive and quantitative RT-qPCR assay was developed and validated for reliable detection of CYVCV. This first detailed report of CYVCV seasonal dynamics provides critical insights for optimizing disease management and improving certification programs in Kinnow mandarin orchards.

Mustard is an economically important oilseed crop in India. Recently, a mosaic viral disease was observed in mustard crop at ICAR-IARI, New Delhi and found to be caused by coinfections of turnip mosaic virus (TuMV) and cucumber mosaic virus (CMV) or by infection of TuMV alone. As both the viruses are transmitted by aphids, manipulation of sowing time is a practical cultural strategy to manage the viral disease by modulating vector pressure. A two-year field experiment (2020-21 and 2021-22) was conducted at IARI, using a randomized complete block design with three replications to assess the impact of three sowing dates (early (September), mid (October), and late (November)) on mosaic disease incidence and severity in terms of agro-economic performance of mustard. Real-time PCR was employed to quantify the viral titre of TuMV and CMV. A negative association was found between TuMV and CMV titer and the yield loss. The late-sown plants exhibited highest disease incidence, high viral titer of both viruses and lower plant growth and yield. Significant differences (P < 0.05) in plant height, main shoot length, and fewer primary and secondary branches were observed among sowing dates in both years. The siliqua density on the main shoot, number of seeds per siliqua, seed yield per plant, and 1000-seed weight, were also negatively affected. Oil content was only marginally affected. In contrast, early sowing minimized disease severity, reduced virus load, maintained superior growth and yield attributes. This study provides first systematic evidence of managing mosaic disease by adjusting sowing time. Early sowing (September) is a simple, effective, and sustainable practice for managing vector-borne viral diseases in mustard production systems.

The geothermal springs of the Garhwal Himalaya represent unique geothermal ecosystems that harbor diverse thermophilic microorganisms; however, their bacterial diversity remains insufficiently characterized using culture-independent sequencing approaches. In this study, a comparative 16S rRNA gene amplicon sequencing analysis was conducted to investigate bacterial community composition in two geographically proximate but physicochemically distinct geothermal spring systems, Badrinath (52°C–56 °C) and Tapovan (67°C–70 °C), located in Uttarakhand, India. A total of 225,109 high-quality non-chimeric sequences were obtained, achieving > 99

Turnip mosaic virus (TuMV) is a major constraint in mustard production, with emerging evidence of its seed-borne nature posing significant risks for long-distance dissemination and disease outbreaks. Rapid and sensitive detection methods tailored for seed health diagnostics are therefore critically needed. In the present study, a reverse transcription recombinase polymerase amplification (RT-RPA) assay targeting the coat protein (CP) gene of TuMV was optimized across multiple mustard tissues, including mature seeds. The assay was standardized at 42 °C for 25 min, and it demonstrated high analytical sensitivity, detecting viral RNA up to 10 fg dilution, particularly from crude extracts, outperforming conventional RT-PCR by 2–3 orders of magnitude. A simplified crude sap extraction using 0.1 M phosphate buffer enabled direct amplification without RNA purification, and assay compatibility with hydroxynaphthol blue (HNB) allowed visual, colorimetric detection suitable for field applications. Validation across diverse genotypes and field samples showed complete concordance of RT-RPA with RT-PCR. To establish practical seed health testing thresholds, seed pool optimization was performed using two mustard varieties differing in seed size. RT-RPA results were quantitatively validated using RT-qPCR, revealing strong agreement between qualitative and quantitative detection. Reliable detection was achieved with crude seed extracts of as few as 2–6 seeds in large-seeded genotypes and 15–25 seeds in small-seeded genotypes, highlighting the influence of seed size on detection sensitivity. This study developed and validated the first crude extract-based RT-RPA assay for detecting TuMV infection in mustard plant parts, including seed samples. It provides an ISTA (International Seed Testing Association)-compatible framework for rapid, sensitive, and field-deployable seed health diagnostics. This study delivers a crude extract based RT-RPA, with RT-qPCR validation, providing a rapid, field-deployable framework for the sensitive detection of turnip mosaic virus in seed-lot testing of mustard.

Chamomile is an annual flower having medicinal, therapeutic, consumption, cosmetic uses since a long time. It is native to southern and eastern Europe and has been grown in many other countries. Here, we identify a novel Deltapartitivirus, chamaemelum cryptic virus (CCV) through publicly available RNA-seq data of chamomile. CCV contains two genomic RNA segments i.e. RNA1 (BK068401) and RNA2 (BK068402). CCV RNA1 (1597 nt) encoded for an RNA dependent RNA polymerase (RdRp) protein (481 aa) while CCV RNA2 (1682 nt) encoded for a coat protein (CP) (478 aa). Homology and phylogenetic analysis of CCV genome showed relatedness with beet cryptic virus 3 (YP009665971) and vitis cryptic virus (BCS51498). Based on the sequence demarcation criteria, CCV represents a newly discovered species within the Deltapartitivirus genus of the Partitiviridae family, associated with a new host i.e. chamomile.

Citrus yellow vein clearing virus (CYVCV) and citrus yellow mottle-associated virus (CiYMaV) frequently co-infect citrus, posing challenges for reliable diagnosis and certification systems. In this study, a duplex reverse transcription recombinase polymerase amplification (RT-RPA) assay was developed for the simultaneous detection of both viruses using crude leaf sap of citrus. The assay operates under isothermal conditions (40 °C, 25 min) and incorporates an endogenous internal control (Elongation factor 1α) to support assay reliability and reduce the likelihood of false-negative results. The duplex RT-RPA assay performed effectively with crude sap, enabling detection without the need for nucleic acid extraction. It specifically amplified CYVCV and CiYMaV without cross-reactivity with other citrus pathogens and showed performance comparable to duplex RT-PCR. A hydroxynaphthol blue (HNB)-based colorimetric format was further evaluated to allow visual identification of positive samples without electrophoresis, although it does not differentiate between the two viruses. Validation using citrus samples confirmed detection of both single and mixed infections, with results consistent with those obtained by duplex RT-PCR. Overall, the combined approach provides a rapid and simplified method for citrus virus detection and may be useful for routine screening and certification programs.

Tomato leaf curl New Delhi virus (ToLCNDV) is a highly adaptable begomovirus with an expansive and ever-increasing host range. Since its first report in the Indian subcontinent, the virus has rapidly spread across Asia, the Mediterranean Basin, North Africa, and other areas, largely due to efficient transmission by the whitefly Bemisia tabaci. The virus causes severe economic losses in tomato and cucurbit crops, with reported yield reductions ranging from 80% to 100% depending on crop stage, host genotype, and epidemic severity. ToLCNDV has a bipartite circular single-stranded DNA genome that encodes proteins involved in replication, movement, pathogenicity, and suppression of host defense responses. Rapid host range expansion, emergence of new strains, and breakdown of resistance have been facilitated by its high mutation rate, frequent recombination, genome reassortment, and interactions with associated DNA satellites. This review summarizes the current knowledge on taxonomy, genome organization, epidemiology, transmission biology, host range, and molecular interactions of ToLCNDV with host plants and vectors. Particular attention is given to natural sources of resistance in tomato and cucurbits, the genetic basis of resistance loci, host susceptibility factors, and viral counter-defense strategies. This review also discusses recent advances in genomics, transcriptomics, proteomics, gene editing, and molecular breeding as promising tools for durable disease management. Although progress has been made in resistance gene discovery and host–virus interaction studies, sustainable management remains challenging due to the rapid evolution of viruses and the adaptability of vectors. The future management of ToLCNDV will be based on a combination of resistant cultivars, clean plant material, correct diagnosis, whitefly control, real-time surveillance, and omics-guided breeding strategies. A systems-level understanding of the host–virus–vector relationship will be essential for developing resilient crop production systems under changing climatic and agricultural conditions.

Citrus yellow vein clearing virus (CYVCV) is an emerging mandarivirus globally, commonly present in citrus orchards in India. Early detection of CYVCV is essential to prevent its spread through propagative material and to support integrated disease management. Conventional RT-PCR, although reliable and widely used, are time-intensive, require RNA extraction, and depend on sophisticated laboratory infrastructure, which limits their application for rapid on-site surveillance and large-scale indexing. In this study, we developed and validated a CRISPR-Cas12a-assisted reverse transcription recombinase polymerase amplification (RT-RPA) assay using crude-sap as template for rapid, sensitive, and sequence-specific detection of CYVCV. A 241 bp RT-RPA amplicon derived from the RNA-dependent RNA polymerase (RdRp) region of CYVCV was specifically recognized by a Cas12a-crRNA-complex, which activated collateral cleavage of a fluorescent single-stranded DNA-reporter, generating robust and unambiguous signals within 40-50 min. The analytical sensitivity of the CRISPR-based system was established at the 10-6 dilution of RT-RPA product by quantitative fluorescence measurement and was further translated into absolute copy numbers using a plasmid-based SYBR Green qPCR standard curve, while endpoint visualization using a UV transilluminator was feasible up to the 10-3 dilution. Validation on symptomatic citrus field samples revealed strong fluorescence signals in infected plants (up-to 91,447 AU), whereas healthy and non-template controls consistently remained at baseline. Importantly, visible fluorescence in infected samples under UV light further underscored the field-deployable potential of the assay. Compared with conventional RT-PCR, the CRISPR-based RT-RPA platform demonstrated an approximately similar to 1.4-fold per-sample cost reduction, supported by itemized reagent-level cost analysis. These attributes establish the assay as robust, user-friendly, and scalable diagnostic-tool for CYVCV detection, offering strong potential for nursery indexing, orchard surveillance, and certification programs.

Citrus tristeza virus (CTV) and ‘Candidatus Liberibacter asiaticus’ (CLas), are two of the most significant systemic pathogens associated with decline threatening citrus crops globally, including those in tropical and subtropical regions. Effective disease management and the prevention of their spread rely on rapid, sensitive, and reliable diagnostic tools aiming at bud wood certification and clean stock propagation. An assay capable of simultaneous and sensitive detection of both the virus and fastidious prokaryotes (CTV and CLas) is expected to simply the routine indexing and certification procedures in citrus. This study describes the development and validation of a highly sensitive and rapid duplex isothermal RT-RPA/RPA assay for the simultaneous detection of CTV and CLas. The assay utilizes a simplified pulverized tissue extract template prepared in a 50 mM NaOH : 2.5 mM EDTA buffer (1 : 1, pH 8.0), making it suitable for field-based or limited-resource laboratory settings. The developed assay resulted in an optimal performance at 37°C for 30 min. A higher sensitivity was observed with the assay detecting CTV and CLas infections at concentrations up to a 10–9 fold dilution (0.1 pg/μL concentration), a significant improvement over conventional duplex RT-PCR/PCR. Validation results revealed mixed infections of CLas and CTV in 83.3

Southern rice black-streaked dwarf virus (SRBSDV), a member of the Fijivirus genus, is an emerging threat to rice production in Asia. Since its first outbreak in 2022, the virus has raised concerns due to its potential impact on rice ecosystems in India. However, limited genomic data exist on its establishment, ecology and evolution, particularly in alternative hosts. In this study, high-throughput sequencing (HTS) and RT-PCR were used to perform a comparative genomic segmental analysis of SRBSDV in symptomatic rice (Oryza sativa) and asymptomatic monocot weeds from the vicinity of rice fields in North India. Complete SRBSDV genomes (segments S1-S10) were recovered from rice samples, while seven near-complete segments were identified in the monocot weeds during the two subsequent rice growing seasons. Viral segment accumulation, copy number and FPKM analyses revealed significantly higher SRBSDV loads in rice than in weeds. SNV profiling indicated active viral replication and intra-host evolution in rice, whereas limited SNV in weeds suggested viral stability and a reservoir role. Phylogenetic analysis of SRBSDV segments S8 and S10 confirmed close relatedness to the Chinese isolates. Diversity analysis of the S8 segment using DnaSP demonstrated high haplotype richness, moderate nucleotide diversity, and strong purifying selection, with Indian isolates forming a low-diversity subgroup relative to highly polymorphic Chinese populations. RT-PCR validation across additional samples supported HTS findings and segment-specific variability in detection. This study provides the first genomic evidence of SRBSDV establishment in weed hosts in Indian rice agroecosystem post its first outbreak and highlights the role of asymptomatic weeds as potential reservoirs. Furthermore, the detection of all ten SRBSDV genomic segments in the white-backed planthopper (WBPH) vector collected from these fields confirms its role in viral transmission. These findings provide the first genomic evidence of SRBSDV persistence in weed hosts in India and underscore the importance of integrated disease and vector management strategies to safeguard rice productivity, contributing to sustainable agriculture.

Infection of viruses and bacteria poses a major threat to citrus fruit production worldwide, leading to significant economic losses. Reliable, quick and accurate detection of the clonally-transmitted pathogens is essential for effective control measures. In India, citrus tristeza virus (CTV) and ‘Candidatus Liberibacter asiaticus’ (CLas) are of notable economic importance, especially CLas, which is responsible for huanglongbing disease (HLB). HLB with its rapid symptom progression and extensive spread throughout citrus tree canopies, along with the infection of CTV leads to citrus decline under field conditions. To tackle this challenge, we devised a one-tube reaction system capable of detecting both CTV and CLas pathogens, respectively. In present study, we report a robust and sensitive detection assay by integrating isothermal recombinase polymerase amplification (RPA) with CRISPR-Cas12a cleavage. The developed method relies on the use of either purified nucleic acid (DNA of CLas infected tissues and RNA of CTV infected tissues) or simplified crude tissue extract of leaf midribs and veins. This diagnostic method can be performed under isothermal conditions (42°C) within a short timeframe of less than 30 minutes. The use of an affordable commercially available fluorescence visualizer further enables rapid and cost-effective field-level disease detection. Our study demonstrates that the in vitro “Specific CRISPR-based Assay for Nucleic acids” (iSCAN-OP) detection assay is highly adaptable for large-scale screening of plant viruses or virus-like pathogens in field settings and holds significant promise in the rapid detection of damaging systemic plant pathogens.

Apple necrotic mosaic virus (ApNMV) (species: Ilarvirus ApNMV), the predominant causal agent of apple mosaic disease in Asia, poses a major threat to apple cultivation, leading to significant yield losses. Considering the graft-transmissibility of ApNMV and the lack of resistant cultivars, reliable detection methods are crucial for managing disease spread through planting materials. In this study, we developed a rapid, sensitive, and field-deployable reverse transcription-recombinase polymerase amplification (RT-RPA) assay for ApNMV detection. Three primer sets targeting the RNA-dependent RNA polymerase (RdRp) and coat protein genes were designed, of which the RdRp-specific primer pair (282 bp) showed high specificity. Crude leaf extracts prepared in NaOH:EDTA (1:1) buffer provided the most suitable template, eliminating the need for RNA purification. The optimized assay performed best at 42 °C for 35 min, detecting ApNMV up to 10–5 dilution in RNA and 10–4 dilution in crude extract template, thereby exhibiting tenfold higher sensitivity than conventional RT-PCR. No cross-reactivity was observed with other common apple viruses (ASPV, ASGV, ACLSV, ApMV). ApNMV was detected by RT-RPA in 75

Citrus is one of the most widely cultivated fruit crops worldwide. Citrus plants affected with Huanglongbing (HLB) disease can endure significant yield and quality losses. For management of HLB and avoiding further losses, a sensitive and rapid detection tool for the pathogen causing HLB is essential. In the present study, a recombinase polymerase amplification (RPA) assay integrated with a lateral flow assay (LFA) optimized for both DNA and crude sap templates was developed to rapidly detect 'Candidatus Liberibacter asiaticus' (CLas), the major species causing HLB in India and worldwide. A specific primer pair and probe designed based on the conserved outer membrane protein (OMP) gene of CLas were employed in the assay. The developed HLB-RPA-LFA was specific to CLas as it did not cross-react other major citrus pathogens. The developed HLB-RPA-LFA performed better when DNA and crude sap templates were incubated at 37 degrees C for 25 min. The maximum detection limit of the assay was 1 pg of CLas DNA and 10(-4) dilution of crude sap derived from CLas-infected plants. Further, the developed assay was used to detect CLas in different citrus cultivars grown in various citrus orchards of India using crude sap as template. Owing to the sensitive, rapid, and specific detection of CLas, the developed HLB-RPA-LFA has a great potential for use by nurserymen, disease surveyors, and plant pathologists as an improved detection tool for CLas.

Cucumber mosaic virus (CMV), a member of the genus Cucumovirus with a broad host range and diverse strain variants, is one of the most prevalent plant viruses and poses a significant threat to global agriculture worldwide, leading to significant yield losses. The only effective way to manage plant viruses is through the use of virus-free planting material and control of vectors. Early and accurate identification of the causal agent is the most crucial step for the effective management of diseases caused by viral pathogens, for which quick, easy, and sensitive diagnostic methods are of the utmost importance. However, conventional methods, viz. the enzyme-linked immunosorbent assay (ELISA) and reverse transcription-polymerase chain reaction (RT-PCR), which are used for the detection of plant viruses, are time-consuming, costly, labor intensive and often require specialized laboratory infrastructure, limiting their utility in resource-limited settings. To address these limitations, a rapid and user-friendly reverse transcription–recombinase polymerase amplification–lateral flow dipstick (RT-RPA-LFD) diagnostic assay for CMV was developed. In the RT-RPA-LFD assay, the coat protein (CP) gene of CMV was successfully amplified via different templates, such as RNA, cDNA, and crude sap extracted from infected banana leaves. The assay showed a high sensitivity of 0.18 pg with RNA extracted from banana leaf samples followed by cDNA ( 18 fg), exhibited a 10⁻5 (1.8 pg) limit of detection with the crude sap and presented a clear visual signal on the LFDs. The developed assay was highly specific in the detection of CMV, and no cross-reactivity was observed with other related plant viruses infecting banana plants. The simplicity and efficacy of the RT-RPA-LFD assay offers significant advances in point-of-care disease detection, not only for crops such as banana for the selection of healthy mother plants but also for other crops that are susceptible to CMV infection.

BACKGROUND:Transcriptome data obtained from plant samples often contain significant numbers of reads originating from viral genomes, which are typically co-isolated during the RNA extraction process. This occurs through the simultaneous presence of viral RNA alongside host plant RNA, leading to the inclusion of viral sequences in the transcriptomic data. METHODS AND RESULTS:Here, we identify a novel member of the genus Ampelovirus, grapevine leafroll-associated virus S (GLRaV-S) by employing the high-throughput sequencing (HTS) of RNA of grape leaves showing leafroll symptoms using a bioinformatic pipeline for plant virus detection. The genomic RNA of GLRaV-S, measured 13,102 nucleotides (nts) and encompasses five open reading frames (ORF). Homology analysis of GLRaV-S genome showed sequence identity of 23.0 - 53.3 % with the sequences of known ampeloviruses. Phylogenetic analysis based on genome sequences showed that GLRaV-S clustered in a same clade of ampeloviruses. However, the RdRp and HSP70h of GLRaV-S clustered with subgroup II while the CP sequences clustered with subgroup I of ampeloviruses. CONCLUSIONS:Based on the species demarcation criteria, GLRaV-S represents a newly discovered species within the genus Ampelovirus of the Closteroviridae family. This study on identification of novel virus will be useful in developing a robust certification program for the production of healthy plants of grapevine.

BACKGROUND: Banana streak MY virus (BSMYV) [Badnavirus gammavirgamusae] is one of the most prevalent badnaviruses associated with streak disease in Musa species. Its infection and symptom development vary across the banana genotypes. Present study, for the first time attempted successful agroinfection of BSMYV in diploid banana progenitor Musa balbisiana cv. Bhimkol (BB) which was earlier considered resistant and elucidated the underlying mechanism of infection. METHODS AND RESULTS: Agroinfection of Bhimkol banana showed delayed infection at 280 days post-BSMYV agroinoculation. High-throughput sequencing (HTS) was carried out to decipher the mechanisms of delayed BSMYV infection. De novo assembly of transcriptome generated 101,961 unigenes with a mean length of 1310 base pairs (bp). Out of the total coding sequence (CDS), 48,797 were annotated against the non-redundant protein database. A total of 3174 differentially expressed genes (DEGs) were identified, of which 1138 up-regulated and 2036 down-regulated genes were observed in comparison of mock inoculated (BB_Mock) and delayed infected (BB_Symptomatic) Bhimkol banana. A heatmap with hierarchical clustering of top 50 significantly differentially expressed genes showed four different clusters. Based on fold changes, and adjusted p-value, twelve selected DEGs were validated using quantitative-PCR (qPCR). Selected DEGs were associated with regulation of plant hormone, host defense system and host machinery hijack. Enrichment analysis of differentially expressed genes hints toward the importance of Ca2+ dependent Ras signaling in M. balbisiana (BB) exhibiting delayed BSMYV infection response. CONCLUSION: The present study revealed a complex cross-talk between Ca2+ dependent Ras, macromolecules localization and auxin responsive genes to regulate primary metabolite production that possibly hinder the spread of virus across the cell, leading to the delayed establishment of BSMYV infection in Bhimkol banana. To the best of our knowledge, this is first report on elucidation of delayed infection of BSMYV in diploid M. balbisiana (BB) through comprehensive transcriptome analysis.

Cucumoviruses and potyviruses are the most destructive viruses of crop plants. In the experimental mustard field of IARI, New Delhi, in 2021 eight genotypes were observed with mosaic, puckering, and stunting symptoms. The next-generation sequencing (NGS) confirmed the infection of two viruses, i.e., turnip mosaic virus (TuMV) and cucumber mosaic virus (CMV), validated through reverse transcription polymerase chain reaction (RT-PCR). In the following year, i.e., 2022, the same genotypes showed only puckering symptoms on the leaves with slight stunting. The association of only TuMV was found via NGS and RT-PCR. A study was undertaken to evaluate the impact of natural mixed infection of TuMV and CMV on the growth and yield of mustard genotypes and compared the same with the impact of natural infection of TuMV alone. The variance analysis results from data collected on various growth parameters, such as plant height and main shoot length, were significant, with mixed infections of TuMV and CMV causing severe stunting. The yield parameters, including the number of seeds per siliqua and the test weight of 1000 seeds, were significantly lower under mixed infection conditions than with TuMV alone. The coinfections have a substantial effect on the seed yield per plant with reduction factor of 2.5–4 across different genotypes compared to single TuMV infections. However, the reduction in oil content was minimal and less significant. This study provides the first comprehensive analysis of the effects of TuMV and CMV mixed infections on mustard growth and yield compared to single infection of TuMV, highlighting the highly negative impact of mixed infections on crop productivity. These findings underscore the need for integrated virus management strategies in mustard cultivation.

Peaches hold great importance as a valuable stone fruit crop, yet the complete viral and viroid populations affecting peach varieties in India remain largely unexplored. To address this gap, transcriptome analyses of four rootstocks (Nemaguard, B6, Meripendent and 13–6) and a scion variety (Cresthaven) of peach was performed. Our study identified near- complete genomic sequences of nine viruses, including two ilarviruses: prune dwarf virus (PDV) and prunus necrotic ringspot virus (PNRSV); two luteoviruses: nectarine stem pitting-associated virus (NSPaV) and peach-associated luteovirus (PaLV); one maculavirus: grapevine red globe virus (GRGV); three marafiviruses: grapevine asteroid mosaic-associated virus (GAMaV), peach virus D (PeVD), and citrus sudden death-associated virus (CSDaV); and a novel marafivirus, peach associated marafivirus (PaMV). The accumulation of viral reads varied among these pathogens, with PDV exhibiting the highest proportion (23.54