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Cotton (Gossypium hirsutum, Malvaceae) is the most important fiber crop in the world. There are published records of many fungal pathogens attacking Gossypium spp., causing numerous diseases, including powdery mildews. Recently, in 2022, non-cultivated spontaneous G. hirsutum plants bearing powdery mildews symptoms were found at roadsides in two municipalities of the state of Minas Gerais (Brazil): Varginha and Ubá. Such localities are situated ca. 260 km apart, suggesting a broader distribution of this fungus-host association in Brazil. Samples were taken to the laboratory, and an Ovulariopsis-like, asexual stage of Phyllactinia, was identified forming amphigenous colonies, that were more evident, white and cottony, abaxially. Morphological and molecular data- of the ITS and LSU regions- have shown that colonies from those two samples were of the same fungus species, belonging to a previously unknown species of Erysiphaceae (Ascomycota). The fungus fits into the Phyllactinia clade and is described herein as the new species Phyllactinia gossypina sp. nov. This new species belongs to the 'basal Phyllactinia group', a lineage that includes species known only from the Americas. This report expands the list of pathogenic fungi on cotton. It is early to anticipate whether this new powdery mildew represents a threat to cultivated cotton, which is a major crop in Brazil. Nevertheless, further studies about its infectivity to commercial cotton varieties are recommended, since all known Erysiphaceae are specialized obligate plant parasites and several species cause major losses to important crops.

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Traditional monitoring of asian soybean rust severity is a time- and labor-intensive task, as it requires visual assessments by skilled professionals in the field. Thus, the use of remote sensing and machine learning (ML) techniques in data processing has emerged as an approach that can increase efficiency in disease monitoring, enabling faster, more accurate and time- and labor-saving evaluations. The aims of the study were: (i) to identify the spectral signature of different levels of Asian soybean rust severity; (ii) to identify the most accurate machine learning algorithm for classifying disease severity levels; (iii) which spectral input provides the highest classification accuracy for the algorithms; (iv) to determine a sample size of leaves that guarantees the best accuracy for the algorithms. A field experiment was carried out in the 2022/2023 harvest in a randomized block design with a 6x3 factorial scheme (ML algorithms x severity levels) and four replications. Disease severity levels assessed were: healthy leaves, 25 % severity, and 50 % severity. Leaf hyperspectral analysis was carried out over a wide range from 350 to 2500 nm. From this analysis, 28 spectral bands were extracted, seeking to distinguish the spectral signature for each severity level with the least input dataset. Data was subjected to machine learning analysis using Artificial Neural Network (ANN), REPTree (DT) and J48 decision trees, Random Forest (RF), and Support Vector Machine (SVM) algorithms, as well as a traditional classification method (Logistic Regression - LR). Two different input datasets were tested for each algorithm: the full spectrum (ALL) provided by the sensor and the 28 spectral bands (SB). Tests with different sample sizes were also conducted to investigate the algorithms' ability to detect severity levels with a reduced sample size. Our findings indicate differences between the spectral curves for the severity levels assessed, which makes it possible to differentiate between healthy plants with low and high severity using hyperspectral sensing. SVM was the most accurate algorithm for classifying severity levels by using all the spectral information as input. This algorithm also provided high classification accuracy when using smaller leaf samples. This study reveals that hyperspectral sensing and the use of ML algorithms provide an accurate classification of different levels of Asian rust severity, and can be powerful tools for a more efficient disease monitoring process.

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Interactions between various microbial pathogens including viruses, bacteria, fungi, oomycetes, and their plant hosts have traditionally been the focus of phytopathology. In recent years, a significant and growing interest in the study of eukaryotic microorganisms not classified among fungi or oomycetes has emerged. Many of these protists establish complex interactions with photosynthetic hosts, and understanding these interactions is crucial in understanding the dynamics of these parasites within traditional and emerging types of farming, including marine aquaculture. Many phytopathogenic protists are biotrophs with complex polyphasic life cycles, which makes them difficult or impossible to culture, a fact reflected in a wide gap in the availability of comprehensive genomic data when compared to fungal and oomycete plant pathogens. Furthermore, our ability to use available genomic resources for these protists is limited by the broad taxonomic distance that these organisms span, which makes comparisons with other genomic datasets difficult. The current rapid progress in genomics and computational tools for the prediction of protein functions and interactions is revolutionizing the landscape in plant pathology. This is also opening novel possibilities, specifically for a deeper understanding of protist effectors. Tools like AlphaFold2 enable structure-based function prediction of effector candidates with divergent protein sequences. In turn, this allows us to ask better biological questions and, coupled with innovative experimental strategies, will lead into a new era of effector research, especially for protists, to expand our knowledge on these elusive pathogens and their interactions with photosynthetic hosts. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

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BACKGROUND: Septoria tritici blotch (STB), caused by the fungus Zymoseptoria tritici, is a foliar disease affecting wheat crops against which conventional control methods are not totally effective. During inter-epidemic periods the fungus survives in wheat residues left on the ground. In this study, we tested the potential of the collembolan Heteromurus nitidus - a springtail species present in field soils and known to interact with different fungal species - as a potential bioregulation agent of Z. tritici on wheat residues through a choice and consumption experiment. RESULTS: Springtails preferred inoculated fresh residues but did not have a preference between inoculated and uninoculated old residues. Springtails grazed on Z. tritici fruiting bodies and reduced pycnidiospore numbers by ten-fold compared to control inoculated fresh residues. Attraction toward fresh inoculated residues and pycnidiospore reduction support the hypothesis that Z. tritici is a food source for springtails. Heteromurus nitidus showed no preference between inoculated and uninoculated 18-month-old residues, probably because they no longer produced ascospores. CONCLUSION: Attraction towards fresh residues and spore reduction support our hypothesis that H. nitidus may contribute to the bioregulation of Z. tritici. Perspectives for field application would be determined by the ability of H. nitidus and Z. tritici to interact at key epidemiological stages. The impact of H. nitidus on the quantity of pathogen primary inoculum over time should be estimated using residues of intermediate age. This would help to identify the optimal period for enhancing the effectiveness of springtails as consumers of Z. tritici. © 2024 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

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Like other crops, different types of diseases affect apple trees. These diseases cause ugly cosmetic changes on the fruit and hence reduce its shelf life and value. To eliminate their impact, they need to be detected well in advance before any control measures are applied. The manual method of disease detection and subsequent classification has flaws as it involves manual scouting and analysis of the affected leaves through the naked eye. Besides, the manual method may result in wrong judgment as the knowledge of an expert limits the accuracy. Deep Learning Models have been successfully implemented for automated disease detection and classification. However, these models need massive datasets for training, testing and validation. This study proposes one such dataset that has been built indigenously by collecting images from the apple cultivation fields of Kashmir valley and subjecting it to cleaning and subsequent annotation by experts. Augmentation techniques have been used to enhance the size and quality of the dataset to prevent over-fitting of deep learning models.

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Introducción. Se ha informado que los hongos fitopatógenos representan las principales pérdidas económicas a nivel global en diferentes tipos de cultivos, entre los que se encuentran hortalizas como Brassica Oleracea var. capitata. Objetivos. Identificar los posibles hongos fitopatógenos asociados a Brassica, los signos y síntomas que estos pueden causar, su posible mecanismo de transmisión y comparar cualitativamente el crecimiento de estos en diferentes medios de cultivo. Materiales y métodos. Se aislaron hojas con y sin síntomas, junto con muestras de suelo. En cuanto a la microscopia se visualizaron las partes reproductivas de los hongos para su clasificación taxonómica. Resultados. Se aislaron un total de 17 morfotipos hasta nivel de género, siendo Botritis y Fusarium los que se encontraron con mayor presencia en las muestras de hojas asintomáticas y con síntomas. Para las muestras de suelo, el género más frecuente fue Penicillium. Conclusiones. De los tres medios evaluados, el agar extracto Sabouraud mostró los mejores resultados para el crecimiento de la mayoría de los hongos. Se establecieron mecanismos de transmisión probables para cada uno de los hongos encontrados en asociación a B. Oleracea var. capitata y se estableció que Botrytis sp. es el posible agente patógeno causante de la sintomatología observada en las muestras.

Introduction. Phytopathogenic fungi represent the main economic losses worldwide in different types of crops, including vegetables such as Brassica Oleracea var. capitata. Objectives. Identify the possible phytopathogenic fungi associated with Brassica, the signs and symptoms they may cause, their possible transmission mechanism, and to qualitatively compare their growth in different culture media. Materials and methods. Leaves with and without symptoms were isolated, together with soil samples to elaborate serial dilutions. As for microscopy, the reproductive parts of the fungi were visualized for taxonomic classification. Results. A total of 17 morphotypes were isolated up to genus level, being Botrytis and Fusarium, the genera found with the highest presence in asymptomatic and symptomatic leaf samples. For soil samples, the most frequent genus was Penicillium. Conclusions. Of the three media evaluated, Sabouraud's extract agar showed the best results for the growth of most fungi. Probable transmission mechanisms were established for each of the fungi found in association with B. oleracea var. capitata and Botrytis sp. was established as the possible pathogen causing the symptoms observed in the samples.

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Different fungal species of the Pleosporaceae family infect rice, causing similar symptoms. Reference genomic sequences are useful tools to study the evolution of these species and to develop accurate molecular diagnostic tools. Here, we report the complete genome sequences of Bipolaris bicolor, Curvularia hawaiiensis, Curvularia spicifera, and Exserohilum rostratum.

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Pulses have gained popularity over the past few decades due to their use as a source of protein in food and their favorable impact on soil fertility. Despite being essential to modern agriculture, these species face a number of challenges, such as agronomic crop management and threats from plant seed pathogens. This review's goal is to gather information on the distribution, symptomatology, biology, and host range of seedborne pathogens. Important diagnostic techniques are also discussed as a part of a successful process of seed health certification. Additionally, strategies for sustainable control are provided. Altogether, the data collected are suggested as basic criteria to set up a conscious laboratory approach.

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Nucleotide-binding and leucine-rich repeat receptors (NLRs) are a diverse family of intracellular immune receptors that play crucial roles in recognizing and responding to pathogen invasion in plants. This review discusses the overall model of NLR activation and provides an in-depth analysis of the different NLR domains, including N-terminal executioner domains, the nucleotide-binding oligomerization domain (NOD) module, and the leucine-rich repeat (LRR) domain. Understanding the structure-function relationship of these domains is essential for developing effective strategies to improve plant disease resistance and agricultural productivity.

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Two new actinobacteria, designated strains IBSBF 2807T and IBSBF 2953T, isolated from scab lesions on potato tubers grown in the southern Brazilian states of Rio Grande do Sul and Santa Catarina, respectively, were characterized and identified through a polyphasic approach. Phylogenetic analyses of 16S rRNA sequences revealed that these two strains belong to the genus Streptomyces. Multilocus sequence analysis using five concatenated genes, atpD, gyrB, recA, rpoB and trpB, allocated strains IBSBF 2807T and IBSBF 2953T in distinct branches of Streptomyces phytopathogenic strains. PCR-RFLP analysis of the atpD gene also confirmed that these strains differ from the type strains of Streptomyces associated with potato scab. The morphological, physiological and biochemical characterization, along with the overall genome-related index properties, indicated that these two strains could be distinguished from their closest phylogenetic relatives and each other. According to the data, IBSBF 2807T and IBSBF 2953T represent two new Streptomyces species related to potato scab. The proposed names for these strains are Streptomyces hilarionis sp. nov. (IBSBF 2807T=CBMAI 2674T=ICMP 24297T=MUM 22.66T) and Streptomyces hayashii sp. nov (IBSBF 2953T=CBMAI 2675T=ICMP 24301T=MUM 22.68T).

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Targeted genome editing technologies are becoming the most important and widely used genetic tools in studies of phytopathology. The "clustered regularly interspaced short palindromic repeats (CRISPR)" and its accompanying proteins (Cas) have been first identified as a natural system associated with the adaptive immunity of prokaryotes that have been successfully used in various genome-editing techniques because of its flexibility, simplicity, and high efficiency in recent years. In this review, we have provided a general idea about different CRISPR/Cas systems and their uses in phytopathology. This review focuses on the benefits of knock-down technologies for targeting important genes involved in the susceptibility and gaining resistance against viral, bacterial, and fungal pathogens by targeting the negative regulators of defense pathways of hosts in crop plants via different CRISPR/Cas systems. Moreover, the possible strategies to employ CRISPR/Cas system for improving pathogen resistance in plants and studying plant-pathogen interactions have been discussed.

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The fungus Ustilaginoidea virens, the causative agent of false smut in rice (Oryza sativa L.), is responsible for one of the severe grain diseases that lead to significant losses worldwide. In this research, microscopic and proteomic analyses were performed by comparing U. virens infected and non-infected grains of the susceptible and resistant rice varieties to provide insights into the molecular and ultrastructural factors involved in false smut formation. Prominent differentially expressed peptide bands and spots were detected due to false smut formation as revealed by sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional gel electrophoresis (2-DE) SDS-PAGE profiles and were identified using liquid chromatography-mass spectrometry (LC-MS/MS). The proteins identified from the resistant grains were involved in diverse biological processes such as cell redox homeostasis, energy, stress tolerance, enzymatic activities, and metabolic pathways. It was found that U. virens produces diverse degrading enzymes such as ß-1, 3-endoglucanase, subtilisin-like protease, putative nuclease S1, transaldolase, putative palmitoyl-protein thioesterase, adenosine kinase, and DNase 1 that could discretely alter the host morphophysiology resulting in false smut. The fungus also produced superoxide dismutase, small secreted proteins, and peroxidases during the smut formation. This study revealed that the dimension of rice grain spikes, their elemental composition, moisture content, and the specific peptides produced by the grains and the fungi U. virens play a vital role in the formation of false smut.

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As available tools for crop disease management are scarce, new, effective, and eco-friendly solutions are needed. So, this study aimed at assessing the antibacterial activity of a dried leaf Eucalyptus globulus Labill. aqueous extract (DLE) against Pseudomonas syringae pv. tomato (Pst), Xanthomonas euvesicatoria (Xeu), and Clavibacter michiganensis michiganensis (Cmm). For this, the inhibitory activity of different concentrations of DLE (0, 15, 30, 45, 60, 75, 90, 105, 120, 135, and 250 g L-1) was monitored against the type strains of Pst, Xeu, and Cmm through the obtention of their growth curves. After 48 h, results showed that the pathogen growth was strongly inhibited by DLE, with Xeu the most susceptible species (15 g L-1 MIC and IC50), followed by Pst (30 g L-1 MIC and IC50), and Cmm (45 and 35 g L-1 MIC and IC50, respectively). Additionally, using the resazurin assay, it was possible to verify that DLE considerably impaired cell viability by more than 86%, 85%, and 69% after Pst, Xeu, and Cmm were incubated with DLE concentrations equal to or higher than their MIC, respectively. However, only the treatment with DLE at 120 g L-1 did not induce any hypersensitive response in all pathogens when treated bacterial suspensions were infiltrated onto tobacco leaves. Overall, DLE can represent a great strategy for the prophylactic treatment of tomato-associated bacterial diseases or reduce the application of environmentally toxic approaches.

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Due to an inevitable disadvantage of chemical or physical synthesis routes, biosynthesis approach to nanoparticles, especially metallic oxide is attractive nowadays. Metallic oxides nanoparticles present a new approach to the control of plant pathogens. ZnO nanoparticles (ZNPs) have very important role in phytopathology. In current study, biosynthesized ZNPs were tested against two devastating bacterial pathogens including Xanthomonas campestris pv. vesicatoria and Ralstonia solanacearum causing bacterial leaf spot and bacterial wilt in tomato. ZNPs were produced using a new extract from the plant Picea smithiana using an environmentally friendly, cost-effective and simple procedure. Zinc acetate was added to P. smithiana extract, stirred and heated to 200 °C. The white precipitation at the bottom were clear indication of synthesis of nanoparticles, which were further dried by subjecting them at 450 °C. X-ray diffraction pattern determined that the ZNPs had a crystallite size of about 26 nm, Fourier transform infrared spectroscopy indicated a peak between 450 and 550 cm-1 and the particle size estimated by dynamic light scattering was about 25 nm on average. Scanning electron microscopic analysis indicated that the particles were hexagonal in shape 31 nm in diameter. Antibacterial tests showed ZNPs synthesized by P. smithiana resulted in clear inhibition zones of 20.1 ± 1.5 and 18.9 ± 1.5 mm and 44.74 and 45.63% reduction in disease severity and 78.40 and 80.91% reduction in disease incidence in X. compestris pv. vesicatoria and R. solanacearum respectively at concentration of 100 µg/ml. Our findings reveal that the concentration of ZNPs was important for their efficient antibacterial activity. Overall, the biosynthesized ZNPs have been found to have effective antimicrobial activities against bacterial wilt and bacterial leaf spot in tomato.

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Aphids and Pseudomonas syringae are a permanent challenge for agriculture, causing severe losses to the crop industry worldwide. Despite the obvious phylogenetic distance between them, both have become predominant colonizers of the plant kingdom. In this study, we reviewed three key steps of spread and colonization that aphids and P. syringae have mastered to successfully colonize the phyllosphere. These steps involve (i) plant-to-plant movement for locating new nutritional sources, (ii) disruption and modification of the apoplast to facilitate nutrient acquisition, and (iii) suppression of host defenses through effector proteins. In addition, we will provide insights about the direct interaction between aphids and P. syringae and how this yet underrated phenomenon could bring new ecological implications for both organisms beyond their pathogenicity.

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Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. We investigated the genetic diversity and reproductive biology of Colletotrichum graminicola isolates which infect maize by sequencing the genomes of 108 isolates collected from 14 countries using restriction site-associated DNA sequencing (RAD-seq) and whole-genome sequencing (WGS). Clustering analyses based on single-nucleotide polymorphisms revealed three genetic groups delimited by continental origin, compatible with short-dispersal of the pathogen and geographic subdivision. Intra- and intercontinental migration was observed between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality, evidence of genetic recombination, and high phenotypic diversity were detected. We show evidence that, although it is rare (possibly due to losses of sexual reproduction- and meiosis-associated genes) C. graminicola can undergo sexual recombination. Our results support the hypotheses that intra- and intercontinental pathogen migration and genetic recombination have great impacts on the C. graminicola population structure. IMPORTANCE Plant pathogens cause significant reductions in yield and crop quality and cause enormous economic losses worldwide. Reducing these losses provides an obvious strategy to increase food production without further degrading natural ecosystems; however, this requires knowledge of the biology and evolution of the pathogens in agroecosystems. We employed a population genomics approach to investigate the genetic diversity and reproductive biology of the maize anthracnose pathogen (Colletotrichum graminicola) in 14 countries. We found that the populations are correlated with their geographical origin and that migration between countries is ongoing, possibly caused by the movement of infected plant material. This result has direct implications for disease management because migration can cause the movement of more virulent and/or fungicide-resistant genotypes. We conclude that genetic recombination is frequent (in contrast to the traditional view of C. graminicola being mainly asexual), which strongly impacts control measures and breeding programs aimed at controlling this disease.

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Abstract Colletotrichum is one of the most economically important fungal genera, which affects a wide range of hosts, specifically tropical and subtropical crops. Thus far, there have been several records of mycovirus infection in Colletotrichum spp., primarily by viruses of the Partitiviridae family. There have also been records of infections by mycoviruses of the Chrysoviridae family. Mycoviruses are (+)ssRNA and dsRNA genome viruses, which may or may not be enveloped. To date, no mycovirus with a DNA genome has been isolated from Colletotrichum spp. Typically, mycoviruses cause latent infections, although hypo- and hypervirulence have also been reported in Colletotrichum spp. In addition to its effects on pathogenic behavior, mycovirus infection can lead to important physiological changes, such as altered morphological characteristics, reduced vegetative growth, and suppressed conidia production. Therefore, research on mycoviruses infecting phytopathogenic fungi can help develop alternative methods to chemical control, which can cause irreversible damage to humans and the environment. From an agricultural perspective, mycoviruses can contribute to sustainable agriculture as biological control agents via changes in fungal physiology, ultimately resulting in the total loss of or reduction in the virulence of these pathogens.

Resumo Colletotrichum é um dos gêneros fúngicos mais importantes economicamente, afetando uma ampla gama de hospedeiros, especialmente em cultivos tropicais e subtropicais. Atualmente já existem diversos registros de infecção por micovírus em Colletotrichum spp., sendo a maioria dos já identificados classificados na família Partitiviridae. Ocorrem registros também de micovírus pertencentes à família Chrysoviridae. Compreendem vírus de genoma de (+)ssRNA e dsRNA que podem ser ou não envelopados. Ainda não foram identificados micovírus com genoma de DNA isolados de Colletotrichum. A infecção por micovírus pode ocorrer de forma latente, mas já foi observado em Colletotrichum spp. o fenômeno de hipo e hipervirulência. Além de influenciar no comportamento patogênico, a infecção pode causar mudanças fisiológicas importantes como alterações das características morfológicas, redução do crescimento vegetativo e redução na produção de conídios. O estudo com micovírus em fungos fitopatogênicos traz uma alternativa ao controle químico que é um método capaz de causar danos irreversíveis ao homem e o meio ambiente. Sob a perspectiva agrícola, os micovírus podem contribuir para agricultura sustentável como agentes de controle biológico. Isso porque obsevam-se mudanças importantes na fisiologia fúngica resultando na perda total ou redução da virulência desses patógenos.

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Colletotrichum is one of the most economically important fungal genera, which affects a wide range of hosts, specifically tropical and subtropical crops. Thus far, there have been several records of mycovirus infection in Colletotrichum spp., primarily by viruses of the Partitiviridae family. There have also been records of infections by mycoviruses of the Chrysoviridae family. Mycoviruses are (+)ssRNA and dsRNA genome viruses, which may or may not be enveloped. To date, no mycovirus with a DNA genome has been isolated from Colletotrichum spp. Typically, mycoviruses cause latent infections, although hypo- and hypervirulence have also been reported in Colletotrichum spp. In addition to its effects on pathogenic behavior, mycovirus infection can lead to important physiological changes, such as altered morphological characteristics, reduced vegetative growth, and suppressed conidia production. Therefore, research on mycoviruses infecting phytopathogenic fungi can help develop alternative methods to chemical control, which can cause irreversible damage to humans and the environment. From an agricultural perspective, mycoviruses can contribute to sustainable agriculture as biological control agents via changes in fungal physiology, ultimately resulting in the total loss of or reduction in the virulence of these pathogens.

Colletotrichum é um dos gêneros fúngicos mais importantes economicamente, afetando uma ampla gama de hospedeiros, especialmente em cultivos tropicais e subtropicais. Atualmente já existem diversos registros de infecção por micovírus em Colletotrichum spp., sendo a maioria dos já identificados classificados na família Partitiviridae. Ocorrem registros também de micovírus pertencentes à família Chrysoviridae. Compreendem vírus de genoma de (+)ssRNA e dsRNA que podem ser ou não envelopados. Ainda não foram identificados micovírus com genoma de DNA isolados de Colletotrichum. A infecção por micovírus pode ocorrer de forma latente, mas já foi observado em Colletotrichum spp. o fenômeno de hipo e hipervirulência. Além de influenciar no comportamento patogênico, a infecção pode causar mudanças fisiológicas importantes como alterações das características morfológicas, redução do crescimento vegetativo e redução na produção de conídios. O estudo com micovírus em fungos fitopatogênicos traz uma alternativa ao controle químico que é um método capaz de causar danos irreversíveis ao homem e o meio ambiente. Sob a perspectiva agrícola, os micovírus podem contribuir para agricultura sustentável como agentes de controle biológico. Isso porque obsevam-se mudanças importantes na fisiologia fúngica resultando na perda total ou redução da virulência desses patógenos.

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Abstract Colletotrichum is one of the most economically important fungal genera, which affects a wide range of hosts, specifically tropical and subtropical crops. Thus far, there have been several records of mycovirus infection in Colletotrichum spp., primarily by viruses of the Partitiviridae family. There have also been records of infections by mycoviruses of the Chrysoviridae family. Mycoviruses are (+)ssRNA and dsRNA genome viruses, which may or may not be enveloped. To date, no mycovirus with a DNA genome has been isolated from Colletotrichum spp. Typically, mycoviruses cause latent infections, although hypo- and hypervirulence have also been reported in Colletotrichum spp. In addition to its effects on pathogenic behavior, mycovirus infection can lead to important physiological changes, such as altered morphological characteristics, reduced vegetative growth, and suppressed conidia production. Therefore, research on mycoviruses infecting phytopathogenic fungi can help develop alternative methods to chemical control, which can cause irreversible damage to humans and the environment. From an agricultural perspective, mycoviruses can contribute to sustainable agriculture as biological control agents via changes in fungal physiology, ultimately resulting in the total loss of or reduction in the virulence of these pathogens.

Resumo Colletotrichum é um dos gêneros fúngicos mais importantes economicamente, afetando uma ampla gama de hospedeiros, especialmente em cultivos tropicais e subtropicais. Atualmente já existem diversos registros de infecção por micovírus em Colletotrichum spp., sendo a maioria dos já identificados classificados na família Partitiviridae. Ocorrem registros também de micovírus pertencentes à família Chrysoviridae. Compreendem vírus de genoma de (+)ssRNA e dsRNA que podem ser ou não envelopados. Ainda não foram identificados micovírus com genoma de DNA isolados de Colletotrichum. A infecção por micovírus pode ocorrer de forma latente, mas já foi observado em Colletotrichum spp. o fenômeno de hipo e hipervirulência. Além de influenciar no comportamento patogênico, a infecção pode causar mudanças fisiológicas importantes como alterações das características morfológicas, redução do crescimento vegetativo e redução na produção de conídios. O estudo com micovírus em fungos fitopatogênicos traz uma alternativa ao controle químico que é um método capaz de causar danos irreversíveis ao homem e o meio ambiente. Sob a perspectiva agrícola, os micovírus podem contribuir para agricultura sustentável como agentes de controle biológico. Isso porque obsevam-se mudanças importantes na fisiologia fúngica resultando na perda total ou redução da virulência desses patógenos.

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High-throughput sequencing (HTS) methods are transforming our capacity to detect pathogens and perform disease diagnosis. Although sequencing advances have enabled accessible and point-of-care HTS, data analysis pipelines have yet to provide robust tools for precise and certain diagnosis, particularly in cases of low sequencing coverage. Lack of standardized metrics and harmonized detection thresholds confound the problem further, impeding the adoption and implementation of these solutions in real-world applications. In this work, we tackle these issues and propose biologically-informed viral genome assembly coverage as a method to improve diagnostic certainty. We use the identification of viral replicases, an essential function of viral life cycles, to define genome coverage thresholds in which biological functions can be described. We validate the analysis pipeline, Viroscope, using field samples, synthetic and published datasets, and demonstrate that it provides sensitive and specific viral detection. Furthermore, we developed Viroscope.io a web-service to provide on-demand HTS data viral diagnosis to facilitate adoption and implementation by phytosanitary agencies to enable precise viral diagnosis.