Plant Virology Research Articles

Flexible spandrels of the global plant virome: Proteomic-wide evolutionary patterns of structural intrinsic protein disorder elucidate modulation at the functional virus-host interplay.

Intrinsically disordered proteins and regions (IDPs/IDRs) make up a large part of viral proteomes, but their real prevalence across the global plant virome is still murky, partly because of their massive diversity. Here, we propose an evolutionary quantitative proteomic approach to foray into genomic signatures that are preserved in the amino acid sequences of orthologous IDRs. Markedly, we found that relatively abundant IDP varies substantially in viral species among and within plant virus families, including according to genome size, partition or replication strategies. We also demonstrate that most encoded proteomic modules of the plant virome contain multiple disordered features that are phylogenomically preserved, and can be correlated to genomic, bio-physical and evolutionary strategies. Furthermore, our focused interactome-wide analysis highlights lines of evidence indicating that various IDPs with similar evolutionary signatures modulate viral multifunctionality. Moreover, estimated fractions of IDR in the vicinity of pivotal evolutionary structural domains embedded in interaction modules are strongly enriched with affinity binding functional annotations and relate to vector-borne virus transmission modes. Importantly, molecular recognition features (MoRFs) are abundantly widespread in IDRs of viral hallmark modules and their binding partners. Finally, we propose a coarse-grained conceptual framework in which evolutionary proteome-wide IDP/IDRs patterns can be, rather, reliably exploited to elucidate their foundational fine-tuning role in plant virus transmission mechanisms. While opening unexplored avenues for consistently predicting virus-host functions for many new or uncharacterized viruses based on their proteomic repertoire, other considerations advocating further structural IDP research in Plant Virology are thoroughly discussed in light of viral modular evolution.

A BRIEF DESCRIPTION OF TOMATO LEAF CURL VIRUS AND ITS MANAGEMENT

The tomato crop is affected by various biotic and abiotic factors. Among the biotic factors, Tomato Leaf Curl Virus (TLCV) is one of the most devastating viruses of tomato. The virus belongs to Begomovirus and family Gemniniviridae. The genome of virus is single-stranded-DNA. It is naturally transmitted through whitefly (Bemisia tabaci). The virus is responsible for causing severe economic losses up to 80% in tomato crop-growing regions and continuously threatening the tomato crops. The increasing severity of TLCV has compelled plant virologists to develop accurate detection and identification of the virus. TLCV is responsible for certain biochemical changes and considerably affecting the plant growth. Tomato Leaf Curl Virus is significantly influenced physiological parameters and metabolic activities of all tomato varieties. The biochemical changes of cellular components are caused due to morphological deviation of infected virus plants, and symptoms expressed by the plants can determine the magnitude of the vegetable losses. It is evident from the previous reports, that nutrients were effective in reducing TLCV from a tomato plant. Moreover, the usage of resistant varieties and controlling of whitefly population and management of TLCV by different nutrients are some of the economical and recommendable ways to manage TLCV. Among the organic management strategies, the compost is also considered best in suppressing disease severity. Moreover, epidemiology plays a vital role in the spread and progress of the disease. Keeping in view the importance of TLCV and its effects on tomato crop, the present review will highlight the etiology, physiology and management of TLCV.

Publishing goes on despite the virus—What is new for 2021

Publishing goes on despite the virus—What is new for 2021

Walking Together: Cross-Protection, Genome Conservation, and the Replication Machinery of Citrus tristeza virus.

“Cross-protection”, a nearly 100 years-old virological term, is suggested to be changed to “close protection”. Evidence for the need of such change has accumulated over the past six decades from the laboratory experiments and field tests conducted by plant pathologists and plant virologists working with different plant viruses, and, in particular, from research on Citrus tristeza virus (CTV). A direct confirmation of such close protection came with the finding that “pre-immunization” of citrus plants with the variants of the T36 strain of CTV but not with variants of other virus strains was providing protection against a fluorescent protein-tagged T36-based recombinant virus variant. Under natural conditions close protection is functional and is closely associated both with the conservation of the CTV genome sequence and prevention of superinfection by closely similar isolates. It is suggested that the mechanism is primarily directed to prevent the danger of virus population collapse that could be expected to result through quasispecies divergence of large RNA genomes of the CTV variants continuously replicating within long-living and highly voluminous fruit trees. This review article provides an overview of the CTV cross-protection research, along with a discussion of the phenomenon in the context of the CTV biology and genetics.

Historical virus isolate collections: An invaluable resource connecting plant virology’s pre‐sequencing and post‐sequencing eras

AbstractMany laboratories maintain historical collections of preserved plant virus isolates that store a wealth of untapped data, including original type isolates, studied in the pre‐sequencing era. Currently, many recently recognized virus species exist with no supporting reference sequences. Also, many virus sequences appear new when compared to available sequences, but, on sequencing pre‐sequencing era isolates, they may coincide. Such linkages allow access to data from previously determined biological and other parameters from pre‐sequencing era studies. These linkages are increasingly being found using high‐throughput sequencing, helping clarify virus taxonomy and improving understanding of virus ecology and evolution. Thus, mistakes can be avoided in naming viruses and in combining or separating them, as well as enabling identification of unknown viruses preserved long ago. With well‐established viruses, success in dating and other evolutionary studies, and discovery of changes in regional virus populations, both depend upon comparisons between recent and old isolate sequences covering the greatest possible time periods. Such studies help reveal the extent that human activities have influenced virus evolution and changed virus populations on a global scale. Sequencing virus genomes from herbarium specimens, archaeological specimens, or living plant collections can provide complementary data. By bringing context to newly detected viruses and supporting plant pest risk analyses, linking new virus discoveries to previously generated disease symptom, host range, virus transmission, and geographical distribution data has important implications for plant health regulation. Also, historical isolates can provide an invaluable resource facilitating biosecurity investigations involving virus introductions, entry pathways, and baseline surveillance.

Population Genomics of Plant Viruses: The Ecology and Evolution of Virus Emergence.

The genomics era has revolutionized studies of adaptive evolution by monitoring large numbers of loci throughout the genomes of many individuals. Ideally, the investigation of emergence in plant viruses requires examining the population dynamics of both virus and host, their interactions with each other, with other organisms and the abiotic environment. Genetic mechanisms that affect demographic processes are now being studied with high-throughput technologies, traditional genetics methods, and new computational tools for big-data. In this review, we discuss the utility of these approaches to monitor and detect changes in virus populations within cells and individuals, and over wider areas across species and communities of ecosystems. The advent of genomics in virology has fostered a multidisciplinary approach to tackling disease risk. The ability to make sense of the information now generated in this integrated setting is by far the most substantial obstacle to the ultimate goal of plant virology to minimize the threats to food security posed by disease. To achieve this goal, it is imperative to understand and forecast how populations respond to future changes in complex natural systems.

High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later.

High-throughput sequencing (HTS) application in the field of plant virology started in 2009 and has proven very successful for virus discovery and detection of viruses already known. Plant virology is still a developing science in most of Africa; the number of HTS-related studies published in the scientific literature has been increasing over the years as a result of successful collaborations. Studies using HTS to identify plant-infecting viruses have been conducted in 20 African countries, of which Kenya, South Africa and Tanzania share the most published papers. At least 29 host plants, including various agricultural economically important crops, ornamentals and medicinal plants, have been used in viromics analyses and have resulted in the detection of previously known viruses and novel ones from almost any host. Knowing that the effectiveness of any management program requires knowledge on the types, distribution, incidence, and genetic of the virus-causing disease, integrating HTS and efficient bioinformatics tools in plant virology research projects conducted in Africa is a matter of the utmost importance towards achieving and maintaining sustainable food security.

Real-time tracking of Tomato brown rugose fruit virus (ToBRFV) outbreaks in the Netherlands using Nextstrain.

Tomato brown rugose fruit virus (ToBRFV) is a Tobamovirus that was first observed in 2014 and 2015 on tomato plants in Israel and Jordan respectively. Since the first description, the virus has been reported from all continents except Oceania and Antarctica, and has been found infecting both tomato and pepper crops. In October 2019, the Dutch National Plant Protection Organization received a ToBRFV infected tomato sample as part of a generic survey targeting tomato pests. Presence of the virus was verified using Illumina sequencing. A follow-up survey was initiated to determine the extent of ToBRFV presence in the Dutch tomato horticulture and identify possible linkages between ToBRFV genotypes, companies and epidemiological traits. Nextstrain was used to visualize these potential connections. By November 2019, 68 companies had been visited of which 17 companies were found to be infected. The 50 ToBRFV genomes from these outbreak locations group in three main clusters, which are hypothesized to represent three original sources. No correlation was found between genotypes, companies and epidemiological traits, and the source(s) of the Dutch ToBRFV outbreak remain unknown. This paper describes a Nextstrain build containing ToBRFV genomes up to and including November 2019. Sharing data with this interactive online tool will enable the plant virology field to better understand and communicate the diversity and spread of this new virus. Organizations are invited to share data or materials for inclusion in the Nextstrain build, which can be accessed at https://nextstrain.nrcnvwa.nl/ToBRFV/20191231.

Emerging Molecular Links Between Plant Photomorphogenesis and Virus Resistance.

Photomorphogenesis refers to photoreceptor-mediated morphological changes in plant development that are triggered by light. Multiple photoreceptors and transcription factors (TFs) are involved in the molecular regulation of photomorphogenesis. Likewise, light can also modulate the outcome of plant–virus interactions since both photosynthesis and many viral infection events occur in the chloroplast. Despite the apparent association between photosynthesis and virus infection, little is known about whether there are also interplays between photomorphogenesis and plant virus resistance. Recent research suggests that plant–virus interactions are potentially regulated by several photoreceptors and photomorphogenesis regulators, including phytochromes A and B (PHYA and PHYB), cryptochromes 2 (CRY2), phototropin 2 (PHOT2), the photomorphogenesis repressor constitutive photomorphogenesis 1 (COP1), the NAM, ATAF, and CUC (NAC)-family TF ATAF2, the Aux/IAA protein phytochrome-associated protein 1 (PAP1), the homeodomain-leucine zipper (HD-Zip) TF HAT1, and the core circadian clock component circadian clock associated 1 (CCA1). Particularly, the plant growth promoting brassinosteroid (BR) hormones play critical roles in integrating the regulatory pathways of plant photomorphogenesis and viral defense. Here, we summarize the current understanding of molecular mechanisms linking plant photomorphogenesis and defense against viruses, which represents an emerging interdisciplinary research topic in both molecular plant biology and virology.

RT-PCR Based Cloning and Sequencing of Potato Leaf Roll Virus-Coat Protein (PLRV-CP) Gene for Characterization as a Bangladeshi PLRV Isolate and Its Phylogenetic Analysis

An experiment was conducted in Molecular Biology and Plant Virology Laboratory under the Department of Plant Pathology, Sher-e-Bangla Agricultural University, Dhaka-1207, Bangladesh. Total RNA was extracted from Potato leaf roll virus (PLRV) positive leaves and complementary DNA (cDNA) were synthesized from total RNA. Reverse transcriptase polymerase chain reaction (RT-PCR) based detection conditions were optimized by using coat protein (CP) gene specific primers. In PCR amplification cDNA and in nucleotide sequencing PCR product was used as a template. A 346 bp amplicon of PLRV- CP gene was amplified and amplified gene region was sequenced. The expected nucleotide sequence of amplified PLRV-CP gene showed 95 to 98% homology when compared with the isolates sequences reported in Gene Bank database. This explored novel PLRV-CP gene was characterized as a PLRV Bangladeshi isolate (Accession number, Bankit 2274496, MN605963). PLRV-CP gene protein modeling was carried out using Expert Protein Analysis System (ExPaSy), DNASTAR’s protein tools server used for 3D protein modeling. Phylogenetic analysis was also carried out, the tree was made by using MEGA 4.0 software and maximum parsimony method was selected to construct phylogenetic tree. The RT-PCR based molecular technique optimized in this study, would be a useful for early detection, epidemiological studies of PLRV as well as in seed tubers certification program and the novel hyper variable sequenced region of PLRV-CP gene will be useful in pathogen derived resistance breeding program against the PLRV local strain.

Deep Roots and Splendid Boughs of the Global Plant Virome.

Land plants host a vast and diverse virome that is dominated by RNA viruses, with major additional contributions from reverse-transcribing and single-stranded (ss) DNA viruses. Here, we introduce the recently adopted comprehensive taxonomy of viruses based on phylogenomic analyses, as applied to the plant virome. We further trace the evolutionary ancestry of distinct plant virus lineages to primordial genetic mobile elements. We discuss the growing evidence of the pivotal role of horizontal virus transfer from invertebrates to plants during the terrestrialization of these organisms, which was enabled by the evolution of close ecological associations between these diverse organisms. It is our hope that the emerging big picture of the formation and global architecture of the plant virome will be of broad interest to plant biologists and virologists alike and will stimulate ever deeper inquiry into the fascinating field of virus-plant coevolution.

Reconsidering causal association in plant virology

Reconsidering causal association in plant virology

30th Brazilian Society for Virology 2019 Annual Meeting-Cuiabá, Mato Grosso, Brazil.

The 30th meeting of the Brazilian Society for Virology (SBV) was held, for the first time in its 30 years of existence, in Cuiabá, the capital of Mato Grosso State, Central Western Brazil, a tropical region between the three richest biomes in the world: Amazon Florest, Cerrado and Pantanal. In recent years, the field of virology has been built in the State. The aim of this report is to support participants and virologists to receive the most up-to-date information about the meeting, which occurred from 16 to 19 October 2019. National and international speakers gave SBV the opportunity to learn about their experience on their virology fields, sharing recent scientific findings, compiling conferences, round table presentations and work presentations in oral and poster sessions. The meeting held over 300 attendants, who were also involved on oral and poster presentations, showing a great variety of recent unpublished studies on environmental, basic, animal, human, plant and invertebrate virology. In addition, SBV offered the Helio Gelli Pereira award for the best research studies in each field presented during the meeting. The 30th meeting of SBV was very productive and has also encouraged scientific partnership and collaboration among virologists worldwide.

Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology.

In the last decades, the evolution of molecular diagnosis methods has generated different advanced tools, like loop-mediated isothermal amplification (LAMP). Currently, it is a well-established technique, applied in different fields, such as the medicine, agriculture, and food industries, owing to its simplicity, specificity, rapidity, and low-cost efforts. LAMP is a nucleic acid amplification under isothermal conditions, which is highly compatible with point-of-care (POC) analysis and has the potential to improve the diagnosis in plant protection. The great advantages of LAMP have led to several upgrades in order to implement the technique. In this review, the authors provide an overview reporting in detail the different LAMP steps, focusing on designing and main characteristics of the primer set, different methods of result visualization, evolution and different application fields, reporting in detail LAMP application in plant virology, and the main advantages of the use of this technique.

Plant virology: Alive and kicking!

Plant virology: Alive and kicking!

John Peter Carr.

John Peter Carr.

First Report of Cotton Leafroll Dwarf Virus Infecting Cotton (Gossypium hirsutum) in Kansas

In the United States, cotton leafroll dwarf disease, caused by cotton leafroll dwarf virus (CLRDV, Polerovirus, Luteoviridae), was first reported from cotton (Gossypium hirsutum L.) fields in Alabama (Avelar et al. 2019) and later Mississippi (Aboughanem-Sabanadzovic et al. 2019) and Georgia (Tabassum et al. 2019). During a survey of cotton fields in Barber County, Kansas, in the 2019 growing season, cotton plants showed virus-like symptoms including leaf yellowing, discoloration, reddening, and short internodes with reduced or small boll sets. Disease incidence based on virus-like symptoms was ∼1 to 15% depending on the affected fields. Eleven symptomatic and seven apparently asymptomatic leaf samples from 18 independent cotton plants (cv. PhytoGen 210) were collected in commercial cotton fields and tested for the presence of the virus in the Plant Virology Lab at the University of Tulsa, Oklahoma. Total RNA was extracted from all 18 samples by the Spectrum Plant Total RNA Kit (Sigma-Aldrich) and was synthesized into complementary DNA (cDNA) using the Superscript IV Reverse Transcription Kit (ThermoFisher Scientific) according to the manufacturer’s instructions. The polymerase chain reaction (PCR) was performed with primers CLRDV3675F and Pol3982R as described previously (Sharman et al. 2015) to amplify a specific PCR product of 310 bp of the ORF3-5 fragment of the CLRDV. cDNA of CLRDV for the specific fragment was obtained from the Plant Disease Diagnostic Lab at Auburn University and was used as a positive control. A PCR product of the predicted size (310 bp) was obtained from seven symptomatic cotton samples and the positive control, whereas no bands were present in four symptomatic and seven asymptomatic samples, as well as the PCR negative control. RT-PCR was repeated twice with these samples and obtained the same results as above. The PCR products of all positive samples were directly sequenced, and sequence comparison showed 97 to 99% identity with the CLRDV-Alabama isolate (MN071395). To further confirm the presence of CLRDV in these samples, two additional pair of primers—AL674F and AL1407R for partial P0/P1 (Avelar et al. 2019) and RdRpF2 and RdRpR1 for partial RdRp (Aboughanem-Sabanadzovic et al. 2019)—were used to amplify the 694- and 770-bp product of the CLRDV genome, respectively. The expected PCR bands were obtained from all seven symptomatic cotton plants but none from asymptomatic samples. PCR products of 694 and 770 bp from two samples (KS-7 and KS-10 isolates) were purified, cloned into pGEM-T Easy vector (Promega), and transformed into Escherichia coli DH5α cells (New England Bio Labs). At least three clones were sequenced using the Applied Biosystem 3130 Genetic Analyzer at the University of Tulsa. Sequences obtained in this study for partial P0/P1and RdRP genes of KS-7 and KS-10 isolates were deposited in GenBank (MN809925 to 28). Nucleotide sequence comparisons and BLASTn analysis of partial P1/P0 (MN809927 to 28) showed 98 to 99% identity with corresponding sequences of Alabama isolates (MH883237 and MN071395) and 92 to 93% identity with typical and 91 to 92% identity with atypical CLRDV isolates from Argentina and Brazil. Similarly, partial RdRP genes (MN809925 to 26) showed 94 to 98% identity with the corresponding sequences of available CLRDV isolates from Mississippi (MK512759, MK512762 to 64) and Alabama (MN071395) and 93 to 96% identity with typical and 92 to 95% identity with atypical CLRDV isolates from Argentina and Brazil. This is the first report of CLRDV infection and occurrence in cotton fields in Kansas. Cotton acreage in Kansas has increased since 2018 by 40% (NASS 2018), and the presence of CLRDV could be a detrimental disease for cotton production. Therefore, further studies are needed, including other cotton-growing counties in Kansas, to determine the distribution, epidemiology, vector transmission, and population structure of this virus, which would be helpful in the management of CLRDV.

Biolistic Approach for Transient Gene Expression Studies in Plants.

Since its inception in the late 1980s, the delivery of exogenous nucleic acids into living cells via high-velocity microprojectiles (biolistic, or microparticle bombardment) has been an invaluable tool for both agricultural and fundamental plant research. Here, we review the technical aspects and the major applications of the biolistic method for studies involving transient gene expression in plant cells. These studies cover multiple areas of plant research, including gene expression, protein subcellular localization and cell-to-cell movement, plant virology, silencing, and the more recently developed targeted genome editing via transient expression of customized endonucleases.

Fundamental Aspects of Plant Viruses-An Overview on Focus Issue Articles.

Given the importance of and rapid research progress in plant virology in recent years, this Focus Issue broadly emphasizes advances in fundamental aspects of virus infection cycles and epidemiology. This Focus Issue comprises three review articles and 18 research articles. The research articles cover broad research areas on the identification of novel viruses, the development of detection methods, reverse genetics systems and functional genomics for plant viruses, vector and seed transmission studies, viral population studies, virus-virus interactions and their effect on vector transmission, and management strategies of viral diseases. The three review articles discuss recent developments in application of prokaryotic clustered regularly interspaced short palindromic repeats/CRISPR-associated genes (CRISPR/Cas) technology for plant virus resistance, mixed viral infections and their role in disease synergism and cross-protection, and viral transmission by whiteflies. The following briefly summarizes the articles appearing in this Focus Issue.

CRISPR Applications in Plant Virology: Virus Resistance and Beyond.

Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated genes (Cas) is a prokaryotic adaptive immune system which has been reprogrammed into a precise, simple, and efficient gene targeting technology. This emerging technology is revolutionizing various areas of life sciences, medicine, and biotechnology and has raised significant interest among plant biologists, both in basic science and in plant protection and breeding. In this review, we describe the basic principles of CRISPR/Cas systems, and how they can be deployed to model plants and crops for the control, monitoring, and study of the mechanistic aspects of plant virus infections. We discuss how Cas endonucleases can be used to engineer plant virus resistance by directly targeting viral DNA or RNA, as well as how they can inactivate host susceptibility genes. Additionally, other applications of CRISPR/Cas in plant virology such as virus diagnostics and imaging are reviewed. The review also provides a systemic comparison between CRISPR/Cas technology and RNA interference approaches, the latter of which has also been used for development of virus-resistant plants. Finally, we outline challenges to be solved before CRISPR/Cas can produce virus-resistant crop plants which can be marketed.