First Report of Southern tomato virus on Tomatoes in Southwest France

Localization of southern tomato virus (STV) in tomato tissues

Southern tomato virus (STV) is a dsRNA virus, which belongs to the newly formed Amalgavirus genus of the Amalgaviridae family. Currently there is no report regarding the presence of STV in tomato tissues. In this study, we performed in situ hybridization to examine the distribution of STV in host tissues. STV was found in the leaves, stems, seeds, shoot apexes and root tips of tomato and localized in the cortex tissue, vascular tissues, pith, seed coat, endosperm, cotyledon (including inner cotyledons and outer cotyledons), hypocotyls and radicles of infected tomato tissues. In addition, STV was detected in the apical part of the stems and roots for the first time. This indicates that STV is a systemic infectious virus.

Molecular Detection of Southern Tomato Amalgavirus Prevalent in Tomatoes and Its Genomic Characterization with Global Evolutionary Dynamics

Southern tomato amalgavirus (STV) is a cryptic pathogen that is abundant in tomato production fields and intensifies the resurgence of tomato yellow stunt disease (ToYSD), together with other phytoviruses. Here, we mapped the geographical and genomic diversity, phylogenetics, and evolutionary dynamics of STV. We found that STV prevailed across China and Pakistan, with a maximum average rate of infection of 43.19% in Beijing, China, and 40.08% in Punjab, Pakistan. Subsequently, we amplified, cloned, and annotated the complete genome sequences of STV isolates from Solanum lycopersicum L. in China (OP548653 and OP548652) and Pakistan (MT066231) using Sanger and next-generation sequencing (NGS). These STV isolates displayed close evolutionary relationships with others from Asia, America, and Europe. Whole-genome-based molecular diversity analysis showed that STV populations had 33 haplotypes with a gene diversity (Hd) of 0.977 and a nucleotide diversity (π) of 0.00404. The genetic variability of RNA-dependent RNA-polymerase (RdRp) was higher than that of the putative coat protein (CP) p42. Further analysis revealed that STV isolates were likely to be recombinant but with a lower-to-moderate level of confidence. With a variable distribution pattern of positively and negatively selected sites, negative selection pressure predominantly acted on p42 and RdRp. These findings elaborated on the molecular variability and evolutionary trends among STV populations across major tomato-producing regions of the world.

Development of polyclonal antibodies-based serological methods and a DIG-labelled DNA probe-based molecular method for detection of the Vicia cryptic virus-M in field plants

Vicia cryptic virus M (VCV-M), a member of the genus Amalgavirus of the family Amalgaviridae, was first identified in 2009 in a Vicia faba Linn. planting in Hangzhou, Zhejiang Province, China. However, there has been no further research on the biological features of VCV-M to date and the viral particles and coat protein (CP) have not been identified. The putative CP of VCV-M was predicted from the viral genomic RNA. In this study, a recombinant version of the putative CP of VCV-M (His-CP^VCV-M) was produced and used to prepare a polyclonal antiserum against the His-CP^VCV-M. Using this antiserum, a Western blot, an immuno-dot-blot and an enzyme-linked immunosorbent assay were developed for testing field samples of V. faba for the presence of VCV-M. Additionally, a digoxigenin (DIG)-labelled DNA probe-based Northern blot assay was established for VCV-M genome detection in field samples. The results showed that both the serological and nucleic acid assays could accurately and sensitively detect VCV-M in V. faba. This research represented the first confirmed expression of the putative CP of VCV-M in infected V. faba tissues. The serological and nucleic acid assays provided two complementary methods for VCV-M detection which could contribute to seed quality control and production increases of V. faba crops.

Detection of Four New Tomato Viruses in Serbia Using Post Hoc High-Throughput Sequencing Analysis of Samples From a Large-Scale Field Survey

Tomato production worldwide is affected by numerous plant virus species. The early and accurate detection of viruses is a critical step for disease control. However, the simultaneous detection of the most known tomato viruses can be difficult because of the high number and diversity of tomato-infecting viruses. Here, we have identified four new viruses in Serbia by applying target-independent small RNA high-throughput sequencing (HTS). HTS was applied on pools of samples and separate samples, in total comprising 30 tomato samples that exhibited (severe) virus-like symptoms and were collected in Serbia during three annual surveys (2011 to 2013). These samples had previously tested negative for the presence of 16 tomato viruses using targeted detection methods. Three divergent complete genome sequences of Physostegia chlorotic mottled virus were obtained from different localities, indicating for the first time that this virus is widespread in Serbia and might represent an emergent viral pathogen of tomato. The tomato torrado virus was detected at one locality with devastating yield losses. The southern tomato virus was detected at two localities, and the spinach latent virus was detected at one locality. In addition, we detected the presence of one already-known virus in Serbia, the tomato spotted wilt orthotospovirus. All the HTS results were subsequently confirmed by targeted detection methods. In this study, the successful application of post hoc HTS testing of a limited number of pooled samples resulted in the discovery of new viruses. Thus, our results encourage the use of HTS in research and diagnostic laboratories, including laboratories that have limited resources to resolve disease etiology.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Effect of asymptomatic infection with southern tomato virus on tomato plants

Southern tomato virus (STV) is often found infecting healthy tomato plants (Solanum lycopersicum). In this study, we compared STV-free and STV-infected plants of cultivar M82 to determine the effect of STV infection on the host plant. STV-free plants exhibited a short and bushy phenotype, whereas STV-infected plants were taller. STV-infected plants produced more fruit than STV-free plants, and the germination rate of seeds from STV-infected plants was higher than that of seeds from STV-free plants. This phenotypic difference was also observed in progeny plants (siblings) derived from a single STV-infected plant in which the transmission rate of STV to progeny plants via the seeds was approximately 86%. These results suggest that the interaction between STV and host plants is mutualistic. Transcriptome analysis revealed that STV infection affects gene expression in the host plant and results in downregulation of genes involved in ethylene biosynthesis and signaling. STV-infected tomato plants might thus be artificially selected due to their superior traits as a crop.

Identification and genome analysis of tomato chlorotic spot virus and dsRNA viruses from coinfected vegetables in the Dominican Republic by high-throughput sequencing

The Tomato chlorotic spot virus (TCSV) was first reported in the 1980s, having its occurrence limited to Brazil and Argentina. Due to an apparent mild severity in the past, molecular studies concerning TCSV were neglected. However, TCSV has disseminated over the USA and Caribbean countries. In Dominican Republic TCSV has been recently reported on important cultivated crops such as pepper and beans. In this work, we provide the first complete genome of a TCSV isolate from symptomatic plants in Dominican Republic, which was obtained by high-throughput sequencing. In addition, three dsRNA viruses from different virus families were identified coinfecting these plants Bell pepper endornavirus (BPEV), Southern tomato virus (STV) and Pepper cryptic virus 2 (PCV-2). Phylogenetic analysis showed that the Dominican Republic TCSV isolate has a close relationship with other TCSV isolates and a reassortant isolate between TCSV and Groundnut ringspot virus (GRSV), all found in USA. BPEV, STV and PCV-2 isolates from Dominican Republic were close related to corresponding American isolates. The possible biological implications of these virus-mixed infections are discussed.

Diversity, Distribution, and Evolution of Tomato Viruses in China Uncovered by Small RNA Sequencing

Tomato is a major vegetable crop that has tremendous popularity. However, viral disease is still a major factor limiting tomato production. Here, we report the tomato virome identified through sequencing small RNAs of 170 field-grown samples collected in China. A total of 22 viruses were identified, including both well-documented and newly detected viruses. The tomato viral community is dominated by a few species, and they exhibit polymorphisms and recombination in the genomes with cold spots and hot spots. Most samples were coinfected by multiple viruses, and the majority of identified viruses are positive-sense single-stranded RNA viruses. Evolutionary analysis of one of the most dominant tomato viruses, Tomato yellow leaf curl virus (TYLCV), predicts its origin and the time back to its most recent common ancestor. The broadly sampled data have enabled us to identify several unreported viruses in tomato, including a completely new virus, which has a genome of ∼13.4 kb and groups with aphid-transmitted viruses in the genus Cytorhabdovirus Although both DNA and RNA viruses can trigger the biogenesis of virus-derived small interfering RNAs (vsiRNAs), we show that features such as length distribution, paired distance, and base selection bias of vsiRNA sequences reflect different plant Dicer-like proteins and Argonautes involved in vsiRNA biogenesis. Collectively, this study offers insights into host-virus interaction in tomato and provides valuable information to facilitate the management of viral diseases.IMPORTANCE Tomato is an important source of micronutrients in the human diet and is extensively consumed around the world. Virus is among the major constraints on tomato production. Categorizing virus species that are capable of infecting tomato and understanding their diversity and evolution are challenging due to difficulties in detecting such fast-evolving biological entities. Here, we report the landscape of the tomato virome in China, the leading country in tomato production. We identified dozens of viruses present in tomato, including both well-documented and completely new viruses. Some newly emerged viruses in tomato were found to spread fast, and therefore, prompt attention is needed to control them. Moreover, we show that the virus genomes exhibit considerable degree of polymorphisms and recombination, and the virus-derived small interfering RNA (vsiRNA) sequences indicate distinct vsiRNA biogenesis mechanisms for different viruses. The Chinese tomato virome that we developed provides valuable information to facilitate the management of tomato viral diseases.

Genome Sequence of Southern tomato virus in Asymptomatic Tomato 'Sweet Hearts'

The genome sequence of Southern tomato virus in asymptomatic Solanum lycopersicum 'Sweet Hearts' (STV-Florida) in Florida was assembled from small RNAs sequenced by Illumina RNA-seq. The STV-Florida genome shared 99.0 to 99.9% similarity with full genome sequences from Bangladesh, China, Mexico, and the United States (Mississippi and North Carolina).

Complete Genome Sequence of Southern tomato virus Naturally Infecting Tomatoes in Bangladesh

The complete genome sequence of a Southern tomato virus (STV) isolate on tomato plants in a seed production field in Bangladesh was obtained for the first time using next-generation sequencing. The identified isolate, STV_BD-13, shares a high degree of sequence identity (99%) with several known STV isolates worldwide.

Complete Genome Sequence of Southern tomato virus Identified in China Using Next-Generation Sequencing

The complete genome sequence of Southern tomato virus (STV), a double-stranded RNA virus that affects tomato in China, was determined using small RNA deep sequencing. This Chinese isolate shares 99% sequence identity to other isolates from Mexico, France, Spain, and the United States. This is the first report of STV infecting tomatoes in Asia.