Complete genome sequence of a novel badnavirus infecting Fatsia japonica in China.

The complete genome sequence of a novel badnavirus, tentatively named "fatsia badnavirus 1" (FaBV1, OM540428), was identified in Fatsia japonica. The infected plant displayed virus-like symptoms on leaves, including yellowing and chlorosis. The genome of FaBV1 is 7313 bp in length and similar in size and organization to other members of the genus Badnavirus (family Caulimoviridae), containing four open reading frames (ORFs), three of which are found in all known badnaviruses, and the other of which is only present in some badnaviruses. The virus has the genome characteristics of badnaviruses, including a tRNAMet binding site (5'-TCTGAATTTATAGCGCTA-3') and two cysteine-rich domains (C-X-C-2X-C-4X-H-4X-C and C-2X-C-11X-C-2X-C-4X-C-2X-C). Pairwise sequence comparisons of the RT+RNase H region indicated that FaBV1 shares 61.4-71.2% nucleotide (nt) sequence identity with other known badnaviruses, which is below the threshold (80% nt sequence identity in the RT+RNase H region) used for species demarcation in the genus Badnavirus. Phylogenetic analysis revealed that FaBV1, ivy ringspot-associated virus (IRSaV, MN850490.1), and cacao mild mosaic virus (CMMV, KX276640.1) together form a separate clade within the genus Badnavirus, suggesting that FaBV1 is a new member of the genus Badnavirus in the family Caulimoviridae. To our knowledge, this is the first report of a badnavirus infecting F. japonica.

Identification of a sugarcane bacilliform virus promoter that is activated by drought stress in plants.

Sugarcane (Saccharum spp.) is an important sugar and biofuel crop in the world. It is frequently subjected to drought stress, thus causing considerable economic losses. Transgenic technology is an effective breeding approach to improve sugarcane tolerance to drought using drought-inducible promoter(s) to activate drought-resistance gene(s). In this study, six different promoters were cloned from sugarcane bacilliform virus (SCBV) genotypes exhibiting high genetic diversity. In ß-glucuronidase (GUS) assays, expression of one of these promoters (PSCBV-YZ2060) is similar to the one driven by the CaMV 35S promoter and >90% higher compared to the other cloned promoters and Ubi1. Three SCBV promoters (PSCBV-YZ2060, PSCBV-TX, and PSCBV-CHN2) function as drought-induced promoters in transgenic Arabidopsis plants. In Arabidopsis, GUS activity driven by promoter PSCBV-YZ2060 is also upregulated by abscisic acid (ABA) and is 2.2-5.5-fold higher when compared to the same activity of two plant native promoters (PScRD29A from sugarcane and PAtRD29A from Arabidopsis). Mutation analysis revealed that a putative promoter region 1 (PPR1) and two ABA response elements (ABREs) are required in promoter PSCBV-YZ2060 to confer drought stress response and ABA induction. Yeast one-hybrid and electrophoretic mobility shift assays uncovered that transcription factors ScbZIP72 from sugarcane and AREB1 from Arabidopsis bind with two ABREs of promoter PSCBV-YZ2060. After ABA treatment or drought stress, the expression levels of endogenous ScbZIP72 and heterologous GUS are significantly increased in PSCBV-YZ2060:GUS transgenic sugarcane plants. Consequently, promoter PSCBV-YZ2060 is a possible alternative promoter for genetic engineering of drought-resistant transgenic crops such as sugarcane.

Cacao sustainability: The case of cacao swollen-shoot virus co-infection.

The cacao swollen shoot virus disease (CSSVD) is among the most economically damaging diseases of cacao trees and accounts for almost 15-50% of harvest losses in Ghana. This virus is transmitted by several species of mealybugs (Pseudococcidae, Homoptera) when they feed on cacao plants. One of the mitigation strategies for CSSVD investigated at the Cocoa Research Institute of Ghana (CRIG) is the use of mild-strain cross-protection of cacao trees against the effects of severe strains. In this study, simple deterministic, delay, and stochastic ordinary differential equation-based models to describe the dynamic of the disease and spread of the virus are suggested. Model parameters are estimated using detailed empirical data from CRIG. The modeling outcomes demonstrate a remarkable resemblance between real and simulated dynamics. We have found that models with delay approximate the data better and this agrees with the knowledge that CSSVD epidemics develop slowly. Also, since there are large variations in the data, stochastic models lead to better results. We show that these models can be used to gain useful informative insights about the nature of disease spread.

The P2 nucleic acid binding protein of Sugarcane bacilliform virus is a viral pathogenic factor.

Background: Saccharum spp. is the primary source of sugar and plays a significant role in global renewable bioenergy. Sugarcane bacilliform virus (SCBV) is one of the most important viruses infecting sugarcane, causing severe yield losses and quality degradation. It is of great significance to reveal the pathogenesis of SCBV and resistance breeding. However, little is known about the viral virulence factors or RNA silencing suppressors and the molecular mechanism of pathogenesis. Methods: To systematically investigate the functions of the unknown protein P2 encoded by SCBV ORF2. Phylogenetic analysis was implemented to infer the evolutionary relationship between the P2 of SCBV and other badnaviruses. The precise subcellular localization of P2 was verified in the transient infiltrated Nicotiana benthamiana epidermal mesophyll cells and protoplasts using the Laser scanning confocal microscope (LSCM). The post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS) RNA silencing suppressor activity of P2 was analyzed, respectively. Furthermore, restriction digestion and RT-qPCR assays were conducted to verify the probable mechanism of P2 on repressing DNA methylation. To explore the pathogenicity of P2, a potato virus X-based viral vector was used to heterologously express SCBV P2 and the consequent H2O2 accumulation was detected by the 3,3'-diaminobenzidine (DAB) staining method. Results: Phylogenetic analysis shows that SCBV has no obvious sequence similarity and low genetic relatedness to Badnavirus and Tungrovirus representatives. LSCM studies show that P2 is localized in both the cytoplasm and nucleus. Moreover, P2 is shown to be a suppressor of PTGS and TGS, which can not only repress ssRNA-induced gene silencing but also disrupt the host RNA-directed DNA methylation (RdDM) pathway. In addition, P2 can trigger an oxidative burst and cause typical hypersensitive-like response (HLR) necrosis in systemic leaves of N. benthamiana when expressed by PVX. Overall, our results laid a foundation for deciphering the molecular mechanism of SCBV pathogenesis and made progress for resistance breeding.

Integration of Rubus yellow net virus in the raspberry genome: A story centuries in the making.

Rubus yellow net virus (RYNV) belongs to genus Badnavirus. Badnaviruses are found in plants as endogenous, inactive or activatable sequences, and/or in episomal (infectious and active) forms. To assess the state of RYNV in Rubus germplasm, we sequenced the genomes of various cultivars and mined eight raspberry whole genome datasets. Bioinformatics analysis revealed the presence of a diverse array of endogenous RYNV (endoRYNV) sequences that differ significantly in their structure; some lineages have nearly complete, yet non-functional genomes whereas others have rudimentary, short sequence fragments. We developed assays to genotype the main lineages as well as the only known episomal lineage present in the United States. This study discloses the widespread presence of endoRYNVs in commercial raspberries, likely because breeding efforts have focused on a limited pool of germplasm that harbored endoRYNVs.

Distribution and Location of BEVs in Different Genotypes of Bananas Reveal the Coevolution of BSVs and Bananas.

Members of the family Caulimoviridae contain abundant endogenous pararetroviral sequences (EPRVs) integrated into the host genome. Banana streak virus (BSV), a member of the genus Badnavirus in this family, has two distinct badnaviral integrated sequences, endogenous BSV (eBSV) and banana endogenous badnavirus sequences (BEVs). BEVs are distributed widely across the genomes of different genotypes of bananas. To clarify the distribution and location of BEVs in different genotypes of bananas and their coevolutionary relationship with bananas and BSVs, BEVs and BSVs were identified in 102 collected banana samples, and a total of 327 BEVs were obtained and categorized into 26 BEVs species with different detection rates. However, the majority of BEVs were found in Clade II, and a few were clustered in Clade I. Additionally, BEVs and BSVs shared five common conserved motifs. However, BEVs had two unique amino acids, methionine and lysine, which differed from BSVs. BEVs were distributed unequally on most of chromosomes and formed hotspots. Interestingly, a colinear relationship of BEVs was found between AA and BB, as well as AA and SS genotypes of bananas. Notably, the chromosome integration time of different BEVs varied. Based on our findings, we propose that the coevolution of bananas and BSVs is driven by BSV Driving Force (BDF), a complex interaction between BSVs, eBSVs, and BEVs. This study provides the first clarification of the relationship between BEVs and the coevolution of BSVs and bananas in China.

Mixed infections with new emerging viruses associated with jujube mosaic disease / Infecciones mixtas con nuevos virus emergentes asociados con la enfermedad del mosaico de azufaifa

Background: Jujube is an economically important fruit tree and native to China. Viral disease is a new threat to jujube production, and several new viruses have been identified infecting jujube plants. During our field survey, jujube mosaic disease was widely distributed in Beijing, but the associated causal agents are still unknown. Methods: Small RNA deep sequencing was conducted to identify the candidate viruses associated with jujube mosaic. Further complete genome sequences of the viruses were cloned, and the genomic characterization of each virus was analyzed. The field distribution of these viruses was further explored with PCR/RT-PCR detection of field samples. Results: Mixed infection of four viruses was identified in a plant sample with the symptom of mosaic and leaf twisting, including the previously reported jujube yellow mottle-associated virus (JYMaV), persimmon ampelovirus (PAmpV), a new badnavirus tentatively named jujube-associated badnavirus (JaBV), and a new secovirus tentatively named jujube-associated secovirus (JaSV). PAmpV-jujube was 14,093 nt in length with seven putative open reading frames (ORFs) and shared highest (79.4%) nucleotide (nt) sequence identity with PAmpV PBs3. Recombination analysis showed that PAmpV-jujube was a recombinant originating from plum bark necrosis stem pitting-associated virus isolates nanjing (KC590347) and bark (EF546442). JaBV was 6449 bp in length with conserved genomic organization typical of badnaviruses. The conserved RT and RNAse H region shared highest 67.6% nt sequence identity with jujube mosaic-associated virus, which was below the 80% nt sequence identity value used as the species demarcation threshold in Badnavirus. The genome of JaSV composed of two RNA molecules of 5878 and 3337 nts in length, excluding the polyA tails. Each genome segment contained one large ORF that shared homology and phylogenetic identity with members of the family Secoviridae...(AU)

Detection of Sugarcane bacilliform virus in diseased sugarcane plants in Andhra Pradesh, India by serological and molecular methods.

Sugarcane leaf fleck incited by Sugarcane bacilliform virus is emerging as a major disease and affecting exchange of sugarcane germplasm and cultivation worldwide. Roving surveys conducted in 162 fields belonging to 81 villages spread over 14 sugarcane growing districts of Andhra Pradesh during 2021-2022 revealed 8 to 44% incidence of the disease. Mean maximum fleck disease incidence was reported in Anakapalli district (33.00%) followed by Srikakulam district (22.66%), whereas least incidence was observed in Alluri Sitharamaraju district (9.33%). The early and sensitive detection of pathogens is vital and necessary to reduce the danger of introducing new diseases or pathogen strains into sugarcane growing regions. Both serological and molecular methods were used in proposed investigation to identify the virus at the protein and nucleic acid levels. DAS-ELISA results were positive for 50 suspected SCBV infected sugarcane leaf samples out of 81, with mean absorbance (A405) values ranging from 0.50 to 2.20. Further PCR assays were performed using SCBV-specific primers targeting RT/RNase H coding region which is frequently employed as a taxonomic marker for species delineation in Badnaviruses. Out of 81 symptomatic samples collected, 61 samples gave positive results, and no amplification was observed in healthy control and negative control. Results made it evident that PCR was more sensitive than DAS-ELISA. Low virus concentration or variation in virus strains may be the reason for the low detection rate in DAS-ELISA in the current study. Extensive roving surveys conducted for the incidence of leaf fleck disease for the first time in the state of Andhra Pradesh revealed severe occurrence of leaf fleck disease under field conditions.

Mixed infections with new emerging viruses associated with jujube mosaic disease.

BACKGROUND: Jujube is an economically important fruit tree and native to China. Viral disease is a new threat to jujube production, and several new viruses have been identified infecting jujube plants. During our field survey, jujube mosaic disease was widely distributed in Beijing, but the associated causal agents are still unknown. METHODS: Small RNA deep sequencing was conducted to identify the candidate viruses associated with jujube mosaic. Further complete genome sequences of the viruses were cloned, and the genomic characterization of each virus was analyzed. The field distribution of these viruses was further explored with PCR/RT-PCR detection of field samples. RESULTS: Mixed infection of four viruses was identified in a plant sample with the symptom of mosaic and leaf twisting, including the previously reported jujube yellow mottle-associated virus (JYMaV), persimmon ampelovirus (PAmpV), a new badnavirus tentatively named jujube-associated badnavirus (JaBV), and a new secovirus tentatively named jujube-associated secovirus (JaSV). PAmpV-jujube was 14,093 nt in length with seven putative open reading frames (ORFs) and shared highest (79.4%) nucleotide (nt) sequence identity with PAmpV PBs3. Recombination analysis showed that PAmpV-jujube was a recombinant originating from plum bark necrosis stem pitting-associated virus isolates nanjing (KC590347) and bark (EF546442). JaBV was 6449 bp in length with conserved genomic organization typical of badnaviruses. The conserved RT and RNAse H region shared highest 67.6% nt sequence identity with jujube mosaic-associated virus, which was below the 80% nt sequence identity value used as the species demarcation threshold in Badnavirus. The genome of JaSV composed of two RNA molecules of 5878 and 3337 nts in length, excluding the polyA tails. Each genome segment contained one large ORF that shared homology and phylogenetic identity with members of the family Secoviridae. Field survey showed JYMaV and JaBV were widely distributed in jujube trees in Beijing. CONCLUSION: Two new viruses were identified from jujube plants, and mixed infections of JYMaV and JaBV were common in jujube in Beijing.

Genome sequence of Chionoecetes opilio bacilliform virus, a nimavirus infecting the snow crab Chionoecetes opilio.

Nimaviridae (class Naldaviricetes) is a family of double-stranded DNA viruses infecting crustaceans, with the only officially recognized representative being white spot syndrome virus (WSSV). Chionoecetes opilio bacilliform virus (CoBV) was isolated as the causative agent of milky hemolymph disease in the snow crab Chionoecetes opilio, an economically important crustacean in the northwestern Pacific. Here, we present the complete genome sequence of CoBV and show that it is unambiguously a nimavirus. The CoBV genome is a 240-kb circular DNA molecule with 40% GC content that encodes 105 proteins, including 76 WSSV orthologs. Phylogenetic analysis based on eight naldaviral core genes established that CoBV is a member of the family Nimaviridae. The availability of the CoBV genome sequence provides a deeper understanding of CoBV pathogenicity and nimavirus evolution.

Cacao Swollen Shoot Viruses in Ghana.

Cacao swollen shoot virus causes cacao swollen shoot disease of Theobroma cacao (cacao) plants. At least six cacao-infecting Badnavirus species-Cacao swollen shoot Togo A virus, Cacao swollen shoot Togo B virus (previously known as Cacao swollen shoot virus), Cacao swollen shoot CE virus, Cacao swollen shoot Ghana M virus, Cacao swollen shoot Ghana N virus, and Cacao swollen shoot Ghana Q virus-are responsible for the swollen shoot disease of cacao in Ghana. Each of these species consists of a multiplicity of strains. The New Juaben strain, the most virulent cacao swollen shoot virus strain in Ghana, belongs to the Cacao swollen shoot Togo B virus species, and is a commonly used strain in laboratory transmission assays. Infection of cacao trees with multiple strains of the virus is common and new evidence suggests that these coinfections may have resulted in the emergence of recombinant strains of the virus. The impact of these emerging recombinant strains on disease severity is uncertain. This review focuses largely on the discovery of cacao swollen shoot virus in Ghana, diversity of the virus strains, molecular characterization, propagation of virus infection in cacao plants, emergence of recombinant virus strains, vector-mediated transmission of the virus, and the management of the cacao swollen shoot disease in Ghana. It also contains sections on the botany and origin of the cacao tree, its introduction to Ghana, the role of cacao swollen shoot disease in facilitating Ghana's independence from Britain, and a brief history of chocolate.

Epidemiology and Diagnostics of Cacao Swollen Shoot Disease in Ghana: Past Research Achievements and Knowledge Gaps to Guide Future Research.

Cacao swollen shoot disease (CSSD) caused by complexes of cacao swollen shoot badnaviruses (family Caulimoviridae, genus Badnavirus) remains highly prevalent and devastating in West Africa. The disease continues to impact substantially on cacao yield loss, cacao tree mortality, and decline in foreign exchange income from cacao bean sales. Currently, the disease is estimated to have a prevalence rate of over 30% in Ghana, as assessed in the ongoing third country-wide surveillance program. Although achievements from past research interventions have greatly elucidated the etiology, biology, epidemiology, diagnostics, and management of the disease, there are some outstanding knowledge gaps. The role of these information gaps and their effect on CSSD epidemiology and prevalence remain unanswered. This paper summarizes existing scientific knowledge from past research achievements that have provided elucidation on CSSD epidemiology, management options, and guided future research. The discussion highlights the need for multidisciplinary research with modern tools and institutional collaborators to holistically bring clarity on knowledge gaps on pathogen biology, virus-host--vector interactions, role of environmental and soil nutrient effects on CSSD severity, evolution pattern, role of alternative hosts on virus species diversity, vector population dynamics, and their overall impact on CSSD prevalence and integrated management in cacao plantations.

Biology and Ultrastructural Characterization of Grapevine Badnavirus 1 and Grapevine Virus G.

The biological characteristics of grapevine viruses, such as their transmission and host range, are important for the adoption of successful prophylaxis strategies. The aim of this study was to investigate the traits of two newly described grapevine viruses widely distributed in Croatia, grapevine badnavirus 1 (GBV-1) and grapevine virus G (GVG). The vine mealybug (Planoccocus ficus) proved to be a vector of GBV-1 and GVG capable of vine-to-vine transmission with overall experimental transmission rates of 61% and 14.6%, respectively. Transmission was also demonstrated by grafting, with an overall transmission rate of 53.8% for GBV-1 and 100% for GVG, as well as by green grafting using the T-budding technique. Symptoms of GBV-1 and GVG were not observed on the woody cylinders of the indicators LN 33, Kober 5BB, 110 Richter and cvs. Chardonnay and Cabernet Sauvignon. Seed transmission and mechanical transmission were not confirmed. Electron microscopy revealed accumulation of GBV-1 particles and viroplasms in the cytoplasm, but no alternations of the cell structure. Infection with GVG revealed the proliferation of tonoplast-associated vesicles inside phloem cells and cell wall thickening.

Epidemiology of Yam Viruses in Guadeloupe: Role of Cropping Practices and Seed-Tuber Supply.

The epidemiology of yam viruses remains largely unexplored. We present a large-scale epidemiological study of yam viruses in Guadeloupe based on the analysis of 1124 leaf samples collected from yams and weeds. We addressed the prevalence of cucumber mosaic virus (CMV), Cordyline virus 1 (CoV1), Dioscorea mosaic associated virus (DMaV), yam asymptomatic virus 1 (YaV1), yam mosaic virus (YMV), yam mild mosaic virus (YMMV), badnaviruses, macluraviruses and potexviruses, and the key epidemiological drivers of these viruses. We provide evidence that several weeds are reservoirs of YMMV and that YMMV isolates infecting weeds cluster together with those infecting yams, pointing to the role of weeds in the epidemiology of YMMV. We report the occurrence of yam chlorotic necrosis virus (YCNV) in Guadeloupe, the introduction of YMMV isolates through the importation of yam tubers, and the absence of vertical transmission of YaV1. We identified specific effects on some cropping practices, such as weed management and the use of chemical pesticides, on the occurrence of a few viruses, but no crop-related factor had a strong or general effect on the overall epidemiology of the targeted viruses. Overall, our work provides insights into the epidemiology of yam viruses that will help design more efficient control strategies.

Transcriptome Analysis Reveals a Comprehensive Virus Resistance Response Mechanism in Pecan Infected by a Novel Badnavirus Pecan Virus.

Pecan leaf-variegated plant, which was infected with a novel badnavirus named pecan mosaic virus (PMV) detected by small RNA deep sequencing, is a vital model plant for studying the molecular mechanism of retaining green or chlorosis of virus-infected leaves. In this report, PMV infection in pecan leaves induced PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI). PMV infection suppressed the expressions of key genes of fatty acid, oleic acid (C18:1), and very-long-chain fatty acids (VLCFA) biosynthesis, indicating that fatty acids-derived signaling was one of the important defense pathways in response to PMV infection in pecan. PMV infection in pecans enhanced the expressions of pathogenesis-related protein 1 (PR1). However, the transcripts of phenylalanine ammonia-lyase (PAL) and isochorismate synthase (ICS) were downregulated, indicating that salicylic acid (SA) biosynthesis was blocked in pecan infected with PMV. Meanwhile, disruption of auxin signaling affected the activation of the jasmonic acid (JA) pathway. Thus, C18:1 and JA signals are involved in response to PMV infection in pecan. In PMV-infected yellow leaves, damaged chloroplast structure and activation of mitogen-activated protein kinase 3 (MPK3) inhibited photosynthesis. Cytokinin and SA biosynthesis was blocked, leading to plants losing immune responses and systemic acquired resistance (SAR). The repression of photosynthesis and the induction of sink metabolism in the infected tissue led to dramatic changes in carbohydrate partitioning. On the contrary, the green leaves of PMV infection in pecan plants had whole cell tissue structure and chloroplast clustering, establishing a strong antiviral immunity system. Cytokinin biosynthesis and signaling transductions were remarkably strengthened, activating plant immune responses. Meanwhile, cytokinin accumulation in green leaves induced partial SA biosynthesis and gained comparatively higher SAR compared to that of yellow leaves. Disturbance of the ribosome biogenesis might enhance the resistance to PMV infection in pecan and lead to leaves staying green.

Complete genome sequence of a new badnavirus infecting a tea plant in China.

The complete genome of a novel virus, provisionally named "Camellia sinensis badnavirus 1" (CSBV1), was identified in tea plant (Camellia sinensis) leaves collected in Anhui Province, China. The genome of CSBV1 consists of 8,195 bp and possesses three open reading frames (ORFs), sharing 68.6 % nucleotide sequence identity with the genome of Camellia lemon glow virus (CLGV) from Camellia japonica. The genome organization of CSBV1 is highly similar to that of members of the genus Badnavirus (family Caulimoviridae). Phylogenetic analysis revealed that CSBV1, CLGV, and cacao swollen shoot virus form a separate clade within the genus Badnavirus, suggesting that CSBV1 is the first badnavirus infecting C. sinensis.

Characterization of the first Rubus yellow net virus genome from blackberry.

Rubus yellow net virus (RYNV) is a badnavirus that infects Rubus spp. Mixed infections with black raspberry necrosis virus and raspberry leaf mottle virus cause raspberry mosaic, a disease that leads to significant losses and even plant death. RYNV has been reported in several European countries and the Americas yet there is substantial lack of knowledge, especially when it comes to virus diversity and the evolutionary forces that affect virus fitness outside its primary host, raspberry. Herein, we report the first RYNV episomal genome isolated from blackberry and this is the first report of the virus in Bosnia and Herzegovina. The isolate has five open reading frames (ORFs) and, when compared with other fully sequenced counterparts, showed 82-97% nucleotide pairwise identity. This communication adds to our limited knowledge on RYNV and addresses some of the gaps in RYNV genetics when it comes to the coding capacity of episomal isolates and the probability of the first fully sequenced isolate of the virus being integrated in the raspberry genome.

Examination of the Virome of Taro Plants Affected by a Lethal Disease, the Alomae-Bobone Virus Complex, in Papua New Guinea.

Alomae-bobone virus complex (ABVC) is a lethal but still understudied disease that is limited to the Solomon Islands and Papua New Guinea. The only virus clearly associated to ABVC is Colocasia bobone disease-associated virus (CBDaV). Taro (Colocasia esculenta) plants with and without symptoms of ABVC disease were sampled from two locations in Papua New Guinea and examined for viruses using high-throughput sequencing (HTS). Similar to previous reports, isolates of CBDaV were present only in symptomatic plants, further supporting its role in the disease. The only other viruses consistently present in symptomatic plants were badnaviruses: taro bacilliform virus (TaBV) and/or taro bacilliform CH virus (TaBCHV). If ABVC requires co-infection by multiple viruses, CBDaV and badnavirus infection appears to be the most likely combination. The complete genomes of two isolates of CBDaV and TaBCHV, and single isolates of TaBV and dasheen mosaic virus, were obtained in this study, furthering our knowledge of the genetic diversity of these relatively understudied taro viruses. HTS data also provided evidence for an agent similar to umbra-like viruses that we are tentatively designating it as Colocasia umbra-like virus (CULV).

Diverse Novel Viruses Coinfecting the Tropical Ornamental Plant Polyscias balfouriana in China.

The viromic profile of Polyscias balfouriana cv. Marginata, a perennial woody and ornamental plant, was determined using ribosomal RNA-depleted total RNA (rRNA-depleted totRNA) sequencing. Five viruses (i.e., polyscias mosaic virus, PoMV; one potential novel rhabdovirus; and three novel viruses of Betaflexiviridae and Closteroviridae) were detected and prevalence-surveyed in Hainan province, China. The genomes of polyscias capillovirus 1 (PCaV-1) and polyscias citrivirus 1 (PCiV-1) of family Betaflexiviridae were completed, and the genomes of polyscias crinivirus 1 (PCrV-1) of Closteroviridae were nearly completed lacking the 5' and 3' termini. PCaV-1 shares 68% genome nucleotide (nt) identity and 66% replicase (Rep) amino acid (aa) identity with homologues in apple stem grooving virus (ASGV). PCiV-1 shares 65% genome nt identity and 64% Rep aa identity with homologs in citrus leaf blotch virus (CLBV). Meeting the species demarcation criteria, PCaV-1 and PCiV-1 were considered to be new species in genera Capillovirus and Citrivirus, respectively. PCrV-1 shares high genome nt identity (62%), heat shock protein 70-like protein (HSP70h) and RNA-dependent RNA polymerase (RdRp) aa identity (78−80%) with homologues in tomato chlorosis virus (ToCV). We tentatively consider PCrV-1 to be an unclassified member of the Crinivirus genus. PoMV, PCaV-1, PCiV-1, and PCrV-1 are the prevalent viruses with >73% occurrence in the Xinglong Tropical Botanical Garden, Hainan, China.

Complete genome sequence of a novel virus belonging to the genus Badnavirus in jujube (Ziziphus jujuba Mill.) in China.

The genome sequence of a novel circular DNA virus related to members of the genus Badnavirus was identified in diseased jujube trees by high-throughput sequencing and verified by conventional Sanger sequencing of cloned PCR products. The name "jujube badnavirus WS" (JuBWS) is proposed for this virus. Diseased jujube leaves showed yellow mosaic and malformation symptoms, with round chlorotic spots found on diseased fruit. The genome of this virus has a length of 6450 nt and has a typical badnavirus genomic structure with three open reading frames (ORFs). JuBWS was identified as a novel badnavirus based on nucleotide differences in the RNase (RT + RNase H) coding region of ORF3. The JuBWS sequence showed 70.48-76.41% nucleotide sequence identity to other known badnaviruses, thus meeting the taxonomic criterion for establishing a new species within the genus Badnavirus. This study suggested that the novel badnavirus might be a pathogen associated with jujube mosaic disease, and this will be investigated in the future.