History and current distribution of begomoviruses in Latin America

Genetic analysis of resistance to bean leaf crumple virus identifies a candidate LRR-RLK gene

Bean leaf crumple virus (BLCrV) is a novel begomovirus (family Geminiviridae, genus Begomovirus) infecting common bean (Phaseolus vulgaris L.), threatening bean production in Latin America. Genetic resistance is required to ensure yield stability and reduce the use of insecticides, yet the available resistance sources are limited. In this study, three common bean populations containing a total of 558 genotypes were evaluated in different yield and BLCrV resistance trials under natural infection in the field. A genome-wide association study identified the locus BLC7.1 on chromosome Pv07 at 3.31 Mbp, explaining 8 to 16% of the phenotypic variation for BLCrV resistance. In comparison, whole-genome regression models explained 51 to 78% of the variation and identified the same region on Pv07 to confer resistance. The most significantly associated markers were located within the gene model Phvul.007G040400, which encodes a leucine-rich repeat receptor-like kinase subfamily III member and is likely to be involved in the innate immune response against the virus. The allelic diversity within this gene revealed five different haplotype groups, one of which was significantly associated with BLCrV resistance. As the same genome region was previously reported to be associated with resistance against other geminiviruses affecting common bean, our study highlights the role of previous breeding efforts for virus resistance in the accumulation of positive alleles against newly emerging viruses. In addition, we provide novel diagnostic single-nucleotide polymorphism markers for marker-assisted selection to exploit BLC7.1 for breeding against geminivirus diseases in one of the most important food crops worldwide.

Influence of Climatic Variables on Incidence of Whitefly-Transmitted Begomovirus in Soybean and Bean Crops in North-Western Argentina

Over the last 20 years, begomoviruses have emerged as devastating pathogens, limiting the production of different crops worldwide. Weather conditions increase vector populations, with negative effects on crop production. In this work we evaluate the relationship between the incidence of begomovirus and weather before and during the crop cycle. Soybean and bean fields from north-western (NW) Argentina were monitored between 2001 and 2018 and classified as moderate (≤50%) or severe (>50%) according to the begomovirus incidence. Bean golden mosaic virus (BGMV) and soybean blistering mosaic virus (SbBMV) were the predominant begomovirus in bean and soybean crops, respectively. Nearly 200 bio-meteorological variables were constructed by summarizing climatic variables in 10-day periods from July to November of each crop year. The studied variables included temperature, precipitation, relative humidity, wind (speed and direction), pressure, cloudiness, and visibility. For bean, high maximum winter temperatures, low spring humidity, and precipitation 10 days before planting correlated with severe incidence. In soybeans, high temperatures in late winter and in the pre-sowing period, and low spring precipitations were found to be good predictors of high incidence of begomovirus. The results suggest that temperature and pre-sowing precipitations can be used to predict the incidence status [predictive accuracy: 80% (bean) and 75% (soybean)]. Thus, these variables can be incorporated in early warning systems for crop management decision-making to reduce the virus impact on bean and soybean crops.

Sida Golden Mosaic Virus, an Emerging Pathogen of Snap Bean (Phaseolus vulgaris L.) in the Southeastern United States

Sida golden mosaic virus (SiGMV) was first detected from snap bean (Phaseolus vulgaris L.) in Florida in 2006 and recently in Georgia in 2018. Since 2018, it has caused significant economic losses to snap bean growers in Georgia. This study, using a SiGMV isolate field-collected from prickly sida (Sida spinosa L.), examined the putative host range, vector-mediated transmission, and SiGMV-modulated effects on host-vector interactions. In addition, this study analyzed the phylogenetic relationships of SiGMV with other begomoviruses reported from Sida spp. Host range studies confirmed that SiGMV can infect seasonal crops and perennial weed species such as snap bean, hollyhock (Alcea rosea L.), marsh mallow (Althaea officinalis L.), okra (Abelmoschus esculentus (L.) Moench), country mallow (Sida cordifolia L.), prickly sida (S. spinosa), and tobacco (Nicotiana tabacum L.). The incidence of infection ranged from 70 to 100%. SiGMV-induced symptoms and virus accumulation varied between hosts. The vector, Bemisia tabaci Gennadius, was able to complete its life cycle on all plant species, irrespective of SiGMV infection status. However, SiGMV infection in prickly sida and country mallow positively increased the fitness of whiteflies, whereas SiGMV infection in okra negatively influenced whitefly fitness. Whiteflies efficiently back-transmitted SiGMV from infected prickly sida, hollyhock, marsh mallow, and okra to snap bean, and the incidence of infection ranged from 27 to 80%. Complete DNA-A sequence from this study shared 97% identity with SiGMV sequences reported from Florida and it was determined to be closely related with sida viruses reported from the New World. These results suggest that SiGMV, a New World begomovirus, has a broad host range that would allow its establishment in the farmscapes/landscapes of the southeastern United States and is an emerging threat to snap bean and possibly other crops.

Applications of environmental DNA (eDNA) in agricultural systems: Current uses, limitations and future prospects

Global food production, food supply chains and food security are increasingly stressed by human population growth and loss of arable land, becoming more vulnerable to anthropogenic and environmental perturbations. Numerous mutualistic and antagonistic species are interconnected with the cultivation of crops and livestock and these can be challenging to identify on the large scales of food production systems. Accurate identifications to capture this diversity and rapid scalable monitoring are necessary to identify emerging threats (i.e. pests and pathogens), inform on ecosystem health (i.e. soil and pollinator diversity), and provide evidence for new management practices (i.e. fertiliser and pesticide applications). Increasingly, environmental DNA (eDNA) is providing rapid and accurate classifications for specific organisms and entire species assemblages in substrates ranging from soil to air. Here, we aim to discuss how eDNA is being used for monitoring of agricultural ecosystems, what current limitations exist, and how these could be managed to expand applications into the future. In a systematic review we identify that eDNA-based monitoring in food production systems accounts for only 4 % of all eDNA studies. We found that the majority of these eDNA studies target soil and plant substrates (60 %), predominantly to identify microbes and insects (60 %) and are biased towards Europe (42 %). While eDNA-based monitoring studies are uncommon in many of the world's food production systems, the trend is most pronounced in emerging economies often where food security is most at risk. We suggest that the biggest limitations to eDNA for agriculture are false negatives resulting from DNA degradation and assay biases, as well as incomplete databases and the interpretation of abundance data. These require in silico, in vitro, and in vivo approaches to carefully design, test and apply eDNA monitoring for reliable and accurate taxonomic identifications. We explore future opportunities for eDNA research which could further develop this useful tool for food production system monitoring in both emerging and developed economies, hopefully improving monitoring, and ultimately food security.

Impact of Bemisia tabaci MEAM1 (Hemiptera: Aleyrodidae) on Soybean Yield and Quality Under Field Conditions

Bemisia tabaci MEAM1 (Hemiptera: Aleyrodidae) is a key insect pest in soybean fields in Brazil but data are lacking on the relationship between pest abundance and crop yield and quality. Controlled infestation studies were conducted on caged soybean plants in the field over a two year period at two sites in Brazil. Differences in temperature in the two years affected population growth of B. tabaci, reaching 413 nymphs per leaflet in the first year, and 179 the second year even when the average temperature was 3ºC higher. Higher temperatures promoted a shorter lifecycle and nearly one more generation. Yield was affected with losses up to 500 kg/ha in 2017/2018 and 1,147 kg/ha in 2018/2019. A decrease in the weight of a thousand grains of 18 and 33 g was observed in the first and second year, respectively. No significant differences were observed in grain germination, but estimated losses in protein content were up to 440 kg/ha at the highest infestation level. Pest density and yield data were used to estimate economic injury levels (EILs). EILs ranged from 2.5 to 25.67 nymphs per leaflet and 0.17-1.79 adults per leaflet over a range of control costs, soybean production values, and control efficacies. These results should provide data useful toward development of pest management decision making tools.

Complete genome sequence of a novel bipartite begomovirus infecting the legume weed Macroptilium erythroloma

The natural occurrence of mixed infections and large populations of the polyphagous vector (Bemisia tabaci) are the main factors associated with the intensification of the genetic flow among begomoviruses in Neotropical areas, contributing to the emergence of novel recombinants. Here, high-throughput sequencing and metagenomic analyses were employed to discover and characterize a novel recombinant bipartite begomovirus, tentatively named "macroptilium bright yellow interveinal virus" (MaBYIV) in the weed Macroptilium erythroloma (Fabaceae). Recombination signals were detected in MaBYIV, involving bean golden mosaic virus (BGMV) and tomato mottle leaf curl virus (ToMoLCV) genome components. All of the original MaBYIV-infected M. erythroloma plants were found to have mixed infections with BGMV. MaBYIV was transmitted to bean and soybean cultivars via B. tabaci MEAM 1, indicating that M. erythroloma may play a role as a year-round reservoir of a potential new viral pathogen of economically important legume crops.

DETECCIÓN MOLECULAR DE BEGOMOVIRUS AISLADOS DE ARVENSES ASOCIADAS AL CULTIVO DE AJÍ (Capsicum spp.) EN EL VALLE DEL CAUCA, COLOMBIA

Los virus Potato yellow mosaic virus (PYMV/Co), Passionfruit leaf distortion virus (PLDV), Pepper rugose mosaic virus (PRMV) y Rhynchosia golden mosaic Colombia virus (RhGMCV) son begomovirus de interés agrícola, aislados y caracterizados molecularmente en el Valle del Cauca. Sin embargo, en la actualidad no hay suficiente información sobre sus hospederos alternos. Dado que las arvenses cumplen un papel importante en la ecología y epidemiología viral, este estudio tuvo como objetivo detectar la presencia de estos begomovirus en arvenses asociadas al cultivo de ají en el Valle del Cauca, Colombia. Se recolectaron 121 plantas arvenses en zonas productoras de ají, localizadas en 7 municipios del Valle del Cauca, las cuales fueron identificadas a nivel taxonómico. A partir del ADN genómico purificado de estas plantas se evaluó la presencia de virus por PCR, usando cebadores universales para el género Begomovirus y específicos para PYMV/Co, PLDV, PRMV y RhGMCV. Se detectaron begomovirus en 15 de las especies de arvenses evaluadas. Esta es la primera vez que las especies Ipomoea tiliacea, Melothria pendula, Caperonia palustris, Desmodium tortuosum, Desmodium intortum, Ammannia coccinea, Panicum polygonatum, Capsicum rhomboideum, Eclipta prostrata y Synedrella nodiflora se reportan como hospederas de begomovirus en Colombia. Se detectaron los begomovirus RhGMCV, PYMV/Co, PRMV y PLDV en infecciones simples y mixtas. Estos resultados aportan nuevos datos sobre los hospederos alternos de begomovirus. Esta información servirá para implementar un plan de manejo integrado de enfermedades virales con el potencial para afectar negativamente el rendimiento del cultivo de ají, y otros cultivos en Colombia.

Development and Adoption of Genetically Engineered Plants for Virus Resistance: Advances, Opportunities and Challenges

Plant viruses cause yield losses to crops of agronomic and economic significance and are a challenge to the achievement of global food security. Although conventional plant breeding has played an important role in managing plant viral diseases, it will unlikely meet the challenges posed by the frequent emergence of novel and more virulent viral species or viral strains. Hence there is an urgent need to seek alternative strategies of virus control that can be more readily deployed to contain viral diseases. The discovery in the late 1980s that viral genes can be introduced into plants to engineer resistance to the cognate virus provided a new avenue for virus disease control. Subsequent advances in genomics and biotechnology have led to the refinement and expansion of genetic engineering (GE) strategies in crop improvement. Importantly, many of the drawbacks of conventional breeding, such as long lead times, inability or difficulty to cross fertilize, loss of desirable plant traits, are overcome by GE. Unfortunately, public skepticism towards genetically modified (GM) crops and other factors have dampened the early promise of GE efforts. These concerns are principally about the possible negative effects of transgenes to humans and animals, as well as to the environment. However, with regards to engineering for virus resistance, these risks are overstated given that most virus resistance engineering strategies involve transfer of viral genes or genomic segments to plants. These viral genomes are found in infected plant cells and have not been associated with any adverse effects in humans or animals. Thus, integrating antiviral genes of virus origin into plant genomes is hardly unnatural as suggested by GM crop skeptics. Moreover, advances in deep sequencing have resulted in the sequencing of large numbers of plant genomes and the revelation of widespread endogenization of viral genomes into plant genomes. This has raised the possibility that viral genome endogenization is part of an antiviral defense mechanism deployed by the plant during its evolutionary past. Thus, GM crops engineered for viral resistance would likely be acceptable to the public if regulatory policies were product-based (the North America regulatory model), as opposed to process-based. This review discusses some of the benefits to be gained from adopting GE for virus resistance, as well as the challenges that must be overcome to leverage this technology. Furthermore, regulatory policies impacting virus-resistant GM crops and some success cases of virus-resistant GM crops approved so far for cultivation are discussed.

Biological and molecular characterization of bean bushy stunt virus, a novel bipartite begomovirus infecting common bean in northwestern Argentina

Common bean plants (Phaseolus vulgaris L.) showing different virus-like symptoms were collected in northwestern Argentina. Dot-blot hybridization tests showed that the begomoviruses bean golden mosaic virus and tomato yellow vein streak virus were the most prevalent, but they also revealed the presence of unknown begomoviruses. The complete genome sequence of one of these unknown begomoviruses was determined. Sequence analysis showed that the virus is a typical New World begomovirus, for which the name "bean bushy stunt virus" (BBSV) is proposed. Biological assays based on biolistic inoculations showed that BBSV induced leaf roll and stunting symptoms similar to those observed in the field-collected common bean sample.

Disease Pandemics and Major Epidemics Arising from New Encounters between Indigenous Viruses and Introduced Crops

Virus disease pandemics and epidemics that occur in the world’s staple food crops pose a major threat to global food security, especially in developing countries with tropical or subtropical climates. Moreover, this threat is escalating rapidly due to increasing difficulties in controlling virus diseases as climate change accelerates and the need to feed the burgeoning global population escalates. One of the main causes of these pandemics and epidemics is the introduction to a new continent of food crops domesticated elsewhere, and their subsequent invasion by damaging virus diseases they never encountered before. This review focusses on providing historical and up-to-date information about pandemics and major epidemics initiated by spillover of indigenous viruses from infected alternative hosts into introduced crops. This spillover requires new encounters at the managed and natural vegetation interface. The principal virus disease pandemic examples described are two (cassava mosaic, cassava brown streak) that threaten food security in sub-Saharan Africa (SSA), and one (tomato yellow leaf curl) doing so globally. A further example describes a virus disease pandemic threatening a major plantation crop producing a vital food export for West Africa (cacao swollen shoot). Also described are two examples of major virus disease epidemics that threaten SSA’s food security (rice yellow mottle, groundnut rosette). In addition, brief accounts are provided of two major maize virus disease epidemics (maize streak in SSA, maize rough dwarf in Mediterranean and Middle Eastern regions), a major rice disease epidemic (rice hoja blanca in the Americas), and damaging tomato tospovirus and begomovirus disease epidemics of tomato that impair food security in different world regions. For each pandemic or major epidemic, the factors involved in driving its initial emergence, and its subsequent increase in importance and geographical distribution, are explained. Finally, clarification is provided over what needs to be done globally to achieve effective management of severe virus disease pandemics and epidemics initiated by spillover events.

Population Dynamics of Whiteflies and Associated Viruses in South America: Research Progress and Perspectives

Simple Summary

Whiteflies are one of the most important and widespread pests in the world. In South America, the currently most important species occurring are Bemisia afer,Trialeurodes vaporariorum, and the cryptic species Middle East-Asia Minor 1, Mediterranean, and New World, from Bemisia tabaci complex. The present review compiles information from several studies conducted in South America regarding these insects, providing data related to the dynamics and distribution of whiteflies, the associated viruses, and the management strategies to keep whiteflies under the economic damage threshold.

Abstract

By having an extensive territory and suitable climate conditions, South America is one of the most important agricultural regions in the world, providing different kinds of vegetable products to different regions of the world. However, such favorable conditions for plant production also allow the development of several pests, increasing production costs. Among them, whiteflies (Hemiptera: Aleyrodidae) stand out for their potential for infesting several crops and for being resistant to insecticides, having high rates of reproduction and dispersal, besides their efficient activity as virus vectors. Currently, the most important species occurring in South America are Bemisia afer, Trialeurodes vaporariorum, and the cryptic species Middle East-Asia Minor 1, Mediterranean, and New World, from Bemisia tabaci complex. In this review, a series of studies performed in South America were compiled in an attempt to unify the advances that have been developed in whitefly management in this continent. At first, a background of the current whitefly distribution in South American countries as well as factors affecting them are shown, followed by a background of the whitefly transmitted viruses in South America, addressing their location and association with whiteflies in each country. Afterwards, a series of management strategies are proposed to be implemented in South American fields, including cultural practices and biological and chemical control, finalizing with a section containing future perspectives and directions for further research.

Global Dimensions of Plant Virus Diseases: Current Status and Future Perspectives

Viral diseases provide a major challenge to twenty-first century agriculture worldwide. Climate change and human population pressures are driving rapid alterations in agricultural practices and cropping systems that favor destructive viral disease outbreaks. Such outbreaks are strikingly apparent in subsistence agriculture in food-insecure regions. Agricultural globalization and international trade are spreading viruses and their vectors to new geographical regions with unexpected consequences for food production and natural ecosystems. Due to the varying epidemiological characteristics of diverent viral pathosystems, there is no one-size-fits-all approach toward mitigating negative viral disease impacts on diverse agroecological production systems. Advances in scientific understanding of virus pathosystems, rapid technological innovation, innovative communication strategies, and global scientific networks provide opportunities to build epidemiologic intelligence of virus threats to crop production and global food security. A paradigm shift toward deploying integrated, smart, and eco-friendly strategies is required to advance virus disease management in diverse agricultural cropping systems.

Tropical food legumes: virus diseases of economic importance and their control

Diverse array of food legume crops (Fabaceae: Papilionoideae) have been adopted worldwide for their protein-rich seed. Choice of legumes and their importance vary in different parts of the world. The economically important legumes are severely affected by a range of virus diseases causing significant economic losses due to reduction in grain production, poor quality seed, and costs incurred in phytosanitation and disease control. The majority of the viruses infecting legumes are vectored by insects, and several of them are also seed transmitted, thus assuming importance in the quarantine and in the epidemiology. This review is focused on the economically important viruses of soybean, groundnut, common bean, cowpea, pigeonpea, mungbean, urdbean, chickpea, pea, faba bean, and lentil and begomovirus diseases of three minor tropical food legumes (hyacinth bean, horse gram, and lima bean). Aspects included are geographic distribution, impact on crop growth and yields, virus characteristics, diagnosis of causal viruses, disease epidemiology, and options for control. Effectiveness of selection and planting with virus-free seed, phytosanitation, manipulation of crop cultural and agronomic practices, control of virus vectors and host plant resistance, and potential of transgenic resistance for legume virus disease control are discussed.

Contrasting genetic structure between two begomoviruses infecting the same leguminous hosts

Begomoviruses are whitefly-transmitted, ssDNA plant viruses and are among the most damaging pathogens causing epidemics in economically important crops worldwide. Wild/non-cultivated plants play a crucial epidemiological role, acting as begomovirus reservoirs and as ‘mixing vessels' where recombination can occur. Previous work suggests a higher degree of genetic variability in begomovirus populations from non-cultivated hosts compared with cultivated hosts. To assess this supposed host effect on the genetic variability of begomovirus populations, cultivated (common bean, Phaseolus vulgaris, and lima bean, Phaseolus lunatus) and non-cultivated (Macroptilium lathyroides) legume hosts were sampled from two regions of Brazil. A total of 212 full-length DNA-A genome segments were sequenced from samples collected between 2005 and 2012, and populations of the begomoviruses Bean golden mosaic virus (BGMV) and Macroptilium yellow spot virus (MaYSV) were obtained. We found, for each begomovirus species, similar genetic variation between populations infecting cultivated and non-cultivated hosts, indicating that the presumed genetic variability of the host did not a priori affect viral variability. We observed a higher degree of genetic variation in isolates from MaYSV populations than BGMV populations, which was explained by numerous recombination events in MaYSV. MaYSV and BGMV showed distinct distributions of genetic variation, with the BGMV population (but not MaYSV) being structured by both host and geography.

Indigenous American species of the Bemisia tabaci complex are still widespread in the Americas

Bemisia tabaci is a complex of at least 36 putative cryptic species. Since the late 1980s, the Middle East-Asia Minor 1 species (MEAM1, formerly known as the B biotype), has emerged in many tropical and subtropical regions of the world and in some areas has displaced the indigenous populations of B. tabaci. Based on analysis of the mtCOI gene, two indigenous species native to America have been reported: New World (NW, formerly the A biotype) and New World 2 (NW2). NW is present at least in Argentina, Brazil, Martinique, Mexico, Texas and Venezuela, and NW2 in Argentina, Bolivia and Brazil. Wild plants (Euphorbia sp. and Ipomoea sp.), as well as important crops such as tomato, bean and cotton, are still hosts for native B. tabaci populations in the Americas. MEAM1 has not completely displaced the native B. tabaci from the Americas.

Complete genome sequences of two novel begomoviruses infecting common bean in Venezuela

The complete genome sequences of isolates of two new bipartite begomoviruses (genus Begomovirus, family Geminiviridae) found infecting common bean in Venezuela are provided. The names proposed for each of these viruses are "bean yellow chlorosis virus" (BYCV) and "bean white chlorosis mosaic virus" (BWCMV). Phylogenetic analysis showed that they segregated in two distinct clades of New World begomoviruses. This is the first report of begomoviruses infecting common bean in Venezuela.

Diversity of dicotyledenous-infecting geminiviruses and their associated DNA molecules in southern Africa, including the South-west Indian ocean islands

The family Geminiviridae comprises a group of plant-infecting circular ssDNA viruses that severely constrain agricultural production throughout the temperate regions of the world, and are a particularly serious threat to food security in sub-Saharan Africa. While geminiviruses exhibit considerable diversity in terms of their nucleotide sequences, genome structures, host ranges and insect vectors, the best characterised and economically most important of these viruses are those in the genus Begomovirus. Whereas begomoviruses are generally considered to be either monopartite (one ssDNA component) or bipartite (two circular ssDNA components called DNA-A and DNA-B), many apparently monopartite begomoviruses are associated with additional subviral ssDNA satellite components, called alpha- (DNA-αs) or betasatellites (DNA-βs). Additionally, subgenomic molecules, also known as defective interfering (DIs) DNAs that are usually derived from the parent helper virus through deletions of parts of its genome, are also associated with bipartite and monopartite begomoviruses. The past three decades have witnessed the emergence and diversification of various new begomoviral species and associated DI DNAs, in southern Africa, East Africa, and proximal Indian Ocean islands, which today threaten important vegetable and commercial crops such as, tobacco, cassava, tomato, sweet potato, and beans. This review aims to describe what is known about these viruses and their impacts on sustainable production in this sensitive region of the world.

Molecular characterization of distinct bipartite begomovirus infecting bhendi (Abelmoschus esculentus L.) in India

Yellow vein mosaic disease of okra is a whitefly transmitted begomovirus causing heavy economic loss in different parts of India. The okra isolate (OY131) of this virus from a bhendi plant [(Abelmoschus esculentus L.) Moench] showing yellow vein mosaic, vein twisting, reduced leaves, and a bushy appearance in the Palem region, New Delhi, India, was characterized in the present study. The complete DNA-A and DNA-B sequences have been determined and are comprised of 2,746 and 2,703 nucleotides, respectively. The betasatellite (DNA-β) component was absent in the sample. The genome organization was typically of biparite begomoviruses, which were characterized earlier. Comparison of DNA-A component with other known begomoviruses suggest that this virus, being only distantly related (<85.9% similarity with its nearest relative, BYVMV) to other known begomoviruses, is a new species. We have tentatively assigned the genome to a novel geminivirus species Bhendi yellow vein mosaic Delhi virus [BYVDV-IN (India: Delhi: okra)]. DNA-B showed highest sequence identity (87.8% identical) to that of a ToLCNDV (AY158080). The phylogenetic analysis of the present isolate is distinct from all other viruses; however clusters with ToLCNDV group infect different crops. The recombination analysis revealed that this isolate has sequences originated from ToLCNDV. This is the first known bhendi yellow vein mosaic disease associated bipartite begomovirus from India.

Further characterization of tomato-infecting begomoviruses in Brazil

Tomato cultivation in Brazil is threatened by a number of tomato-infecting viruses belonging to the genus Begomovirus of the family Geminiviridae. Here, we report the full DNA-A sequences of three Brazilian begomoviruses: a potentially new tomato-infecting viruses, tomato interveinal chlorosis virus (ToICV), and two previously proposed begomoviruses for which only partial DNA-A sequences are available in the databases: tomato mottle leaf curl virus (TMoLCV) and tomato golden vein virus (TGVV). The complete sequences of the DNA-B components of TMoLCV and TGVV and the DNA-A components of a number of tomato severe rugose virus variants are also presented. Collectively, all of the analyzed sequences were phylogenetically clustered within the two major groups of Brazilian tomato-infecting begomoviruses.

Recombination in eukaryotic single stranded DNA viruses

Although single stranded (ss) DNA viruses that infect humans and their domesticated animals do not generally cause major diseases, the arthropod borne ssDNA viruses of plants do, and as a result seriously constrain food production in most temperate regions of the world. Besides the well known plant and animal-infecting ssDNA viruses, it has recently become apparent through metagenomic surveys of ssDNA molecules that there also exist large numbers of other diverse ssDNA viruses within almost all terrestrial and aquatic environments. The host ranges of these viruses probably span the tree of life and they are likely to be important components of global ecosystems. Various lines of evidence suggest that a pivotal evolutionary process during the generation of this global ssDNA virus diversity has probably been genetic recombination. High rates of homologous recombination, non-homologous recombination and genome component reassortment are known to occur within and between various different ssDNA virus species and we look here at the various roles that these different types of recombination may play, both in the day-to-day biology, and in the longer term evolution, of these viruses. We specifically focus on the ecological, biochemical and selective factors underlying patterns of genetic exchange detectable amongst the ssDNA viruses and discuss how these should all be considered when assessing the adaptive value of recombination during ssDNA virus evolution.

Molecular and biological characterization of a new Brazilian begomovirus, euphorbia yellow mosaic virus (EuYMV), infecting Euphorbia heterophylla plants

To date, no begomovirus has been fully characterized from Euphorbia heterophylla, a widely distributed weed, in Brazil. Here, we show the occurrence of a new begomovirus on E. heterophylla plants showing bright yellow mosaic. The bipartite viral genome was cloned from 10 samples, and all clones are almost identical to each other (95.6-98.8% nucleotide sequence identity). The DNA-A sequences shared a maximum nucleotide sequence identity of 87.3% with euphorbia mosaic Peru virus (EuMPV) and thus were classified as belonging to a novel begomovirus species, tentatively named Euphorbia yellow mosaic virus (EuYMV). The EuYMV DNA-B sequences share a maximum nucleotide sequence identity of 56.2% with a euphorbia mosaic virus (EuMV) isolate from Mexico. Phylogenetic analysis demonstrated that this new virus belongs to a different lineage than EuMV isolates from Central America.

The first DNA 1-like alpha satellites in association with New World begomoviruses in natural infections

From Brazilian weeds with typical symptoms of a geminivirus infection, the DNAs of two new virus species, two new strains with two variants of already known bipartite begomoviruses were sequenced. Moreover, the first two DNA 1-like satellites (alpha satellites) occurring naturally in the New World were identified. They are related to nanoviral DNA components and show a typical genome organization with one open reading frame coding potentially for a replication-associated protein (Rep), a conserved hairpin structure, and an A-rich region. After coinoculation with their helper begomoviruses (Euphorbia mosaic virus, EuMV or Cleome leaf crumple virus, ClLCrV) the satellite DNAs were transmitted to experimental and natural host plants. Three of the begomovirus isolates (EuMV and ClLCrV) infected Arabidopsis thaliana plants, induced mild symptoms, and one of these (ClLCrV) transreplicated the satellite efficiently. As a result, several novel tools for molecular analyses of this important model plant are provided.

The complete nucleotide sequence of a new bipartite begomovirus from Brazil infecting Abutilon

The complete nucleotide sequence of Abutilon mosaic Brazil virus (AbMBV), a new bipartite begomovirus from Bahia, Brazil, is described and analyzed phylogenetically. Its DNA A is most closely related to those of Sida-infecting begomoviruses from Brazil and forms a phylogenetic cluster with pepper- and Euphorbia-infecting begomoviruses from Central America. The DNA B component forms a cluster with different Sida- and okra-infecting begomoviruses from Brazil. Both components are distinct from those of the classical Abutilon mosaic virus originating from the West Indies. AbMBV is transmissible to Nicotiana benthamiana and Malva parviflora by biolistics of rolling-circle amplification products and induces characteristic mosaic and vein-clearing symptoms in M. parviflora.

Maintenance of an old world betasatellite by a new world helper begomovirus and possible rapid adaptation of the betasatellite

Begomoviruses (family Geminiviridae) cause major losses to crops throughout the tropical regions of the world. Begomoviruses originating from the New World (NW) and the Old World (OW) are genetically distinct. Whereas the majority of OW begomoviruses have monopartite genomes and whereas most of these associate with a class of symptom-modulating satellites (known as betasatellites), the genomes of NW begomoviruses are exclusively bipartite and do not associate with satellites. Here, we show for the first time that a betasatellite (cotton leaf curl Multan betasatellite [CLCuMuB]) associated with a serious disease of cotton across southern Asia is capable of interacting with a NW begomovirus. In the presence of CLCuMuB, the symptoms of the NW cabbage leaf curl virus (CbLCuV) are enhanced in Nicotiana benthamiana. However, CbLCuV was unable to interact with a second betasatellite, chili leaf curl betasatellite. Although CbLCuV can transreplicate CLCuMuB, satellite accumulation levels in plants were low. However, progeny CLCuMuB isolated after just one round of infection with CbLCuV contained numerous mutations. Reinoculation of one such progeny CLCuMuB with CbLCuV to N. benthamiana yielded infections with significantly higher satellite DNA levels. This suggests that betasatellites can rapidly adapt for efficient transreplication by a new helper begomovirus, including begomoviruses originating from the NW. Although the precise mechanism of transreplication of betasatellites by begomoviruses remains unknown, an analysis of betasatellite mutants suggests that the sequence(s) required for maintenance of CLCuMuB by one of its cognate begomoviruses (cotton leaf curl Rajasthan virus) differs from the sequences required for maintenance by CbLCuV. The significance of these findings and, particularly, the threat that betasatellites pose to agriculture in the NW, are discussed.

Three distinct begomoviruses associated with soybean in central Brazil

We report the complete nucleotide sequences of geminiviruses of the genus Begomovirus infecting soybean (Glycine max) in central Brazil. Samples obtained from soybean plants collected at Santo Antonio de Goiás, Goiás State, showing typical symptoms of viral infection, were analyzed. Infection was confirmed by PCR-based amplification of a DNA-A fragment with universal begomovirus primers. Total DNA from infected plants was then subjected to rolling-circle amplification (RCA), and 2.6-kb molecules were cloned into plasmid vectors. Sequencing of the three DNA-A and two DNA-B clones thus obtained confirmed infection by three distinct begomoviruses: bean golden mosaic virus, Sida micrantha mosaic virus and okra mottle virus, the last of which was reported recently to be a novel virus infecting okra plants in Brazil. Begomovirus infection of soybean plants has been reported sporadically in Brazil and has generally not been considered to be of economic relevance.

Plant virus emergence and evolution: origins, new encounter scenarios, factors driving emergence, effects of changing world conditions, and prospects for control

This review focuses on virus-plant pathosystems at the interface between managed and natural vegetation, and describes how rapid expansion in human activity and climate change are likely to impact on plants, vectors and viruses causing increasing instability. It starts by considering virus invasion of cultivated plants from their wild ancestors in the centres of plant domestication in different parts of the world and subsequent long distance movement away from these centres to other continents. It then describes the diverse virus-plant pathosystem scenarios possible at the interface between managed and natural vegetation and gives examples that illustrate situations where indigenous viruses emerge to damage introduced cultivated plants and newly introduced viruses become potential threats to biodiversity. These examples demonstrate how human activities increasingly facilitate damaging new encounters between plants and viruses worldwide. The likely effects of climate change on virus emergence are emphasised, and the major factors driving virus emergence, evolution and greater epidemic severity at the interface are analysed and explained. Finally, the kinds of challenges posed by rapidly changing world conditions to achieving effective control of epidemics of emerging plant viruses, and the approaches needed to address them, are described.

Geminiviruses

Plant pathogenic geminiviruses have been proliferating worldwide and have, therefore, attracted considerable scientific interest during the past three decades. Current knowledge concerning their virion and genome structure, their molecular biology of replication, recombination, transcription, and silencing, as well as their transport through plants and dynamic competition with host responses are summarized. The topics are chosen to provide a comprehensive introduction for animal virologists, emphasizing similarities and differences to the closest functional relatives, polyomaviruses and circoviruses.

Multiple introductions of the Old World begomovirus Tomato yellow leaf curl virus into the New World

A phylogenetic analysis of three genomic regions revealed that Tomato yellow leaf curl virus (TYLCV) from western North America is distinct from TYLCV isolated in eastern North America and the Caribbean. This analysis supports a second introduction of this Old World begomovirus into the New World, most likely from Asia.

RNAi-mediated resistance to Bean golden mosaic virus in genetically engineered common bean (Phaseolus vulgaris)

Bean golden mosaic virus (BGMV) is transmitted by the whitefly Bemisia tabaci in a persistent, circulative manner, causing the golden mosaic of common bean (Phaseolus vulgaris L.). The characteristic symptoms are yellow-green mosaic of leaves, stunted growth, or distorted pods. The disease is the largest constraint to bean production in Latin America and causes severe yield losses (40 to 100%). Here, we explored the concept of using an RNA interference construct to silence the sequence region of the AC1 viral gene and generate highly resistant transgenic common bean plants. Eighteen transgenic common bean lines were obtained with an intron-hairpin construction to induce post-transcriptional gene silencing against the AC1 gene. One line (named 5.1) presented high resistance (approximately 93% of the plants were free of symptoms) upon inoculation at high pressure (more than 300 viruliferous whiteflies per plant during the whole plant life cycle) and at a very early stage of plant development. Transgene-specific small interfering RNAs were detected in both inoculated and non-inoculated transgenic plants. A semiquantitative polymerase chain reaction analysis revealed the presence of viral DNA in transgenic plants exposed to viruliferous whiteflies for a period of 6 days. However, when insects were removed, no virus DNA could be detected after an additional period of 6 days.