The monopartite genomic DNA is similar in sequence and genome organization to the DNA-A component of bipartite begomoviruses, with one gene on the v-sense strand encoding the CP, and four genes on the c-sense strand encoding Rep, TrAP, Ren and the C4/AC4 protein. The DNA-B component of the bipartite begomoviruses has two genes, BV1 and BC1, which encodes a nuclear shuttle protein and movement protein, respectively . The sequence of the DNA-B component is typically more divergent than that of the DNA-A component , and also has a hypervariable region . This HVR extends from the 5’ end of the CR to the initiation codon of the BC1 open reading frame and is the most variable region in the genome of bipartite begomoviruses. Begomoviruses also show a phylogeographic distribution, with most bipartite species occurring in the New World and rarely associated with satellites DNAs, and most monopartite species occurring in the Old World and often in association with satellite DNAs that are either required for disease development or have no obvious effect inmodulating disease symptoms . However, there are exception to this, including the introduction of TYLCV into the NW in the early 1990s and the recent identification of indigenous NW monopartite begomoviruses infecting tomato in Peru, Ecuador, Venezuela and Northern Brazil . Begomoviruses have a remarkable flexibility in genome evolution and a long evolutionary history. It is generally believed that the ancestor of modern-day begomoviruses was monopartite and that the bipartite genome likely evolved before the breakup of the supercontinent Pangea because bipartite begomoviruses occur in the NW and OW .
In this scenario, growth rack these viruses have co-evolved with plants for millions of years, i.e., well before the emergence of flowering plants and the domestication of crops . The subsequent diversification and evolution of OW and NW begomoviruses involved genetic mechanisms such as mutation and recombination, which are known as the major contributors to the genetic divergence of viruses . In terms of these mechanisms, recombination has played, and continues to play, an important role in the emergence of begomoviruses. Extensive analysis of begomovirus/satellite sequences have shown that several species of monopartite and bipartite begomoviruses have evolved extensively through recombination . Furthermore, these studies also revealed that recombination hot spots exist in the begomovirus genome, especially the region spans the 5’ end of the AC1 gene, the entire overlapping AC4 gene and the left side of the CR . Begomovirus genomes also showed high level of within-host variation and substitution rates inferred for these viruses are equivalent to those of RNA viruses . More recently, it was shown that mutation is likely the main source of genetic variation for begomovirus genomes . The evolution of begomoviruses also involves pseudore combination . Pseudorecombinants are typically formed between isolates and strains of the same begomovirus species, but in some cases, they can also be formed with DNA components from different species .
Additionally, begomovirus genomes have the capacity to acquire and modify small circular ssDNA components. For example, acquisition of satellite DNAs has played a major role in evolution of OW monopartite begomoviruses, whereas acquisition and modification of the DNA-B components acquired by pseudore combination has played a role bipartite begomoviruses evolution . Finally, begomovirus also evolved locally through the world, resulting in the emergence of multiple begomovirus species that infect one particular host and cause similar symptoms . The emergence and evolution of new begomovirus species has been facilitated by the polyphagous behavior of the whitefly supervector, especially the B. tabaci species MEAM1. Moreover, human activities have led to the long-distance movement of numerous begomoviruses, blurring the geographic separation of OW and NW begomoviruses, e.g., introduction of squash leaf curl virus into the Middle East from the NW, introduction of tomato leaf curl New Delhi virus into the Western Mediterranean Basin from the subcontinent of Asia . However, none of these cases has been as important as the introduction of the invasive TYLCV into the NW during the early 1990s . From there, TYLCV quickly invaded the Southern US, Mexico and the rest of the world . In general, individual begomoviruses tend to have relative narrow host ranges . However, as a group, they can infect a wide range of food and fiber crops, ornamental plants and non-cultivated plants in the OW and NW .
Plants affected include crops such as tomato, cassava, common bean, cotton, cucurbits and pepper; ornamentals such as Abutilon spp. and Lonicera spp. ; and weeds such as Malachra spp., Sida spp., Macroptilium spp. and Malva spp. .In terms of production, tomato has become one of the most important vegetables crops in the world . Tomato is infected by more begomovirus species than any other crop , and this can be attributed to a number of factors. First, production of tomato has grown quickly over the world . Second, domesticated tomato is highly susceptible to begomovirus infection . Third, local evolution has resulted in the emergence of multiple begomoviruses that infect tomato and cause similar symptoms . Together this has accelerated the emergence of numerous tomato-infecting begomoviruses in the NW and OW . The NW begomovirus disease of tomato are mainly caused by bipartite species, although monopartite are becoming more important . Several tomato-infecting begomoviruses have been reported from North and Central America, including tomato mottle virus, pepper golden mosaic virus , pepper huasteco yellow vein virus, chino del tomate virus, tomato golden mottle virus, tomato leaf curl Sinaloa virus , tomato yellow mottle virus , tomato mosaic Havana virus , tomato severe leaf curl virus and the invasive TYLCV . Furthermore, these begomoviruses are often found in mixed infections , which allows for further virus evolution via recombination and pseudore combination . In South America, tomato-infecting begomoviruses emerged in Brazil and other countries after the introduction of the highly polyphagous B. tabaci species MEAM1 in the 90s . The first tomato begomovirus disease in Brazil was cause by the tomato golden mosaic virus , which was reported in the early 1960s . Since then, clone rack at least 14 tomato-infecting begomoviruses have been described and characterized . For example, tomato severe rugose virus is important in central regions, whereas tomato mottle leaf curl virus is more prevalent in north-eastern regions of Brazil . Additionally, since 2010, NW monopartite tomato-infecting monopartite begomoviruses continue to be discovered in BR, Ecuador, Peru and Venezuela . In the OW, tomato yellow leaf curl disease has emerged as one of the most important diseases of tomato . The disease is caused by a complex of species of monopartite and bipartite begomoviruses . Among these viruses, TYLCV and tomato yellow leaf curl Sardinia virus have cause significant crop losses in the Mediterranean Basin . Furthermore, these viruses have been shown to participate in genetic exchanges giving rise to resistance-breaking strains of TYLCV . The bipartite ToLCNDV, the causal agent of tomato leaf curl disease , is one of the most important tomato-infecting begomovirus in the Indian subcontinent . Moreover, in recent years, the virus has expanded its host range and spread into new geographical regions, e.g., North Africa and Southern Europe . Finally, several monopartite tomato-infecting begomoviruses have been described in Asia, including tomato yellow leaf curl China virus, tomato leaf curl China virus, tobacco curly shoot virus, tobacco leaf curl Yunnan virus, tomato leaf curl Guangxi virus, tomato leaf curl Malaysia virus, tobacco leaf curl Japan virus and tomato yellow leaf curl Thailand virus .In addition to infecting crop plants such as tomato, begomoviruses infect a diversity of non-cultivated plants, mostly weeds, in tropical and subtropical regions of the world . Numerous begomoviruses have been reported infecting weed species in the families Asteraceae, Capparaceae, Convolvulaceae, Euphorbiaceae, Fabaceae, Malvaceae, Nyctaginaceae and Solanaceae . Non-cultivated plants have long been believed to serve as a reservoir or alternative hosts for crop-infecting begomoviruses . However, most begomoviruses characterized from weeds are highly adapted to these hosts, and typically infect crop plants less efficiently or not at all . Although there are some exceptions such as tobacco leaf curl Cuba virus infecting Malachra alceifolia in Jamaica , and Nicandra physaloides infected with tomato severe rugose virus in Brazil . Begomoviruses populations in non-cultivated plants are subject to a range of distinct selective pressures compared with those in crop species, as the genetic background of these wildspecies is wider than those of crop species . As a result, begomovirus populations in non-cultivated plants tend to be divergent compared with those of crop-infecting begomoviruses .
Together, this suggest that begomoviruses infecting crops and weeds have coevolved with their hosts over a long period of time, such that the crop-infecting viruses inefficiently infect weeds. More likely, these weeds serve as sources of begomovirus diversity for the emergence of crop-infecting begomoviruses . In this scenario, crop-infecting begomoviruses have originated from ancestral viruses infecting non-cultivated plants, e.g., during spillover events and subsequently evolving and adapting to crops, some of which are highly susceptible, e.g., tomato . Several lines of evidence support this later hypothesis. First, crop-infecting begomoviruses can generally be associated with geographical regions, e.g., begomoviruses that infect crops in Brazil appear to have been indigenous . Second, characterization of some crop-infecting begomoviruses have shown the capacity to infect weeds . Third, the well-established phenomenon of local evolution is consistent with crop-infecting begomoviruses having evolved from weed-infecting progenitors . Together, these findings indicate the importance of weeds in the epidemiology of crop plants and help explains the substantial divergence of weed- and crop-infecting begomoviruses.TYLCV is the most devastating tomato-infecting begomovirus worldwide . Under high whitefly pressure, outbreaks can result in yield losses of up to 100%, especially when plants are infected early in development . Tomato plants infected with TYLCV are stunted, and show abnormal upright grow, and leaves developed upward curling with yellowing, interveinal chlorosis, crumpling and often a bushy appearance . Moreover, flowers on infected plants commonly do not develop and abscise before fruit set, leading to major yield losses, as high as 100%. So far, TYLCV has been reported infecting other solanaceous crops, such as pepper and tobacco; fabaceous crops, such as common bean; and non-cultivated plants, such as Ageratum conyzoides, Chenopodium murale, Cuscuta europaea, Malva parviflora and Sida acuta. However, tomato is by far the most economically important host of this virus, and most of the weeds are symptomless hosts and have low virus titers .Management of TYLCV requires an integrated pest management program that involves measures before, during and after the growing season . Before the growing season, TYLCV can be controlled by using virus- and whitefly-free transplants and propagative stocks and there are now commercially available resistant cultivars generated through conventional breeding . In addition, a variety of transgenic strategies have been used to develop TYLCV-resistant varieties, although these are not currently grow commercially . The use of insecticides to reduce whitefly populations is one of the most important, and commonly used components of a successful IPM approach during the growing season, but monitoring and proper timing of insecticide application is critical . Insecticides such as neonicotenoids and cyazypyr have been used effectively to control the whitefly vector in open fields and greenhouses . Unfortunately, continue usage of insecticides has led to the rapid emergence of insect vector population with resistance to various insecticides . Alternative measures during the growing season also involve roguing of virus-infected plants and row covers and reflective mulches . After the growing season, sanitation, weed management and implementation of a host-free period can be used to reduce the viral inoculumsource and vector populations . Indeed, these approaches have been successfully used to managed TYLCV in the DO .Tomato yellow leaf curl disease can cause devastating losses to tomato production worldwide . The disease is widely distributed in the Old World and New World , and is caused by several begomoviruses, including tomato yellow leaf curl virus . Regardless of the virus involved, symptoms of TYLCD include severe stunting, distorted and upright growth and leaves with upcurling, crumpling, interveinal chlorosis, and yellowing . Tomato is highly susceptible to TYLCV infection and, under high disease pressure , outbreaks can result in substantial yield losses, especially when plants are infected at early stages of development . Because the whitefly vector is difficult to control, an important strategy for disease management is planting of resistant tomato varieties that possess resistance loci introgressed fromwild species .