Six novel begomoviruses infecting tomato and associated weeds in Southeastern Brazil

The incidence of tomato-infecting begomoviruses has sharply increased in Brazil following the introduction of the B biotype of the whitefly vector in the early 1990s. Five definitive species and six tentative species have been described since then. Here, we report the detection of members of an additional six novel species, three in tomato and three infecting weeds that are commonly associated with tomato fields: Blainvillea rhomboidea, Sida rhombifolia and Sida micrantha. Tomato and weed samples were collected in two major tomato-growing regions of southeastern Brazil in 2005 and 2007. Two of the novel viruses were present in tomato plants collected in Paty do Alferes, Rio de Janeiro state. Three novel viruses were present in weed samples collected in Coimbra, Minas Gerais state. One virus was present in tomato samples collected at both locations. Genome features indicate that all six species are typical New World, bipartite begomoviruses. However, the viruses belonging to two of the novel species did not cluster with the Brazilian viruses in a phylogenetic tree. These species could represent a distinct lineage of New World begomoviruses, found in Brazil for the first time. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. The sequences reported in this paper have been deposited in the GenBank under the accession numbers EU710749–EU710757.     

Characterization and distribution of tomato yellow margin leaf curl virus, a begomovirus from Venezuela

A begomovirus causing mottling and leaf deformation in tomato from the State of Mérida was cloned and sequenced. The virus has a bipartite genome comprised of a DNA-A (2,572 nucleotides) and a DNA-B (2,543 nucleotides) with a genome organization typical of New World begomoviruses. Both components share a common region of 115 nucleotides with 98 % sequence identity. Phylogenetic analysis indicated that while no virus sequences were closely related, the A component was distantly related to those of two other tomato-infecting viruses, tomato leaf deformation virus and Merremia mosaic virus; and the DNA-B, to those of pepper huasteco yellow vein virus and Rhynchosia golden mosaic Yucatan virus. The DNA-A and DNA-B sequences were submitted to GenBank (accession no. AY508993 and AY508994, respectively) and later accepted by the International Committee on Taxonomy of Viruses as the genome of a member of a unique virus species with the name Tomato yellow margin leaf curl virus (TYMLCV). Tomato (Solanum lycopersicum L. ‘Fl. Lanai’) plants inoculated with cloned TYMLCV DNA-A and DNA-B became systemically infected and showed chlorotic margins and leaf curling. The distribution of TYMLCV in tomato-producing states in Venezuela was determined by nucleic acid spot hybridization analysis of 334 tomato leaf samples collected from ten states using a TYMLCV-specific probe and confirmed by PCR and sequencing of the PCR fragment. TYMLCV was detected in samples from the states of Aragua, Guárico, and Mérida, suggesting that TYMLCV is widely distributed in Venezuela.     

Unique grouping of the Far East Asian begomovirus complex based on sequence analyses of the DNA-A genome and associated DNAβ satellite molecules isolated from tomato, honeysuckle and Eupatorium plants in Japan

Nucleotide (nt) sequencing has contributed to the identification of virus species and has also proved diagnostically useful in the control of tomato-infecting begomoviruses disease. We determined the complete nt sequences of the DNA-A genome and its cognate DNAβ satellite molecules in isolates of Tobacco leaf curl Japan virus, Honeysuckle yellow vein mosaic virus, Eupatorium yellow vein virus in Japan. Pairwise comparison analyses based on the nt sequences of DNA-A from the genetic group of these viruses tentatively named as TbLCJV, HYVMV and EpYVV (TbJV/HYV/EpV) revealed that this group had a significance threshold of 84 % identity. Phylogenetic relationship analyses of the nt sequences of DNA-A and DNAβ revealed that their isolates were separated into a discrete Far East Asian clade, distinct from all other begomoviruses. This clade was divided into two distinct clusters comprising the subgroups TbJV/HYV and EpV. Furthermore, recombination analysis revealed that members of the TbJV/HYV/EpV group had the genetic variation indicative of many recombination events. Our study demonstrates that this group forms a unique species complex, but that members have discrete lineages depending on their natural perennial host plants. The nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under accession number AB236321–AB236327, AB300463, AB300464.     

Distribution and genetic diversity of tomato-infecting begomoviruses in Brazil<Superscript>*</Superscript>

Summary.  Tomato-infecting begomoviruses have been reported throughout Brazil since the introduction of the B biotype of Bemisia tabaci. Here, we report a large scale survey on the distribution and genetic diversity of tomato-infecting begomoviruses. Tomato samples with typical begomovirus symptoms were collected in seven different states, comprising the major tomato growing areas of the country. Viruses were detected by polymerase chain reaction (PCR) using universal primers for the genus Begomovirus. PCR-amplified fragments were cloned and sequenced. Based on sequence comparisons and phylogenetic analyses, at least seven previously undescribed species of begomoviruses were found. Four of the new viruses were found exclusively in the Southeastern states, two exclusively in the Northeastern states, and one was found in both regions. Sequence comparisons reveal strong evidence of recombination among the Brazilian begomoviruses. Together, the results indicate the existence of a high degree of pre-existing genetic diversity among tomato-infecting begomoviruses in Brazil and suggest that these viruses have emerged after being transferred from natural hosts to tomatoes, due to the introduction into Brazil of a novel polyfagous biotype of the whitefly vector. Received December 21, 2001; accepted September 1, 2002     

A novel cassava-infecting begomovirus from Madagascar: cassava mosaic Madagascar virus

Cassava mosaic geminiviruses (CMGs) are implicated in cassava mosaic disease (CMD), the main constraint to cassava production in Africa. Here, we report the complete nucleotide sequences of the DNA-A and DNA-B of a newly characterized CMG found infecting cassava in Madagascar, for which we propose the tentative name cassava mosaic Madagascar virus. With the exception of two recombinant regions that resembled a CMG, we determined that the non-recombinant part of the DNA-A component is distantly related to the other CMGs. Whereas the DNA-B component possesses one recombinant region originating from an unidentified virus, the rest of the genome was seen to be closely related to members of the species East African cassava mosaic Zanzibar virus (EACMZV). Phylogenetic analysis based on complete genome sequences demonstrated that DNA-A and DNA-B components are outliers related to the clade of EACMV-like viruses and that DNA-A is related to the monopartite tomato leaf curl begomoviruses described in islands in the south-west Indian Ocean.     

Genetic variability of begomoviruses associated with cotton leaf curl disease originating from India

Summary. Cotton leaf curl disease (CLCuD) causing viruses belong to the Begomovirus genus of the family Geminiviridae. Most begomoviruses are bipartite with two molecules of circular single stranded DNA (A and B) encapsidated in icosahedral geminate particles. However, the begomoviruses associated with CLCuD have DNA- instead of DNA-B. In this communication we report the complete genomic sequence of DNA-A component of two CLCuD-causing begomoviruses, cotton leaf curl Kokhran virus-Dabawali (CLCuKV-Dab), tomato leaf curl Bangalore virus-Cotton [Fatehabad] (ToLCBV-Cotton [Fat]) and partial sequences of two other isolates cotton leaf curl Rajasthan virus-Bangalore (CLCuRV-Ban) and cotton leaf curl Kokhran virus-Ganganagar (CLCuKV-Gang). A phylogenetic analysis of these isolates along with other related begomoviruses showed that ToLCBV-Cotton [Fat] isolate was closest to the tomato leaf curl Bangalore virus-5 (ToLCBV-Ban5) where as CLCuKV-Dab isolate was close to the cotton leaf curl Kokhran virus-Faisalabad1 (CLCuKV-Fai1), cotton leaf curl Kokhran virus-72b (CLCuKV-72b) and cotton leaf curl Kokhran virus-806b (CLCuKV-806b) isolates from Pakistan. The phylogenetic analysis further showed that the ToLCBV-Cotton [Fat] and CLCuKV-Dab isolates along with CLCuKV-Fai1, CLCuKV-72b and CLCuKV-806b are closer to the ToLCBV, tomato leaf curl Gujarat virus (ToLCGV), tomato leaf curl Gujarat virus-Varanasi (ToLCGV-Var) and tomato leaf curl Sri Lanka virus (ToLCSLV) isolates, where as cotton leaf curl Alabad virus-804a (CLCuAV-804a), cotton leaf curl Multhan virus (CLCuMV) cluster with the isolates from cotton leaf curl Rajasthan virus (CLCuRV) and okra yellow vein mosaic virus (OYVMV). These results demonstrate the extensive variability observed in this group of viruses. The AC4 ORF is the least conserved among these viruses. In order to further asses the variability in the CLCuD-causing begomoviruses, the region showing minimum similarity in the DNA-A sequence was first determined by a comparison of segments of different lengths of the aligned sequences. The results indicated that region 2411–424 (771nt) was the least conserved. A phylogenetic tree constructed using the sequences of all the CLCuD causing begomoviruses, corresponding to the least conserved region showed that they form two distinct clusters.     

Strains of a new bipartite begomovirus, pepper yellow leaf curl Indonesia virus, in leaf-curl-diseased tomato and yellow-vein-diseased ageratum in Indonesia

The complete nucleotide sequences of begomoviruses from pepper with leaf curl and yellowing symptoms, tomato with leaf curl symptoms, and ageratum with yellow vein in Indonesia were determined. On the basis of genome organization and sequence homology, they were proposed to belong to a new species, Pepper yellow leaf curl Indonesia virus (PepYLCIV), which includes the new strains PepYLCIV-Tomato and PepYLCIV-Ageratum. These viruses had bipartite genomes. Pepper virus DNAs from Indonesia (PepYLCIV, PepYLCIV-Tomato and PepYLCIV-Ageratum DNA-As) were noticeably distinct, forming a separate branch from the viruses infecting pepper. Considerable divergence was observed in the common region (CR) of the genomic components of PepYLCIV (77%), PepYLCIV-Tomato (82%) and PeYLCIV-Ageratum (75%). A stem-loop-forming region and a Rep-binding motif were identical in the CR of the three viruses. The CRs of PepYLCIV-Ageratum DNA-A was approximately 10 nucleotides longer than that of PepYLCIV DNA-A and PepYLCIV-Tomato DNA-A. A similar insertion was also found in the CR of PepYLCIV-Ageratum DNA-B. PepYLCIV DNA-A alone was infectious in pepper and Nicotiana benthamiana plants, and association with DNA-B increased symptom severity.     

Sequence characterization of Tomato leaf curl Sinaloa virus and <Emphasis Type="Italic">Tomato severe leaf curl virus</Emphasis>: Phylogeny of New World begomoviruses and detection of recombination

Summary. Diseases caused by begomoviruses (family Geminiviridae, genus Begomovirus) constitute a serious constraint to tomato production in Nicaragua. In this study, the complete nucleotide (nt) sequences of the DNA-A and DNA-B components were determined for the first time for Tomato leaf curl Sinaloa virus (ToLCSinV). In addition, the complete nt sequence was determined for the DNA-A component of two isolates of Tomato severe leaf curl virus (ToSLCV). The genome organization of ToLCSinV and ToSLCV was identical to the bipartite genomes of other begomoviruses described from the Americas. A phylogenetic analysis of DNA-A including 45 begomovirus species showed that the indigenous begomoviruses of the New World can be divided into three major clades and an intermediate group: AbMV clade, SLCV clade, “Brazil clade”, and BGYMV group. Phylogenetic analyses of the DNA-A and DNA-B components and their open reading frames indicated that ToLCSinV and ToSLCV belong to different clades: ToLCSinV to the AbMV clade, and ToSLCV to the SLCV clade. The two Nicaraguan isolates of ToSLCV showed a close relationship with ToSLCV from Guatemala (ToSLCV-[GT96-1]) and Tomato chino La Paz virus (ToChLPV), but differed significantly in the AV1 and AC1 regions, respectively. Computer-based predictions indicated that recombination with another begomovirus had taken place within AV1 of ToSLCV dividing this species into two strains. A high probability was also found that ToChLPV is involved in the evolution of ToSLCV.     

Evidence of local evolution of tomato-infecting begomovirus species in West Africa: characterization of tomato leaf curl Mali virus and tomato yellow leaf crumple virus from Mali

Tomato yellow leaf curl (TYLC) and tomato leaf curl (ToLC) diseases are serious constraints to tomato production in Mali and other countries in West Africa. In 2003 and 2004, samples of tomato showing virus-like symptoms were collected during a survey of tomato virus diseases in Mali. Three predominant symptom phenotypes were observed: (1) TYLC/ToLC (stunted upright growth and upcurled leaves with interveinal yellowing and vein purpling), (2) yellow leaf crumple and (3) broccoli or bonsai (severe stunting and distorted growth). Squash blot (SB) hybridization with a general begomovirus probe and/or SB/PCR analyses revealed begomovirus infection in plants with each of these symptom phenotypes and no evidence of phytoplasma infection. Sequence analysis of PCR-amplified begomovirus fragments revealed two putative new begomovirus species associated with the TYLC/ToLC and yellow leaf crumple symptom phenotypes, respectively. Full-length clones of these begomoviruses were obtained using PCR and overlapping primers. When introduced into N. benthamiana and tomato plants, these clones induced upward leaf curling and crumpling (the TYLC/ToLC-associated begomovirus) or downward leaf curl/yellow mottle (yellow leaf crumple-associated begomovirus) symptoms. Thus, these begomoviruses were named tomato leaf curl Mali virus (ToLCMLV) and tomato yellow leaf crumple virus (ToYLCrV). The genome organization of both viruses was similar to those of other monopartite begomoviruses. ToLCMLV and ToYLCrV were most closely related to each other and to tobacco leaf curl Zimbabwe virus (TbLCZV-[ZW]) and tomato curly stunt virus from South Africa (ToCSV-ZA). Thus, these likely represent tomato-infecting begomoviruses that evolved from indigenous begomoviruses on the African continent. Mixed infections of ToLCMLV and ToYLCrV in N. benthamiana and tomato plants resulted in more severe symptoms than in plants infected with either virus alone, suggesting a synergistic interaction. Agroinoculation experiments indicated that both viruses induced symptomatic infections in tomato and tobacco, whereas neither virus induced disease symptoms in pepper, common bean, small sugar pumpkin, African eggplant, or Arabidopsis. Virus-specific PCR primers were developed for detection of ToLCMLV and ToYLCrV and will be used to further investigate the distribution and host range of these viruses.     

Molecular characterization of a distinct bipartite begomovirus species infecting tomato in India

A distinct bipartite begomovirus was found associated with tomato plants showing yellowing, curling, and crumpling of the leaves, in a sub-temperate region in India. The complete DNA-A and DNA-B components were amplified through rolling circle amplification (RCA) using Φ-29 DNA polymerase and characterized. The DNA-A of the isolate was comprised of 2,756 nucleotides, encoding six open reading frames (ORFs) and DNA-B that of 2,725 nucleotides, encoding two ORFs. Genome organization of the isolate was typical of an old world bipartite begomovirus. Comparisons showed that DNA-A and its intergenic region (IR) have the highest sequence identity (86% and 84%, respectively) with the Tomato leaf curl New Delhi virus (ToLCNDV; DQ116885) and some other begomoviruses (>84%) reported from cucurbits and tomato. This data suggested that the isolate is a distinct begomovirus species for which a name Tomato leaf curl Palampur virus (ToLCPMV) is proposed. DNA-B showed the maximum sequence identity (73%) with Tomato leaf curl New Delhi virus-India-[Pakistan:Dargai:T5/6:2001] (AY150305). The common region (CR) of DNA-A and DNA-B showed 94% sequence similarity with each other. In the present study, phylogenetic relationship of this new species was also established with different begomoviruses reported from tomato and other begomoviruses showing highest homologies with complete DNA-A and DNA-B sequences. ToLCPMV is being reported from a sub-temperate region in India which was previously unaffected by begomoviruses and its whitefly vector. An erratum to this article can be found at     

PCR-based detection and partial genome sequencing indicate high genetic diversity in Bangladeshi begomoviruses and their whitefly vector, <Emphasis Type="Italic">Bemisia tabaci</Emphasis>

The population diversity of Bangladeshi begomoviruses and their vector, Bemisia tabaci was analysed by PCR-based detection and partial genome sequencing. B. tabaci adults and plants expressing symptoms of virus infection were collected from locations representing diverse agro-ecological regions of the country. Universal and species-specific primers were used to detect begomoviruses in seven crops (chilli, okra, papaya, pumpkin, sponge gourd, tomato and yardlong bean) and two common weeds (Ageratum conyzoides and Croton bonplandianum). At least five distinct species of tomato leaf curl viruses infected tomato and other host-plants. Phylogenetic analyses of their nucleotide sequences (∼530 bases) from the intergenic region and capsid protein of DNA-A indicated the existence of five distinct clusters of begomoviruses. Begomoviruses infecting tomato, chilli and dolichos have been reported previously, and those infecting Ageratum, Croton, okra, papaya, pumpkin and yardlong bean are described for the first time. Phylogenetic analyses based on mitochondrial cytochrome oxidase I gene sequences of 21 B. tabaci from Bangladesh and other reference sequences grouped them into at least two independent clusters. Some sequences from different countries, e.g., Bangladesh, China, India, Nepal, Pakistan and Thailand were almost identical while others collected from plants within the same field diverged by as much as 15%, indicating high diversity even at the local level. None of the B. tabaci from Bangladesh grouped with the reference B- and Q-biotype sequences, thus these two aggressive biotypes were apparently absent from Bangladesh.     

Transreplication of a Tomato yellow leaf curl Thailand virus DNA-B and replication of a DNAbeta component by Tomato leaf curl Vietnam virus and Tomato yellow leaf curl Vietnam virus

The genomes of two tomato-infecting begomoviruses from Vietnam were cloned and sequenced. A new variant of Tomato leaf curl Vietnam virus (ToLCVV) consisting of a DNA-A component and associated with a DNAbeta molecule as well as an additional begomovirus tentatively named Tomato yellow leaf curl Vietnam virus (TYLCVV) consisting also of a DNA-A component were identified. To verify if monopartite viruses occurring in Vietnam and Thailand are able to transreplicate the DNA-B component of Tomato yellow leaf curl Thailand virus-[Asian Institute of Technology] (TYLCTHV-[AIT]) infectivity assays were performed via agroinoculation and mechanically. As result, the DNA-B component of TYLCTHV-[AIT] was transreplicated by different DNA-A components of viruses from Vietnam and Thailand in Nicotiana benthamiana and Solanum lycopersicum. Moreover, the TYLCTHV-[AIT] DNA-B component facilitated the mechanical transmission of monopartite viruses by rub-inoculation as well as by particle bombardment in N. benthamiana and tomato plants. Finally, defective DNAs ranging from 735 to 1457 nucleotides were generated in N. benthamiana from those combinations containing TYLCTHV-[AIT] DNA-B component.     

High genetic variability and recombination in a begomovirus population infecting the ubiquitous weed Cleome affinis in northeastern Brazil

Diseases caused by begomoviruses are a serious constraint to crop production in many tropical and subtropical areas of the world, including Brazil. Begomoviruses are whitefly-transmitted, single-stranded DNA viruses that are often associated with weed plants, which may act as natural reservoirs of viruses that cause epidemics in crop plants. Cleome affinis (family Capparaceae) is an annual weed that is frequently associated with leguminous crops in Brazil. Samples of C. affinis were collected in four states in the northeast of Brazil. Analysis of 14 full-length DNA-A components revealed that only one begomovirus was present, with 91-96% identity to cleome leaf crumple virus (ClLCrV). In a phylogenetic tree, ClLCrV forms a basal group relative to all other Brazilian begomoviruses. Evidence of multiple recombination events was detected among the ClLCrV isolates, which also display a high degree of genetic variability. Despite ClLCrV being the only begomovirus found, its phylogenetic placement, high genetic variability and recombinant nature suggest that C. affinis may act as a source of novel viruses for crop plants. Alternatively, ClLCrV could be a genetically isolated begomovirus. Further studies on the biological properties of ClLCrV should help to clarify the role of C. affinis in the epidemiological scenario of Brazilian begomoviruses.     

Host-specific adaptation of diverse betasatellites associated with distinct Indian tomato-infecting begomoviruses

Tomato leaf curl viruses cause major crop loss hindering tomato cultivation worldwide. The ‘Old World’ begomoviruses are often associated with circular ssDNA satellite molecules called betasatellites. In the present study, replication compatibility of five different betasatellites with three distinct Indian tomato-infecting begomoviruses representing each of a monopartite, a mono-bipartite and a bipartite begomoviruses was studied. All the betasatellites could be trans-replicated by the begomoviruses in Nicotiana benthamiana plants, however, not uniformly in tomato. Tomato leaf curl Joydebpur betasatellite—Magrahat could not induce symptom with any of these begomoviruses in tomato, whereas only Tomato leaf curl Gujarat virus could trans-replicate Radish leaf curl betasatellite in this plant species. However, none of the betasatellites were found to complement the movement function of a bipartite begomovirus in tomato. Unlike tomato, the trans-replication/maintenance of betasatellites by these begomoviruses in N. benthamiana could be due to its compromised host defence machinery. Co-infection of betasatellites with these viruses did not enhance the helper virus accumulation, but the incubation period was reduced. The possible factors involved in this host-driven adaptability of betasatellites were also discussed.     

Further evidence reveals that okra mottle virus arose from a double recombination event

As a result of surveys of okra begomoviruses (genus Begomovirus, family Geminiviridae) conducted over the last five years in Central Brazil, we report the complete genome sequence of an isolate of okra mottle virus (OMoV). The DNA-A and DNA-B components were 2660 and 2653 nucleotides (nt) long, respectively, and they were most closely related to the DNA-A (~99 % nt identity) and DNA-B (~98 % nt identity) components of an OMoV isolate from a soybean plant. A phylogenetic tree was generated based on these sequences, and it was shown that both of the OMoV DNA components were grouped in a branch with Brazilian begomoviruses known to infect weeds. By recombination analysis, strong evidence was observed that the OMoV genome may have been the product of a double inter-species recombination event.     

Molecular characterization of a new begomovirus that infects Euphorbia heterophylla and Solanum lycopersicum in Venezuela

We report the complete nucleotide sequence of a begomovirus isolate infecting Euphorbia heterophylla and tomato (Solanum lycopersicum) in central Venezuela. Based on the current taxonomic criteria for the genus Begomovirus, the isolate was shown to represent a novel species, tentatively named Euphorbia mosaic Venezuela virus (EuMVV). Its DNA-A is most closely related to those of Euphorbia-infecting begomoviruses from the Caribbean and Central America. The DNA B component forms a phylogenetic cluster with Euphorbia and Sida-infecting begomoviruses from the squash leaf curl virus (SLCV) cluster. EuMVV is transmissible to S. lycopersicum and Capsicum annuum by biolistics of infectious cloned DNA-A and DNA-B components and induces characteristic leaf downward curling and yellowing in S. lycopersicum and and yellowing and leaf distortion in Capsicum annuum.     

Molecular characterization and phylogeny of two begomoviruses infecting <Emphasis Type="Italic">Malvastrum americanum</Emphasis> in Jamaica: evidence of the contribution of inter-species recombination to the evolution of malvaceous weed-associated begomoviruses from the Northern Caribbean

Two distinct full-length begomovirus DNA-A components and a DNA-B component were PCR amplified, cloned and sequenced from Jamaican Malvastrum americanum plants exhibiting yellow mosaic symptoms. Whereas one of the DNA-A components is from a potentially new species that we have tentatively named Malvastrum yellow mosaic Helshire virus (MaYMHV), the other DNA-A and the DNA-B form a cognate pair and represent a new virus species tentatively named Malvastrum yellow mosaic Jamaica virus (MaYMJV). The MaYMJV genome components together infected M. americanum and produced yellow mosaic symptoms similar to those seen in naturally infected plants. Both the MaYMJV and MaYMHV DNA-A components are typical of those of bipartite begomoviruses from the Western Hemisphere. The DNA-As of MaYMJV and MaYMHV are most closely related to each other (sharing 84% sequence identity) and cluster phylogenetically with begomoviruses found infecting malvaceous weeds in Cuba and Florida. The DNA-B component of MaYMJV is most similar to that of Sida golden mosaic virus-[USA:Florida] (SiGMV-[US:Flo]) and Sida golden mosaic Costa Rica virus-[Costa Rica] (SiGMCRV-[CR]). As with many other geminivirus species, the genomes of MaYMJV and MaYMHV bear traces of inter-species recombination.     

A novel begomovirus isolated from sida contains putative cis- and trans-acting replication specificity determinants that have evolved independently in several geographical lineages

A novel begomovirus isolated from a Sida rhombifolia plant collected in Sinaloa, Mexico, was characterized. The genomic components of sida mosaic Sinaloa virus (SiMSinV) shared highest sequence identity with DNA-A and DNA-B components of chino del tomate virus (CdTV), suggesting a vertical evolutionary relationship between these viruses. However, recombination analysis indicated that a short segment of SiMSinV DNA-A encompassing the plus-strand replication origin and the 5´-proximal 43 codons of the Rep gene was derived from tomato mottle Taino virus (ToMoTV). Accordingly, the putative cis- and trans-acting replication specificity determinants of SiMSinV were identical to those of ToMoTV but differed from those of CdTV. Modeling of the SiMSinV and CdTV Rep proteins revealed significant differences in the region comprising the small β1/β5 sheet element, where five putative DNA-binding specificity determinants (SPDs) of Rep (i.e., amino acid residues 5, 8, 10, 69 and 71) were previously identified. Computer-assisted searches of public databases led to identification of 33 begomoviruses from three continents encoding proteins with SPDs identical to those of the Rep encoded by SiMSinV. Sequence analysis of the replication origins demonstrated that all 33 begomoviruses harbor potential Rep-binding sites identical to those of SiMSinV. These data support the hypothesis that the Rep β1/β5 sheet region determines specificity of this protein for DNA replication origin sequences.     

Tomato dwarf leaf virus, a New World begomovirus infecting tomato in Argentina

Begomovirus infection is becoming a threat in fresh-market tomato in Argentina, where mixed infections with begomoviruses are common. The complete sequence of a begomovirus isolate infecting tomato sampled in Salta was molecularly characterized. Phylogenetic analysis showed that this virus isolate is closely related to previously reported Brazilian, Bolivian and Argentinean begomoviruses. The associated symptoms in Nicotiana benthamiana and Solanum lycopersicum were determined by biolistic delivery of infectious DNA-A and DNA-B clones. This begomovirus isolate induced leaf mottling, rugosity and dwarfing, and growth retardation in tomato. Based on these symptoms, we propose the name of tomato dwarf leaf virus (ToDLV) for this new begomovirus.     

Tomato chlorotic leaf distortion virus,a new bipartite begomovirus infecting <Emphasis Type="Italic">Solanum lycopersicum</Emphasis> and <Emphasis Type="Italic">Capsicum chinense</Emphasis> in Venezuela

Virus isolate T217L was obtained from a diseased tomato (Solanum lycopersicum) plant showing leaf deformation and chlorotic mottle symptoms near Maracaibo in the state of Zulia, Venezuela. Full-length DNA-A and DNA-B molecules of T217L were cloned and sequenced. The genome organization of T217L was identical to the bipartite genomes of other begomoviruses described from the Americas. Characteristic disease symptoms were reproduced in S. lycopersicum and Capsicum annum plants inoculated using the cloned viral DNA-A and DNA-B components, confirming disease aetiology. A sequence analysis of DNA-A showed that the T217L isolate has the highest sequence identity (84%) with sida yellow mosaic Yucatan virus (SiYMYuV), sida golden mosaic Honduras virus (SiGMHV) and bean dwarf mosaic virus (BDMV) isolates. This is less than the 89% identity in the DNA-A component that has been defined as the threshold value for the demarcation of species in the genus Begomovirus. The molecular data show that isolate T217L belongs to a novel tentative begomovirus species, for which the name tomato chlorotic leaf distortion virus is proposed. TCLDV was also detected in symptomatic C. chinense plants growing near the T217L-infected plant.