Monopartite Begomovirus Research Articles

Compatibility and interaction of begomoviruses and DNA-satellites causing leaf curl disease in Asia, Africa and Mediterranean Region

A complex of begomoviruses and their associated DNA-satellites is causing leaf curl diseases in Asia, Africa and the Mediterranean Region. Begomoviruses and DNA-satellites native to Asia and Africa are distinct from each other. Different combinations of geographically distinct monopartite begomoviruses, betasatellites and an alphasatellite were analyzed in infection experiments: cotton leaf curl Kokhran virus (CLCuKoV) and cotton leaf curl Multan virus (CLCuMuV) from Pakistan along with their associated cotton leaf curl Multan betasatellite (CLCuMuB); okra yellow crinkle virus (OYCrV), cotton leaf curl Gezira betasatellite (CLCuGeB), ageratum leaf curl Cameroon betasatellite (ALCCMB) and ageratum leaf curl Cameroon alphasatellite (ALCCMA) from Cameroon; tomato yellow leaf curl virus (TYLCV) from the Mediterranean Region. The infectivity assays were carried out in the model host species Nicotiana benthamiana and agro-infectious clones containing partial tandem repeats of the begomovirus and satellite genomes. The tested begomoviruses from different regions could functionally interact with non-cognate betasatellites and alphasatellite. Plants co-inoculated with CLCuKoV/CLCuGeB or CLCuMuV/CLCuGeB developed, for both combinations, more severe symptoms than with the begomovirus alone and the infection was verified by Southern blot hybridization. Nonetheless, CLCuKoV and CLCuMuV were shown also to support infection by ALCCMB, whereas OYCrV and TYLCV were able to support infection with CLCuMuB, ALCCMB and CLCuGeB. Moreover, all begomoviruses from different geographical origins supported ALCCMA from Africa. The results confirm that geographically diverse begomoviruses can functionally interact with non-cognate DNA-satellites, which may cause the emergence of new begomovirus-satellite complexes. Possibly, exchange of DNA-satellites may occur across continents leading to the emergence of new viral diseases.

Cryo-EM Structure of a Begomovirus Geminate Particle.

Tobacco curly shoot virus, a monopartite begomovirus associated with betasatellite, causes serious leaf curl diseases on tomato and tobacco in China. Using single-particle cryo-electron microscopy, we determined the structure of tobacco curly shoot virus (TbCSV) particle at 3.57 Å resolution and confirmed the characteristic geminate architecture with single-strand DNA bound to each coat protein (CP). The CP–CP and DNA–CP interactions, arranged in a CP–DNA–CP pattern at the interface, were partially observed. This suggests the genomic DNA plays an important role in forming a stable interface during assembly of the geminate particle.

Tomato Twisted Leaf Virus: A Novel Indigenous New World Monopartite Begomovirus Infecting Tomato in Venezuela.

Begomoviruses are one of the major groups of plant viruses with an important economic impact on crop production in tropical and subtropical regions. The global spread of its polyphagous vector, the whitefly Bemisia tabaci, has contributed to the emergence and diversification of species within this genus. In this study, we found a putative novel begomovirus infecting tomato plants in Venezuela without a cognate DNA-B component. This begomovirus was genetically characterized and compared with related species. Furthermore, its infectivity was demonstrated by agroinoculation of infectious clones in tomato (Solanum lycopersicum) and Nicotiana benthamiana plants. The name Tomato twisted leaf virus (ToTLV) is proposed. ToTLV showed the typical genome organization of the DNA-A component of New World bipartite begomoviruses. However, the single DNA component of ToTLV was able to develop systemic infection in tomato and N. benthamiana plants, suggesting a monopartite nature of its genome. Interestingly, an additional open reading frame ORF was observed in ToTLV encompassing the intergenic region and the coat protein gene, which is not present in other closely related begomoviruses. A putative transcript from this region was amplified by strand-specific reverse transcription-PCR. Along with recent studies, our results showed that the diversity of monopartite begomoviruses from the New World is greater than previously thought.

Tomato leaf curl Patna virus causing tomato leaf curl disease in Bangladesh

Tomato leaf curl virus (ToLCV) has appeared as a potential threat to the tomato production in the world. ToLCV, a member of the family Geminiviridae may contain either bipartite or monopartite genome. The genetic nature of a monopartite ToLCV isolate characterized from the tomato leaf curl diseased samples of Jamalpur district, Bangladesh (ToLCV-JB) has been reported. The products of rolling circle amplification (RCA) were digested, cloned and sequenced. Sequence analysis revealed the features of begomovirus genome organization in the ToLCV-JB isolate, containing six open reading frames. BLAST analysis showed 100% sequence similarity with tomato leaf curl Patna virus (EU862323.1) and more than 80% similarity with other reported monopartite begomoviruses. Hence, the virus isolate was registered as Tomato leaf Curl Patna virus-[Bangladesh:Jamalpur:2014] isolate ToLCV-JB (Genebank Accession: KU933675.1) according to the suggestion of NCBI. Recombination analysis also did not show any genetic exchange between ToLCV-JB and ToLCV-Patna virus. Moreover, they belong to the same cluster as observed in phylogenetic analysis. The present work suggests the possibility of cross-border spread of ToLCV-Patna viruses without mutation and this could pose a threat to tomato production in Bangladesh as well as in the Asian continent.

Identification of pea leaf distortion virus and Ludwigia leaf distortion betasatellite associated with yellow leaf curl disease of lima bean in Nepal

Lima bean (Phaseolus lunatus) plants exhibiting yellow mosaic and stunted growth symptoms, typical of begomovirus infection, were collected in Rampur city Nepal. Symptomatic plants were shown to be infected by a monopartite begomovirus in association with a betasatellite. The two begomovirus isolates associated with the disease showed 98.7% nucleotide sequence identity to previously characterized isolates of the recently identified begomovirus species Pea leaf distortion virus (PLDV) from Nepal. The associated betasatellite isolates showed highest nucleotide sequence identity at 99% to Ludwigia leaf distortion betasatellite (LuLDB) from Nepal. This is the first identification of PLDV and LuLDB infecting the grain legume Phaseolus lunatus.

Ty-6, a major begomovirus resistance gene on chromosome 10, is effective against Tomato yellow leaf curl virus and Tomato mottle virus

Key messageTy-6 is a major resistance gene on chromosome 10 of tomato that provides resistance against monopartite and bipartite begomoviruses and complements resistance conferred by the known Ty-3 and ty-5 genes.Resistance to monopartite and bipartite begomoviruses is an important breeding objective for cultivated tomato. Several begomovirus resistance genes have been introgressed from related Solanum species and are available for breeding purposes. In the present study, we mapped an additional locus, Ty-6, to chromosome 10 of tomato. Ty-6 is effective against both monopartite Tomato yellow leaf curl virus (TYLCV) and bipartite Tomato mottle virus (ToMoV). Gene action is incomplete dominance, with an intermediate resistance response when Ty-6 is heterozygous. Analysis of populations segregating for Ty-6 along with Ty-3 or ty-5 indicates that the highest level of resistance against TYLCV is attained when Ty-6 is combined with an additional resistance allele. Our results also demonstrate that ty-5 is ineffective against ToMoV. Although multiple SNPs linked to Ty-6 were identified and can be used for breeding purposes, none of these were consistently polymorphic between Ty-6 and ty-6 breeding lines. Further research is underway to generate resequencing data for several Ty-6 inbred lines for the discovery of additional sequence polymorphisms that can be used for fine mapping and characterizing the Ty-6 locus.

Identification of Chilli leaf curl virus associated with tomato leaf curl betasatellite infecting Mentha in Oman

Mint (Mentha sp.; family: Lamiaceae) plants showing yellowing and stunting symptoms from Salalah, Dhofar region, Oman were shown to be infected by a monopartite begomovirus (family: Geminiviridae). Cloning and sequencing of restriction endonuclease digested rolling-circle amplified viral DNA identified a begomovirus associated with the symptomatic mint plants. Further analysis of complete sequences showed the virus to be a variant of the ‘Oman’ strain of Chili leaf curl virus (ChLCV-OM), a virus prevalent in a number of crops across Oman. However, the ChLCV-OM identified in mint has a recombination pattern distinct from all other ChLCV isolates. Additionally, PCR amplification and sequencing showed the mint plants to also harbour the betasatellite, Tomato leaf curl betasatellite (ToLCB). This is the first identification of ChLCV in association with ToLCB infecting mint. The distinct recombination pattern of ChLCV-OM from mint suggests that the host is epidemiologically important in the spread of ChLCV-OM to other crops in Oman.

The antisense 5' end of the V2 gene confers enhanced resistance against the monopartite begomovirus cotton leaf curl Kokhran virus-Burewala strain.

Whitefly-transmitted viruses of the genus Begomovirus (the family Geminiviridae) have become a limiting factor for agricultural productivity in many warmer parts of the world. The economies of Pakistan and India have, since the early 1990s, suffered losses due to cotton leaf curl disease (CLCuD). The disease is caused by begomoviruses, the most important of which at this time is cotton leaf curl Kokhran virus strain Burewala (CLCuKoV-Bu), and a disease-specific betasatellite, cotton leaf curl Multan betasatellite (CLCuMuB). Efforts to minimize losses due to CLCuD rely mainly on the use of insecticides to kill the whitefly vector; no resistant cotton varieties are currently commercially available. The study described here has investigated RNA interference technology for its potential to yield resistance against CLCuKoV-Bu and three other begomoviruses; CLCuKoV, tomato leaf curl New Delhi virus (ToLCNDV) and Pedilanthus leaf curl virus (PeLCV). Three fragments of the virion-sense V2 gene of CLCuKoV-Bu were transformed into Nicotiana benthamiana in antisense orientation and transgenic lines expressing virus-specific short RNAs were assessed for their ability to yield resistance. Only CLCuKoV-Bu with the V2 sequence closest to the promoter was resistant. Inoculation of CLCuKoV-Bu with CLCuMuB into transgenic plants did not significantly affect the outcome, although viral DNA was detected in number of plants, suggesting that the betasatellite may impair RNAi resistance. Overall the results indicate that targeting the 5' end of V2 gene using antisense-RNA has the potential to deliver resistance against begomoviruses and that RNAi-based resistance imparts some degree of resistance to heterologous viruses. Keywords: geminivirus; begomovirus; RNAi; resistance; CLCuKoV-Burewala; CLCuMuB.

Occurrence and molecular detection of bipartite begomovirus on tomato in Southern India

Begomoviruses are major constraint in tomato production across the world. In India, tomato production is affected by both monopartite and bipartite begomoviruses. Monopartite were reported to infect tomato crop across India. However, bipartite were reported to infect tomato in Nothern India. In the current study, seventy begomovirus symptomatic tomato samples were collected from southernstates of India and analysed using PCR-based specific primer. The analysis revealed that 45 of them were monopartite, 23 of them were bipartite and 8 bipartite also showed the presence of betasatellite. This is the first report of bipartite begomovirus infecting tomato in Southern India.

The V2 protein encoded by a monopartite begomovirus is a suppressor of both post-transcriptional and transcriptional gene silencing activity

Papaya leaf curl virus (PaLCuV) is a begomovirus (genus Begomovirus; family Geminiviridae) with a monopartite genome that is usually associated with beta- and alphasatellites in plants. Geminiviruses are DNA viruses with small circular genomes that occur as minichromosomes in the nucleus and are susceptible to post-transcriptional gene silencing (PTGS) and transcriptional gene silencing (TGS). Transient expression of the PaLCuV V2 (PV2) protein together with the green fluorescent protein (GFP) in Nicotiana benthamiana resulted in enhanced levels of GFP fluorescence and GFP mRNA, indicative of suppression of PTGS. Expression of PV2 from a Potato virus X vector restored GFP expression in N. benthamiana plants harbouring a transcriptionally silenced GFP transgene, indicative of suppression of TGS. The results show that the PV2 protein encoded by PaLCuV has both suppressor of PTGS and TGS activity and is an important factor in overcoming host RNA-silencing based defenses.

Tomato leaf curl Mahé virus: a novel tomato-infecting monopartite begomovirus from the Seychelles.

This is the first description of the complete genome sequence of a new monopartite begomovirus isolated from tomato with symptoms of tomato (yellow) leaf curl disease collected in the Seychelles. The DNA-A-like nucleotide sequences share the highest nucleotide sequence identity (84%) with tomato leaf curl Anjouan virus (ToLCAnjV) from the Comoros islands. Phylogenetic analysis confirmed its recombinant nature and its relationship to Old World monopartite and bipartite begomoviruses. This discovery of a new member of a species confirms the high genetic diversity of begomoviruses in the south-western Indian Ocean islands.

Transcriptome analysis of Nicotiana benthamiana infected by Tobacco curly shoot virus

BackgroundTobacco curly shoot virus (TbCSV) is a monopartite begomovirus associated with betasatellite (Tobacco curly shoot betasatellite, TbCSB), which causes serious leaf curl disease on tomato and tobacco in China. It is interesting that TbCSV induced severe upward leaf curling in Nicotiana benthamiana, but in the presence of TbCSB, symptoms changed to be downward leaf curling. However, the mechanism of interactions between viral pathogenicity, host defense, viral-betasatellite interactions and virus-host interactions remains unclear.MethodsIn this study, RNA-seq was used to analyze differentially expressed genes (DEGs) in N. benthamiana plants infected by TbCSV (Y35A) and TbCSV together with TbCSB (Y35AB) respectively.ResultsThrough mapping to N. benthamiana reference genome, 59,814 unigenes were identified. Transcriptome analysis revealed that a total of 4081 and 3196 DEGs were identified in Y35AB vs CK (control check) and Y35A vs CK, respectively. Both GO and KEGG analyses were conducted to classify the DEGs. Ten of the top 15 GO terms were enriched in both DEGs of Y35AB vs CK and Y35A vs CK, and these enriched GO terms mainly classified into three categories including biological process, cellular component and molecular function. KEGG pathway analysis indicated that 118 and 111 pathways were identified in Y35AB vs CK and Y35A vs CK, respectively, of which nine and six pathways were significantly enriched. Three major pathways in Y35AB vs CK involved in metabolic pathways, carbon metabolism and photosynthesis, while those in Y35A vs CK were related to Ribosome, Glyoxylate and dicarboxylate metabolism and DNA replication. We observed that 8 PR genes were significantly up-regulated and 44 LRR-RLK genes were significantly differentially expressed in Y35A treatment or in Y35AB treatment. In addition, 7 and 13 genes were identified to be significantly changed in biosynthesis and signal transduction pathway of brassinosteroid (BR) and jasmonic acid (JA) respectively.ConclusionsThese results presented here would be particularly useful to further elucidate the response of the host plant against virus infection.

Complete nucleotide sequence of a novel monopartite begomovirus infecting Ageratum conyzoides in China.

Two isolates of a novel monopartite begomovirus were obtained from naturally infected Ageratum conyzoides plants showing typical leaf curling and enation symptoms in Sichuan Province, China. The complete DNA sequences of two isolates were determined to be 2749 nucleotides in length. Sequence analysis showed that the two isolates shared 99.5% identity, and the highest identity (89.5-89.6%) was with the DNA sequence of tomato leaf curl Hainan virus (ToLCHaiV). No other begomoviruses or satellite molecules were detected in the two samples. Based on the species demarcation criterion for the genus Begomovirus established by the Geminiviridae Study Group, the virus is a novel monopartite begomovirus, and the tentative name "ageratum leaf curl Sichuan virus" (ALCScV) is proposed. Phylogenetic analysis showed that it clustered with ToLCHaiV, and recombination analysis showed that ALCScV might have arisen by recombination between viruses related to ToLCHaiV, ageratum leaf curl virus (ALCuV), and sida leaf curl virus (SiLCuV).

First Report of Papaya leaf curl China virus infecting Acalypha australis in China

Papaya leaf curl China virus (PaLCCNV), a monopartite begomovirus (genus Begomovirus, family Geminiviridae), was originally reported on Carica papaya in Guangxi province of China (Wang et al. 2004). The virus has been reported to infect C. papaya, Solanum lycopersicum, Nicotiana tabacum, Corchoropsis tomentosa, Siegesbeckia orientalis, and Ageratum conyzoides. In January 2015, plants of Acalypha australis, a common and widespread weed species, were found exhibiting yellow vein symptoms in fields of Nanning city, Guangxi province. Five symptomatic leaf samples were collected from each of five diseased plants. Total DNA was extracted from the five samples with the EasyPure Plant DNA kit (TransGen Biotech, Beijing, China) and was used as a template for polymerase chain reaction with the degenerate begomovirus primers AV494 (5′-gccyatrtayagraagccmag-3′) and CoPR (5′-gangsatghgtrcadgccatata-3′). The expected approximately 570-bp fragment was detected from all five samples, indicating that A. australis plants showing yellow vein symptoms were infected by a begomovirus. Begomoviral genomes were amplified from the total DNA using rolling circle amplification (RCA) (TempliPhi kit; GE Healthcare, Buckinghamshire, UK), followed by digestion with endonucleases BamH I, EcoR I, Hind III or Pst I, respectively. Amplicons corresponding to full-length begomoviral genomic components, obtained from RCA products digested with Hind III, were gel purified, ligated into the plasmid pGEM-3Z (previously digested with the corresponding restriction enzyme mentioned above), and transformed into Escherichia coli DH5α. Three clones from each sample were selected for sequencing (Invitrogen, Shanghai, China). Sequencing results were assembled and analyzed using DNAStar software version 5.0 (DNAStar, Madison, WI). A similarity search for each sequence was carried out using BLASTn to identify related sequences in the GenBank database (https://www.ncbi.nlm.nih.gov/). Pairwise nucleotide (nt) sequence identities were determined using the Species Demarcation Tool (SDT1.0). Full-length begomoviral genomic sequences were 2,735 nt long and encoded six putative open reading frames. The cloned genomic sequences shared 99.5 to 100% nt identities with each other. One representative sequence was deposited in GenBank as the accession number KX273343, which shared 91.8 to 99.6% nt identities with isolates of PaLCCNV in the database, with the highest nt identities to PaLCCNV-G111 [CN:Gx:Age:14] (HG003651). In accordance with the threshold of 91% for begomovirus species demarcation (Brown et al. 2015), the virus associated with A. australis yellow vein disease is an isolate of PaLCCNV. According to the obtained sequences, the specific primer pairs W-F2 (5′-GTATACACGCCACTCTCGCATTG-3′) and W-R2 (5′-CTGGACAATCAAAAATCCCCTAT-3′) were designed to amplify the full-length genome and detect the presence of PaLCCNV in A. australis samples. The expected approximately 2.7-kb full-length genomic fragment was amplified from all five samples, indicating that A. australis plants showing yellow vein symptoms were infected by PaLCCNV. To our knowledge, this is the first report of natural occurrence of PaLCCNV on A. australis in China. A. australis may play an important role as a reservoir of PaLCCNV, especially during the non-crop-planting period, but additional studies analyzing a large number of plant samples from different geographical locations within China are necessary to establish the role of this host as a virus reservoir.

In-Silico Investigation of Betasatellite Complexity in Papaya Leaf Curl Disease Complex

Papaya leaf curl disease complex (PLCD) impose heavy losses to papaya farmers across India. It is mainly reported to be caused by Papaya leaf curl virus and associated begomoviruses carrying a DNA-A and betasatellite molecules. Both components are required for infliction of severe symptoms. The investigation into molecular diversity is necessary to devise intervention techniques against these begomoviruses. Based on the outcome of diversity, preferred resistance strategy against a disease complex should be generic in nature, which provides an advantage of a broad range resistance against a variety of plant virus causing same disease symptoms. For this purpose, we studied the molecular diversity through investigation of genetic complexity of the betasatellite genome using various computational methods and probed genetic complexity of betasatellite component. Multiple sequence alignment and recombination analysis were performed to understand the evolutionary relationship of betasatellite components with a DNA-A present as a helper genome in case of monopartite begomoviruses. The overall results indicate that the betasatellite molecules have evolved independently of DNA-A component and their association is a result of co-infection and due to inter- and intraspecific interaction with various forms of virus infection in plants. The information generated through this study has potential application in designing intervention strategies against PLCD, which is widespread in Indian sub-continent region that includes countries like India, Pakistan, Nepal and Bangladesh.

Molecular characterization of ageratum enation virus and DNA-satellites associated with yellowing and leaf curl symptoms on mulberry in Pakistan

The whitefly-transmitted begomoviruses (family Geminiviridae) infect dicotyledonous plants and occur in tropical and sub-tropical regions. Although most commonly found in herbaceous plants, recently begomoviruses have increasingly been identified in woody plants. Leaf samples from five mulberry (Morus alba L.) plants with leaf yellowing and curling symptoms were collected in Lahore (Pakistan) and shown by PCR to be associated with a begomovirus, an alphasatellite and a betasatellite. The complete sequences of two begomovirus clones, as well as an alphasatellite clone and a betasatellite clone, were determined. The begomovirus clones were shown to be isolates of ageratum enation virus (AEV), a virus most commonly identified in weeds but increasingly being identified in crops such as tomato, soybean and fenugreek. Analyses of the sequences of the alphasatellite and betasatellite clones showed them to be isolates of Guar leaf curl alphasatellite and Papaya leaf curl betasatellite, respectively. Both the virus and the alphasatellite sequences showed evidence of a recombination. This is the first report of the weed-infecting monopartite begomovirus AEV, and associated satellites, infecting the woody plant mulberry.

DNA Methylation Suppression by Bhendi Yellow Vein Mosaic Virus

Bhendi yellow vein mosaic virus (BYVMV) belongs to the monopartite begomovirus associated with the β satellite. As a single-stranded DNA (ssDNA) virus, it should be amenable to transcriptional and post-transcriptional gene silencing (TGS and PTGS). Previously, we had demonstrated C2, C4 and βC1 to be having different levels of influence on PTGS. Hence in the present study, a series of experiments such as agroinfiltration, chop-polymerase chain reaction (PCR), quantitative PCR (qPCR) and bisulfite next generation sequencing (NGS) were designed to analyse the involvement of BYVMV proteins on DNA methylation suppression. From the preliminary studies, we concluded that BYVMV genes were responsible for TGS suppression and C2, C4 genes from BYVMV were selected for further studies. Agroinfiltration experiments with mutant C2 and C4 partial tandem repeat (PTR) constructs of BYVMV have confirmed the role of C2 and C4 in DNA methylation impairment. The protoplast replication assay has shown that C4 was not an impediment for viral DNA replication and subsequent agroinfiltration studies with the C4 mutant BYVMV PTR construct have revealed the involvement of C4 in viral DNA movement.

PCR based detection of betasatellite associated with the begomoviruses using improved universal primers

Betasatellite is mostly associated with monopartite begomovirus and is known to play a key role in expression of severe form of disease of infected dicotyledonous plants. Begomoviruses are transmitted by whitefly, causing most severe diseases in a wide range of crops. Diagnosis of the virus and the associated betasatellites is very important while breeding for resistant varieties. The current study reports an improved set of universal primers viz., CLB36F and CLB37R, with an ability to detect vast range of begomoviruses across the crops. About 31 samples of diverse plant species showing distinct symptoms of begomovirus collected from various geographical regions of India were analyzed to validate the improved universal primer pair. The results showed that the improved universal primer pair could detect the betasatellites of all the samples, whereas, the presently available primer pair viz., beta01/beta02 could detect only five out of fifteen samples. This data can be considered as a clear indication that the improved primer pair reported in the current study is a superior substitution for the detection of diverse betasatellites.

FIRST REPORT OF TOBACCO CURLY SHOOT VIRUS (TbCSV) AND ITS ASSOCIATED SATELLITES FROM WATERMELON IN CHINA

Tobacco curly shoot virus (TbCSV), a monopartite begomovirus (genus Begomovirus, family Geminiviridae), is a serious threat to many crops and weeds in China and India. In this study, a begomovirus disease complex was identified from a watermelon sample displaying severe leaf curling and yellowing symptoms. The genome of this TbCSV isolate Y3560 contained 2,744 nucleotides (nt) and shared 97.9% identity with the TbCSV YN4519 isolate. The complete nucleotide sequence of the betasatellite DNA molecule associated to isolate Y3560 contained 1,342 nt and shared 91.0% sequence identity with the Tomato yellow leaf curl China virus betasatellite isolate TYLCCNB-Y319. The nucleotide sequence of the alphasatellite contained 1,372 nt and shared the highest levels of identity (94.0%) with Tobacco curly shoot virus associated DNA1 (TbCSA). This is the first report of a monopartite begomovirus and associated satellites from watermelon.

Distribution and diversity of begomoviruses in tomato and sweet pepper plants in Costa Rica

AbstractBegomoviruses (genus Begomovirus, family Geminiviridae) have emerged as important plant pathogens in tropical and subtropical regions worldwide. Although these viruses were reported during the 1970s in Costa Rica, they are still poorly known. Therefore, the objective of this study was to analyse the diversity and distribution of begomoviruses in commercial tomato and sweet pepper fields from different agricultural production systems of the major growing regions of Costa Rica. A total of 651 plants were randomly sampled from greenhouses and open field crops during 2011 and 2012 in three different geographical locations. The bipartite begomoviruses Tomato yellow mottle virus, Tomato leaf curl Sinaloa virus and Pepper golden mosaic virus, and the monopartite begomovirus Tomato yellow leaf curl virus were detected in the collected samples. The complete genome of isolates from each species was cloned and sequenced. The frequency of detection of these four begomoviruses in the analysed samples ranged from 0 to 9%, the presence, and the prevalent virus varied largely according to the geographical location, the host (tomato and pepper), and the production system (greenhouses or open fields). An association between geographical region and begomovirus species was observed suggesting that in Costa Rica the heterogeneity on climate, topography and agricultural system might influence the distribution of begomovirus species in the country. A broader survey needs to be conducted to confirm it, although these preliminary results may contribute to the management of begomoviruses in Costa Rica.