Investigation, KT989862) on D. stramonium [14], was predominant among tomato crops and some arable weed species. Your efforts are highly appreciated. PLOS ONE promises fair, rigorous peer review, The relationship between tomato production, monthly average temperature and seasonal average temperature in Limpopo province, South Africa during the period of 1971 - 2006 were investigated using statistical regression analysis methods. Whiteflies collected from field and tunnel sites across South Africa indicated the presence of Bemisia and Trialeurodes species from nymph and adult phenotypic analysis. â¢Mozambique- Mozambique is a net importer of tomatoes, with South Africa supplying 99 percent of the 2266 tons of tomatoes imported during 2010 (ITC, 2012).Tomato production has increased from 7117 tons in 2000 to an estimated 16000 tons in 2010. Product Big type Fresh Tomatos Size 6-8cm packaging carton/plastic basket/ Packaging according to customer requirement Place of origin South Africa Supply capacity 3000tons/month Quality No cracks, no insect bites, mature, modest,sweet and sour taste Supplying period All the year round Plant out in late spring, when the weather is settled and warm. RNA templates were incubated at 65°C for 5 min and placed on ice prior to the addition of a master mix component as indicated by the manufacturer. ORF-8 (nucleotides 7124–7822) encodes a 27 kDa (P27) protein that is conserved among members of the Crinivirus genus, however, the amino acid similarity among species is low [27]. Although the fruit remained symptomless and is of marketable standards, many commercial farmers in South Africa reported a significant reduction in their overall yield. Furthermore, they provided detailed information outlining the spread and severity of the disease in various countries and continents in which South Africa was mentioned although no official studies have been conducted to date. Therefore, understanding the role of primary spread is fundamental to the development of effective cultural methods that reduce sources of inoculum. 35 23
Two microliters of each ligation reaction were added to TOP10 chemically competent E. coli cells and heat shocked at 42°C for 30 s. Successful transformants were selected (from blue/white colony screening) and cultured using LB (Luria-Bertani) broth in a shaking incubator at 37°C overnight. The putative 9 kDa (P9) protein encoded by ORF-5 (nucleotides 4096–4332) has no assigned function. Against this background, a follow-up study was carried out to investigate the prevalence and epidemiology of criniviruses infecting tomato crops in South Africa. Five positive amplicons were excised from the agarose gel, purified using a Zymoclean Gel DNA Recovery Kit (Zymo Research, USA) and ligated onto a PCR 2.1 cloning vector. 0000003328 00000 n
South Africa The season has ended in the summer region and the total tonnage is estimated at 40,000 tonnes, as previously. Symptoms resembling those described in previous studies on the epidemiology and etiology of ToCV were observed in many of South Africa's major tomato growing areas [3; 7; 10; 11]. No, Is the Subject Area "South Africa" applicable to this article? Similarly, ToCR2-186 did not cluster with any of the isolates and formed a unique clade. RNA was extracted from 20 mg of frozen leaf tissue samples using a Quick-RNA MiniPrep kit (Zymo Research, USA) according to the manufacturers’ guidelines. D: The occurrence of weeds such as Datura stramonium growing along rows of tomato crops exhibiting interveinal leaf chlorosis and stunting in the presence of whiteflies. https://doi.org/10.1371/journal.pone.0220298.t005. You can discover details including top producing & exporting countries, real-time market prices, local product varieties, seasonality, production & export volumes, and more. Sequence analysis of the 265 bp region located on the ORF-1b gene revealed a high level of similarity among all six ToCV isolates analyzed in this study with Nel-186Cr (KT989862) previously reported on D. stramonium in South Africa [14]. No, Is the Subject Area "Farms" applicable to this article? Samples were placed on dry ice and transported to the University of KwaZulu Natal virology lab for further analysis. Covid-19 brings with it an economic deep freeze the world over. A further investigation of the molecular characteristics of ToCV from South Africa provided insight into the possibility of genetic recombination and reassortment. Contigs that matched to ToCV RNA-1 and RNA-2 sequences as per NCBI GenBank, ranged from 98% to 99%. Various agro-ecological areas and microclimates across the globe possess a set of unique environmental parameters that directly or indirectly affect vector population dynamics. B: Significant reduction in the yield and fruit size in symptomatic crops, however, fruit remain symptomless. Their robust nature and adaptive capacity to survive and reproduce in adverse conditions is an evolutionary trend that indirectly contributes to the epidemiology of vectors such as whiteflies and viruses such as ToCV throughout the world. Although multiplex RT-PCR assays were carried out to determine the presence of four crinivirus species (i.e. Protected horticulture in South Africa is relatively small in size. Contributed equally to this work with: The production of tomato is growing dramatically in the world as like its consumption. A: Interveinal leaf chlorosis, chlorotic flecking, and leaf bronzing symptoms on the lower mature leaves of tomato crops. Macedo et al. The small percentage of asymptomatic tomato samples that tested positive for ToCV infections may be the result of early or latent stages of infection. 0000001130 00000 n
Since tomato samples were collected in the presence of whiteflies it was necessary to test all samples (symptomatic/asymptomatic) to reduce the disparity/bias associated with prevalence studies. History Of Tomato Cultivation. Symptomatic tomato plants typically exhibited interveinal leaf chlorosis, chlorotic flecking and leaf bronzing. Phylogenetic analysis (Figs 5 and 6) shows that the RNA-1 segment (ToCR1-186) groups most closely with Spanish isolates, however, the RNA-2 (ToCR2-186) diverges from and shows the highest identity with South Korean isolate JJ which ultimately group with Spanish isolates. A 59 kDa protein (P59), thought to associate with virion tails and movement is encoded by ORF-4 located at nucleotide position 2561–4114. Yes 0000001049 00000 n
Results from the survey indicated that ToCV is presently the only crinivirus species infecting tomatoes in South Africa. https://doi.org/10.1371/journal.pone.0220298.t003. This also suggests a possible connection between Spanish and some South Korean isolates, specifically JJ. Open field and greenhouse cultivated tomato crops were surveyed during the 2015 and 2016 growing seasons. Much of their efforts were further hampered by the absence of skilled government extension workers able to bridge the gap between the technical jargon associated with research and farmers. Limpopo province is the major production area with 3 590 ha (Northern Lowveld at 2 700 ha and far Northern areas of Limpopo at 890 ha). Yes Although tomato cultivation is concentrated in the Limpopo, Mpumalanga (Lowveld and Highveld), Northern KwaZulu Natal, Eastern Cape, and Western Cape provinces, all nine provinces were surveyed which included commercial, smallholder, and subsistence farms (Fig 1 and Table 1). For more information about PLOS Subject Areas, click A sterile scalpel was used to make an incision along the midrib of a fresh symptomatic leaf tissue sample. For these reasons, a multiplex RT-PCR approach was used to detect single or mixed infections of crinivirus species that commonly infect solanaceous hosts. Factoring all possible variables influencing vector dynamics through collaborative efforts may provide a more dynamic approach to the management of ToCV in South Africa and abroad. Each sample was lysed in a sterile 1.5 ml microcentrifuge tube containing plastic beads, and 500 μl of lysis buffer, using a BioSpec Mini-Beadbeater-16 high-energy cell disrupter (USA). Methodology, Recently, Moodley et al. Resources, The province account for more than 50% of the total area planted to tomatoes. By about 500 BC, tomato was already being cultivated in southern Mexico and a few other areas. https://doi.org/10.1371/journal.pone.0220298.g002. broad scope, and wide readership – a perfect fit for your research every time. PCR positive samples were validated by cloning (using a TA cloning kit [Invitrogen, USA] according to the manufacturers’ guidelines) and sequencing. A total of 787 tomato samples, and 182 weed samples exhibiting virus-like symptoms in the presence of whitefly populations, as well as asymptomatic leaf tissue, were collected and stored in zip-lock plastic bags. These viruses were serendipitously identified using next-generation sequence analysis. Nucleotide and amino acid similarities of coding and non-coding regions were generated using the sequence identity and similarity tool SIAS (http://imed.med.ucm.es/Tools/sias.html). originated in the Andes mountains of Peru, from where it spread as a weed to extensive areas in South and Central America. compared to ⦠Interestingly, the RNA-1 segment of the South Korean isolate JJ clusters within a group of South Korean isolates. The tomato is a very important vegetable crop in South Africa. Using the reference genome assembler: Bowtie2 version2.3.4 [18], an index reference database was constructed, and the sequence reads that did not align to the reference genome was collected for meta-assembly. Explore detailed information about the global Tomato markets. Is the Subject Area "Tomatoes" applicable to this article? endstream
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Each of these areas have their own characteristics related to climate and type of products. It is hoped that the information generated from this study can be used to develop effective strategies to reduce the spread of ToCV. The Aztecs of South America used the fruit in their dishes as per evidence. Visualization, The exact GPS coordinates of each sampling site are represented by a star. Phylogenetic analysis of the RNA-1 segment showed that the South African ToCV isolate ToCR1-186 (Accession no. The use of high-throughput sequencing was a rapid and effective method to generate the full genome sequence of ToCV from South Africa. Although recombination events were not detected, phylogenetic studies showed inconsistencies in the grouping of RNA-1 and RNA-2 segments for some of the ToCV isolates analyzed in this study. The functional role of this protein is presently not known. xref
They serve as overwintering hosts that reduce the quality of soils in arable land. ToCV was identified as the only crinivirus species infecting tomato crops in South Africa (Table 3). 0000010485 00000 n
Both weed species belong to the Solanaceae family and can be found throughout much of South Africa. Trialeurodes abutilonea and Bemisia tabaci (MEAM1, formerly biotype B) are highly effective vectors in comparison to Trialeurodes vaporariorum and Bemisia tabaci (New World, formerly biotype A) [21]. All samples were sequenced in the forward and reverse direction at Inqaba Biotec (Pretoria, South Africa) using a 3500xL Genetic Analyzer (Applied Biosystems, USA). You can discover details including real-time market prices, local product varieties, seasonality, production & export volumes, and more. Cape Town has a Mediterranean climate and No, Is the Subject Area "Weeds" applicable to this article? Nucleic acid extracts from a total of 787 tomato samples and 182 weed samples from 15 species belonging to six botanical families (Amaranthaceae, Asteraceae, Brassicaceae, Euphorbiaceae, Malvaceae, and Solanaceae) were tested for crinivirus infection using multiplex RT-PCR to detect single or mixed infections of crinivirus species (ToCV, TICV, BPYV, and PYVV) that are known to infect solanaceous hosts. South Africa is regarded as a leader in the use of tomato production best practices. Tomato chlorosis crinivirus (ToCV) is vectored by several whitefly species that damage tomato crops throughout the world. �Y�0��*-�VA�� Horticulture products are produced throughout the entire country, however the three main regions are around Cape Town, Johannesburg and Durban. In addition, it is almost impossible to control the spread of a virus without a profound understanding of its molecular genetics and factors that influence its virulence and distribution. To remove the host sequence reads, the trimmed data were mapped against the reference genome: Solanum lycopersicum strain: Heinz 1706 (accession: GCF_000188115), where the whole genome sequence of Solanum lycopersicum strain: Heinz 1706 was downloaded from NCBI. The isolate of ToCV previously reported from South Africa (Nel-186Cr; Accession no. were observed in most greenhouses and sampling sites located in the North-West province. Therefore, it is important to use molecular methods to validate symptoms in the field. [7], reports of the ‘yellow leaf disorder’ as the disease resulting from ToCV infection dates back to 1989 from the Columbia and Suwannee counties in Florida (USA). https://doi.org/10.1371/journal.pone.0220298.g006. A gene-specific Solanaceae reverse primer designed by Wintermantel and Hladky [15] was used at a final concentration of 1 ng/μl in each 20 μl RT reaction. trailer
ORF-2 (7664–8245) encodes a 22 kDa protein (P22) which is a suppressor of gene silencing [25], and ORF-3 (8265–8420) encodes a 6 kDa protein (P6) at the 3ʹ terminus of RNA-1, possessing a transmembrane domain similarly recognized in other crinivirus species [23]. ORF-1a (5838 nt/1945 aa) located at position 304 to 6141 encodes a 221 kDa multifunctional protein comprising a protease, methyltransferase and helicase domain. ORF-3 (nucleotides 2406–2609) encodes a putative 8 kDa protein with no known function to date. h�b```"WV�HAd`��0pt00(0l:���{����t�Vy-_Q��(s�'�pB�$˒9��r�|Ҍ8�%k�4�e�J``� �������d3�-�B;��-H@���X���eL?c�0=e�a������'��L�����O���Uh� �fb[ Vb`2W Ҍ@�
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Next-generation sequencing (NGS) was used to generate the complete genome of ToCV from South Africa. No, PLOS is a nonprofit 501(c)(3) corporation, #C2354500, based in San Francisco, California, US, https://doi.org/10.1371/journal.pone.0220298, http://www.tomatonews.com/en/background_47.html/7/5/2019, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/4/10/2018. Apricots do well in temperate zones but thrive in areas with cold, dry winters and dry, hot summers. and Trialeurodes sp. [2]. The fruit is rich in lycopene and Vitamin C. Tomatoes are used in various ways. In this study, mixed whitefly populations belonging to the genera Bemisia and Trialeurodes were identified in open field and greenhouse-produced tomatoes that tested positive for ToCV infection. Major production areas in South Africa Tomatoes are grown all over the country in summer and in winter in frost-free areas, and their production is concentrated in Limpopo, the Mpumalanga Lowveld and Middleveld, the Pongola area of Kwazulu-Natal, the southern parts ⦠Almost half (47%) of the tomato samples analyzed in this study tested positive for ToCV infections and the majority of these were collected from symptomatic tomato plants. Tomato is grown either on open field or under greenhouse technology. Augustine Gubba, This genetic diversity of the RNA-1 and RNA-2 segments of ToCV isolates throughout the world may have resulted from recombination. For example, tomatoes infected with TICV or ToCV are indistinguishable based on visual inspection. Of the 2,101 contigs, 68 contigs were similar to known viral sequences. To determine the possibility of infection by all known criniviruses, a multiplex system targeting the RNA-dependent RNA polymerase (RdRP) encoded by the ORF-1b gene was used [15]. Limpopo Province is the major production area with 3 590 ha (Northern Lowveld at 2 700 ha and far Northern areas of Limpopo at 890 ha). In recent years, South Africa has experienced increasingly high whitefly populations that overwhelmed much of the country’s commercial and smallholder tomato farming communities [9]. Additionally, bell pepper (Capsicum annuum L.) crops were also screened for crinivirus infection, especially those in adjacent tomato farms, however, criniviruses were not detected on any of the samples from South Africa. Inconsistencies in the grouping of the RNA-1 and RNA-2 segments belonging to the same ToCV isolate suggest the possibility of intraspecific genetic acquisition through reassortment and recombination. A 7 kDa protein (P7) encoded by ORF-9 (nucleotides 7831–8028) has a transmembrane domain and is exclusive to the ToCV species. Bemisia sp. S. nigrum and D. stramonium belonging to the Solanaceae family tested positive for ToCV. 0000008160 00000 n
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