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Öğe Assessment of susceptibility of different rootstock/variety combinations of pear to Candidatus Phytoplasma pyri and experimental transmission studies by Cacopsylla pyri(Springer, 2022) Caglayan, Kadriye; Gazel, Mona; Serce, Cigdem Ulubas; Kaya, KamuranIn this study, efficient transmission ways of 'Ca. P. pyri' which causes Pear Decline (PD) disease and response of different rootstock-scion combinations to this pathogen were evaluated. For graft transmission trials, fifty BA29 clonal rootstocks were grafted with buds taken from a 'Ca. P. pyri' infected pear tree, cv. Deveci, and the transmission rate was found to be 8% according to PCR/RFLP analyses. Growth retardation was detected in some grafted plants but the specific reddening symptoms for PD were not observed during the 2 years of observation. Cacopsylla pyri L., playing important role for the transmission of pear decline phytoplasma in open field, was used for experimental transmission trials. It has been shown that it can acquire phytoplasma (in 1 day) and transmit it (in 2 weeks to healthy pear saplings). Therefore it was revealed that C. pyri plays an important role in pear decline epidemiology. When the response of several rootstock-scion combinations to 'Ca. P. pyri'was evaluated over two vegetative periods by visual monitoring of symptom development and by PCR analyses, two Santa Maria and one Williams plants grafted on OHF333 and one Deveci plant grafted on P. communis were found infected by 'Ca. P. pyri', but no infection was detected in a local cv. Ankara grafted on any rootstocks. Among the commercial cultivars, our local cv. Deveci was found the most sensitive and cv. Ankara was the most tolerant. The use of healthy plant materials, as well as the appropriate control of the vector will play an important role in disease control.Öğe Comparison by Sequence-Based and Electron Microscopic Analyses of Fig mosaic virus Isolates Obtained from Field and Experimentally Inoculated Fig Plants(Amer Phytopathological Soc, 2010) Caglayan, Kadriye; Serce, Cigdem Ulubas; Barutcu, Eminur; Kaya, Kamuran; Medina, Vicente; Gazel, Mona; Soylu, SonerFig mosaic disease (FMD) and the fig mite, Aceria ficus, are widespread in different fig growing provinces of Turkey. Fig trees (Ficus carica) cv. Bursa siyahi (D1) and an unknown seedling (D2) that showed typical FMD symptoms and was heavily infested by fig mites were used as donor plants for attempted mite transmissions to healthy fig seedlings. Transmission electron microscopy observations of donor plant samples prior to the transmission tests were performed and showed the presence of double membrane bodies (DMBs) in the palisade mesophyll cells. Electron microscopy of all experimentally inoculated fig seedlings showed the same bodies. This result reinforced the suggestion that an agent that elicits the production of DMBs in infected cells is involved in the etiology of FMD. Double-stranded (ds)RNA analyses were also performed from experimentally inoculated plants, and dsRNAs with sizes approximately 1.30 and 1.96 kb were obtained. Reverse transcription polymerase chain reaction (RT-PCR) products of 468 and 298 bp specific to Fig mosaic virus (FMV) were amplified from both donor and experimentally inoculated plants. BLAST analyses of nucleotide sequences of these fragments showed 90% identity with FMV for the donor plant and 94 to 96% for experimentally inoculated plants. According to these results, FMV is present in both donor and experimentally inoculated plants in Turkey, and this virus is transmissible by A. ficus from fig plant to fig plant.Öğe Detection and characterization of diverse phytoplasmas in ornamental and cultivated pomegranate species in Turkey(Academic Press Ltd- Elsevier Science Ltd, 2022) Caglayan, Kadriye; Kocabag, Hamide Deniz; Gazel, Mona; Sipahiog, Hikmet MuratYellowing, leaf curling and shoot-dieback symptoms on pomegranates have been observed in Turkey in last decade, however, the association of phytoplasmas to symptoms in pomegranates has been not fully understood. In the present study, 130 cultivated and 65 ornamental pomegranate trees were sampled from three provinces (Hatay, Adana, Sanliurfa) from southern part of Turkey. Nested-PCR assay and restriction fragment length polymorphism analysis were employed to identify the phytoplasma strains detected in symptomatic and asymptomatic pomegranate trees. Among 195 tested samples, three ornamental and six cultivated pomegranates were found positive for phytoplasmas by Nested-PCR. Based on virtual RFLP analysis of 16S rDNA sequences, the strains detected in cultivated pomegranates were related to 'Candidatus Phytoplasma asteris' (16SrI-S), 'Ca. P. solani' (16SrXII-A) and 'Ca. P. mali' (16SrX-A) whereas in the ornamental pomegranates only to 'Ca. P. prunorum' (16SrX-B) was detected. The association of 'Ca. P. mali' and 'Ca. P. asteris' related strains on cultivated pomegranates and as well as 'Ca. P. prunorum' in ornamental pomegranates have been identified for the first time worldwide. The presence of distinct phytoplasmas in pomegranates could result a high diversity of phytoplasmas within single plant species.Öğe Detection and Identification of Phytoplasmas in Pomegranate Trees with Yellows Symptoms(Wiley, 2016) Gazel, Mona; Caglayan, Kadriye; Baspinar, Huseyin; Mejia, Juan F.; Paltrinieri, Samanta; Bertaccini, Assunta; Contaldo, NicolettaSymptoms resembling those associated with phytoplasma presence were observed in pomegranate (Punica granatum L.) trees in June 2012 in the Aegean Region of Turkey (Aydn province). The trees exhibiting yellowing, reduced vigour, deformations and reddening of the leaves and die-back symptoms were analysed to verify phytoplasma presence. Total nucleic acids were extracted from fresh leaf midribs and phloem tissue from young branches of ten symptomatic and five asymptomatic plants. Nested polymerase chain reaction assays using universal phytoplasma-specific 16S rRNA and tuf gene primers were performed. Amplicons were digested with Tru1I, Tsp509I and HhaI restriction enzymes, according to the primer pair employed. The phytoplasma profiles were identical to each other and to aster yellows (16SrI-B) strain when digestion was carried out on 16Sr(I)F1/R1 amplicons. However, one of the samples showed mixed profiles indicating that 16SrI-B and 16SrXII-A phytoplasmas were present when M1/M2 amplicons were digested, the reamplification of this sample with tuf cocktail primers allowed to verify the presence of a 16SrXII-A profile. One pomegranate aster yellows strain AY-PG from 16S rRNA gene and the 16SrXII-A amplicon from tuf gene designed strain STOL-PG were directly sequenced and deposited in GenBank under the Accession Numbers KJ818293 and KP161063, respectively. To our knowledge, this is the first report of 16SrI-B and 16SrXII-A phytoplasmas in pomegranate trees.Öğe Detection and partial characterization of grapevine leafroll-associated virus 1 in pomegranate trees in Turkey(Springer, 2016) Caglayan, Kadriye; Elci, Eminur; Gazel, MonaFoliar virus-like symptoms consisting of yellowing, chlorotic spots, oak-leaf and vein clearing were observed on pomegranate cultivar Hicaz in Hatay province of Turkey in 2013. Three symptomatic out of 23 pomegranate samples reacted to Grapevine leafroll-associated virus 1 (GLRaV-1) antibodies in DAS-ELISA. In order to confirm the presence of GLRaV-1 in pomegranate, total RNA extracted from petiole samples was used in RT-PCR using specific primers designed on sequences of the heat-shock protein 70 homolog (HSP70h), coat protein (CP), coat protein duplicate 2 (CPd2) and open reading frame 9 (p24) genes of GLRaV-1. Amplicons were only obtained from symptomatic pomegranate samples for the CP, CPd2, and p24 genes but, unlike for GLRaV-1 isolates from grapevine, no amplicon was obtained for the HSP70h gene of GLRaV-1 isolates from pomegranate. The CP, CPd2 and p24 genes of GLRaV-1 from pomegranate (accession no. KP411914-KP411922) had 91-94 % nucleotide sequence identity with GLRaV-1 isolates from grapevine. Phylogenetic analyses reconstructed using the neighbor joining method showed a clustering of GLRaV-1 isolates from pomegranate and grapevine. These results suggest that pomegranate could be an alternate host for GLRaV-1.Öğe Detection of 'Candidatus phytoplasma pyri' in Turkey(Alma Mater Studiorum, Univ Bologna, 2007) Gazel, Mona; Serce, Cigdem Ulubas; Caglayan, Kadriye; Ozturk, HarunTypical 'Candidatus Phytoplasma pyri' (Pear Decline, PD) symptoms were first observed in 2005 in pear orchards of Bursa province, which is an important pear growing area in Turkey. The present report resulted from a survey of pear varieties to investigate the infection level of PD in Bursa in 2006. The observed symptoms were foliar reddening in late summer and fall, leaf roll, leaf curl, poor growth and slow or quick decline. The presence of PD phytoplasma in pear trees was investigated by polymerase chain reaction using universal P1/P7 and R16F2/R2 primers and the identification was performed by RFLP analyses. A total of 116 pear trees were tested and 61 samples were found infected by the phytoplasma. 'Ca. P. pyri' was identified using RsaI, SspI and MseI restriction enzymes. PD is widely distributed in pear trees with a high incidence and it is a big threat for pear production in Turkey.Öğe Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies(Peerj Inc, 2023) Rollin, Johan; Bester, Rachelle; Brostaux, Yves; Caglayan, Kadriye; De Jonghe, Kris; Eichmeier, Ales; Foucart, YoikaRecent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area. For this purpose, HTS has greatly facilitated the sequencing of new genomes of detected viruses and their comparison. However, bioinformatics analyses allowing reconstruction of genome sequences and detection of single nucleotide polymorphisms (SNPs) can potentially create bias and has not been widely addressed so far. Therefore, more knowledge is required on the limitations of predicting SNPs based on HTS-generated sequence samples. To address this issue, we compared the ability of 14 plant virology laboratories, each employing a different bioinformatics pipeline, to detect 21 variants of pepino mosaic virus (PepMV) in three samples through large-scale performance testing (PT) using three artificially designed datasets. To evaluate the impact of bioinformatics analyses, they were divided into three key steps: reads pre-processing, virus-isolate identification, and variant calling. Each step was evaluated independently through an original, PT design including discussion and validation between participants at each step. Overall, this work underlines key parameters influencing SNPs detection and proposes recommendations for reliable variant calling for plant viruses. The identification of the closest reference, mapping parameters and manual validation of the detection were recognized as the most impactful analysis steps for the success of the SNPs detections. Strategies to improve the prediction of SNPs are also discussed.Öğe Diversity, Distribution, and Current Status(Elsevier, 2023) Tiwari, A.K.; Caglayan, Kadriye; Al-Sadi, Abdullah M.; Azadvar, Mehdi; Abeysinghe, SamanDiversity, Distribution, and Current Status is the first volume in a three-volume series dedicated to the analysis of this important group of plant pathogens across Asia with a particular focus on geographic distribution. This book offers updated data on the most prevalent phytoplasma diseases specific to each region. Phytoplasmas are emerging plant pathogens all around the world, causing significant economic losses to crops, as well as affecting international trade. The chapters in Volume 1 look closely at different countries and regions across Asia, providing data on country-wide distribution, phytoplasma groups, insect vectors and transmission. The Phytoplama Diseases in Asian Countries series will be an essential read for university students, researchers and agriculturalists interested in Plant Pathology. Volume 1 will be of particular interest to those needing the latest data on the distribution and transmission rates specific to the various regions of Asia. © 2023 Elsevier Inc. All rights reserved.Öğe Endophytic bacterial community living in roots of healthy and 'Candidatus Phytoplasma mali'-infected apple (Malus domestica, Borkh.) trees(Springer, 2012) Bulgari, Daniela; Bozkurt, Adem I.; Casati, Paola; Caglayan, Kadriye; Quaglino, Fabio; Bianco, Piero A.'Candidatus Phytoplasma mali', the causal agent of apple proliferation (AP) disease, is a quarantine pathogen controlled by chemical treatments against insect vectors and eradication of diseased plants. In accordance with the European Community guidelines, novel strategies should be developed for sustainable management of plant diseases by using resistance inducers (e.g. endophytes). A basic point for the success of this approach is the study of endophytic bacteria associated with plants. In the present work, endophytic bacteria living in healthy and 'Ca. Phytoplasma mali'-infected apple trees were described by cultivation-dependent and independent methods. 16S rDNA sequence analysis showed the presence of the groups Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Chlamydiae, and Firmicutes. In detail, library analyses underscored 24 and 17 operational taxonomic units (OTUs) in healthy and infected roots, respectively, with a dominance of Betaproteobacteria. Moreover, differences in OTUs number and in CFU/g suggested that phytoplasmas could modify the composition of endophytic bacterial communities associated with infected plants. Intriguingly, the combination of culturing methods and cloning analysis allowed the identification of endophytic bacteria (e.g. Bacillus, Pseudomonas, and Burkholderia) that have been reported as biocontrol agents. Future research will investigate the capability of these bacteria to control 'Ca. Phytoplasma mali' in order to develop sustainable approaches for managing AP.Öğe Evaluations of apricot trees infected by Candidatus Phytoplasma prunorum for horticultural characteristics(2009) Gazel, Mona; Caglayan, Kadriye; Serce, Cigdem Ulubas; Son, LeventApricot, Prunus armeniaca L., is an important stone fruit species in Turkey. The Mediterranean coastal area in Turkey has advantageous climatic conditions for early table apricot production. New orchards with both local and foreign cultivars are being established in this region. The disease caused by phytoplasma is a critical threat for apricot growers. In this study, pomological data were collected from three apricot trees (cv. 'Precoce de Tyrinthe') that are infected by Candidatus Phytoplasma prunorum disease and from healthy plants under field conditions. The variables evaluated included yield, fruit width, length, height and weight, seed weight, seed/fruit ratio, soluble solids and acidity between 2004 and 2007. Analyses of variance indicated that all infected trees had lower yield when compared to the uninfected trees for four experimental years. The reduction in yield reached up to 77% in some cases. Significant differences were also recovered for variables for infected versus control comparisons. In some cases, the means of the trees also differed among infected ones. The results suggested that Ca. Phytoplasma prunorum negatively affects the 'Precoce de Tyrinthe' apricot for both yield and pomological characteristics in different ratios. Copyright © 2009 Bucharest University.Öğe First report of the Olpidium virulentus-mediated transmission of blueberry mosaic-associated virus in blueberries in Turkey(Springer, 2021) Caglayan, Kadriye; Akkan, Rengin; Gazel, Mona; Tok, Fatih Mehmet[Abstract Not Available]Öğe Further characterization of a new recombinant group of Plum pox virus isolates, PPV-T, found in orchards in the Ankara province of Turkey(Elsevier, 2009) Serce, Cigdem Ulubas; Candresse, Thierry; Svanella-Dumas, Laurence; Krizbai, Laszlo; Gazel, Mona; Caglayan, KadriyeSixteen Plum pox virus (PPV) isolates collected in the Ankara region of Turkey were analyzed using available serological and molecular typing assays. Surprisingly, despite the fact that all isolates except one, which was a mix infection, were typed as belonging to the PPV-M strain in four independent molecular assays, nine of them (60%) reacted with both PPV-M specific and PPV-D specific monoclonal antibodies. Partial 5' and 3' genomic sequence analysis on four isolates demonstrated that irrespective of their reactivity towards the PPV-D specific monoclonal antibody, they were all closely related to a recombinant PPV isolate from Turkey, Ab-Tk. All three isolates for which the relevant genomic sequence was obtained showed the same recombination event as Ab-Tk in the HC-Pro gene, around position 1566 of the genome. Complete genomic sequencing of Ab-Tk did not provide evidence for additional recombination events in its evolutionary history. Taken together, these results indicate that a group of closely related PPV isolates characterized by a unique recombination in the HC-Pro gene is prevalent under field conditions in the Ankara region of Turkey. Similar to the situation with the PPV-Rec strain, we propose that these isolates represent a novel strain of PPV, for which the name PPV-T (Turkey) is proposed. Given that PPV-T isolates cannot be identified by currently available typing techniques, it is possible that their presence has been overlooked in other situations. Further efforts should allow a precise description of their prevalence and of their geographical distribution in Turkey and, possibly, in other countries. (C) 2009 Elsevier B.V. All rights reserved.Öğe Further investigation of a genetically divergent group of plum pox virus-M strain in Turkey(Springer, 2019) Gurcan, Kahraman; Teber, Saffet; Caglayan, KadriyeIn the past several years, a limited number of isolates of a diverse group of Plum pox virus (PPV) strain -M were discovered in the European part of Istanbul, Turkey. In this study, stone fruit samples were collected from the European part of Istanbul and investigated by PCR typing and sequence analyses for determining prevalence and genetic diversity of this divergent PPV-M isolates. Out of the 230 sampled trees, 97 were determined to be infected with PPV. Strains of 88 isolates were identified and 67 of them (76%) were divergent PPV-M isolates, detected in apricot, peach and plum trees revealing that they could be evolutionarily successful divergent PPV-M isolates prevalent in Istanbul. The divergent Istanbul M isolates formed a monophyletic clade thereby named as PPV-MIs. Additionally, recombination analysis suggested that PPV-MIs isolates could be the donor of the PPV-M-type recombinant fragment of the PPV-Rec strain.Öğe Genetic diversity and a long evolutionary history of plum pox virus strain rec in Turkey(Springer, 2021) Gurcan, Kahraman; Teber, Saffet; Akbulut, Mikail; Caglayan, KadriyePlum pox virus strain Recombinant (PPV-Rec) is hypothetically considered as homologous recombinant between strains PPV-M and PPV-D. The nucleotide position 8450 up to end of genome is considered to come from PPV-M, and the remaining major genomic part is PPV-D-derived. It is regarded as third major PPV strain due to its wide distribution and prevalence in Europe. However, among over a thousand PPV isolates genetically identified in Turkey, only 10 of them (<1%) were characterized as PPV-Rec. The nearly complete genome of eight of the PPV-Rec isolates from European part of Turkey were obtained and analyzed together with PPV-Rec isolates of other countries. All major genomic features were conserved among Turkish PPV-Rec isolates. The genetic diversity of PPV-Rec isolates in Turkey (n = 8, 0.015 +/- 0.001%) was found to be comparable to that observed for the isolates from eight countries (n = 10, 0.014 +/- 0.001%). Particularly, genetic diversity of the minor recombinant fragment for Turkish PPV-Rec isolates was apparently higher (0.016 +/- 0.001%) than the value for the 10 isolates from eight countries (0.011 +/- 0.001%). The high genetic diversity was also demonstrated by high phylogenetic variation in Turkish isolates, indicating a long evolutionary history of PPV-Rec isolates in Turkey. After including Turkish isolates in the recombination analysis, the major putative recombination event of PPV-Rec isolates with a breakpoint around position 8450 was identified again, however the other recently reported putative recombination events were not supported in this study by the algorithms implemented in the RDP software.Öğe Genetic Variation and Possible Mechanisms Driving the Evolution of Worldwide Fig mosaic virus Isolates(Amer Phytopathological Soc, 2014) Walia, Jeewan Jyot; Willemsen, Anouk; Elci, Eminur; Caglayan, Kadriye; Falk, Bryce W.; Rubio, LuisFig mosaic virus (FMV) is a multipartite negative-sense RNA virus infecting fig trees worldwide. FMV is transmitted by vegetative propagation and grafting of plant materials, and by the eriophyid mite Aceria ficus. In this work, the genetic variation and evolutionary mechanisms shaping FMV populations were characterized. Nucleotide sequences from four genomic regions (each within the genomic RNAs 1, 2, 3, and 4) from FMV isolates from different countries were determined and analyzed. FMV genetic variation was low, as is seen for many other plant viruses. Phylogenetic analysis showed some geographically distant FMV isolates which clustered together, suggesting long-distance migration. The extent of migration was limited, although varied, between countries, such that FMV populations of different countries were genetically differentiated. Analysis using several recombination algorithms suggests that genomes of some FMV isolates originated by reassortment of genomic RNAs from different genetically similar isolates. Comparison between nonsynonymous and synonymous substitutions showed selection acting on some amino acids; however, most evolved neutrally. This and neutrality tests together with the limited gene flow suggest that genetic drift plays an important role in shaping FMV populations.Öğe Geographical Distribution of Viroids in Africa and the Middle East(Academic Press Ltd-Elsevier Science Ltd, 2017) El-Dougdoug, Khaled A.; Caglayan, Kadriye; Elleuch, Amine; Al-Tuwariqi, Hani Z.; Gyamera, Ebenezer A.; Hadidi, Ahmed[Abstract Not Available]Öğe Graft and vegetative transmission of phytoplasma-associated diseases in Asia and their management(Elsevier, 2023) Caglayan, Kadriye; Choueiri, Elia; Rao, Govind PratapThe propagation materials infected with phytoplasmas, such as rootstocks and other types of grafting materials used as scions play an important role in the dissemination of phytoplasma-associated diseases in new areas. Since the phytoplasma infection is systemic in the plants, the vegetative propagation of many horticultural crops allows their spread through cuttings, bud wood, tubers, runners, and bulbs. Grafting is therefore an efficient method of phytoplasma spreading and establishing infection in vegetatively propagated plants. The phytoplasma spreads through vegetative plant propagation and occurs in nature over short and long distances by natural scattering and transportation of infected propagation materials. The transmission of phytoplasmas in Asian countries is also mainly attributed to grafting of infected propagation materials in woody and herbaceous plant species. In Asia, the phytoplasma associated with stone fruits, pome fruits, citrus, jujube, ornamentals, other trees species, and grapevine are majorly transmitted by grafting. However, possibility of phytoplasma vegetative propagation through basal shoots, stems, rhizomes, tubers, stolons, corms, buds, and bulbs is reported in sugarcane, cassava, potato, sweet potato, and many ornamentals such as rose, carnations, marigold, chrysanthemum. Dodder species are also efficiently utilized for vegetative phytoplasma transmission. The importance of phytoplasma infection spread by grafting, vegetatively propagated plants, and possible management practices are discussed in this chapter. © 2023 Elsevier Inc. All rights reserved.Öğe Identification and Characterization of a Novel Robigovirus Species from Sweet Cherry in Turkey(Mdpi, 2019) Caglayan, Kadriye; Roumi, Vahid; Gazel, Mona; Elci, Eminur; Acioglu, Mehtap; Plesko, Irena Mavric; Reynard, Jean-SebastienHigh throughput sequencing of total RNA isolated from symptomatic leaves of a sweet cherry tree (Prunus avium cv. 0900 Ziraat) from Turkey identified a new member of the genus Robigovirus designated cherry virus Turkey (CVTR). The presence of the virus was confirmed by electron microscopy and overlapping RT-PCR for sequencing its whole-genome. The virus has a ssRNA genome of 8464 nucleotides which encodes five open reading frames (ORFs) and comprises two non-coding regions, 5 ' UTR and 3 ' UTR of 97 and 296 nt, respectively. Compared to the five most closely related robigoviruses, RdRp, TGB1, TGB2, TGB3 and CP share amino acid identities ranging from 43-53%, 44-60%, 39-43%, 38-44% and 45-50%, respectively. Unlike the four cherry robigoviruses, CVTR lacks ORFs 2a and 5a. Its genome organization is therefore more similar to African oil palm ringspot virus (AOPRV). Using specific primers, the presence of CVTR was confirmed in 15 sweet cherries and two sour cherries out of 156 tested samples collected from three regions in Turkey. Among them, five samples were showing slight chlorotic symptoms on the leaves. It seems that CVTR infects cherry trees with or without eliciting obvious symptoms, but these data should be confirmed by bioassays in woody and possible herbaceous hosts in future studies.Öğe Identification of Pomegranate as a New Host of Passiflora Edulis Symptomless Virus (PeSV) and Analysis of PeSV Diversity(Mdpi, 2020) Caglayan, Kadriye; Gazel, Mona; Roumi, Vahid; Kocabag, Hamide Deniz; Tunc, Bahar; Reynard, Jean Sebastien; Ruiz-Garcia, Ana BelenPomegranate is an important crop in the Mediterranean Basin that can be affected by a range of pathogens. With the aim to better understand the impact of viral diseases on pomegranate, two leaf samples from Turkey showing virus-like symptoms such as chlorotic spots and oak-leaf patterns were subjected to high throughput sequencing (HTS). Data analysis indicated the presence of passiflora edulis symptomless virus (PeSV: genus Roymovirus, Potyviridae family) in these two pomegranate samples, consistent with the observation by electron microscopy of flexuous filamentous viral particles 760 to 780 nm long. Further analysis of HTS reads revealed the presence of five PeSV variants in one of the samples and another single variant in the other. PeSV occurrence was also identified from publicly available SRA pomegranate RNA-Seq transcriptomic data from India and China. The genome of these PeSV-pomegranate variants share 78.0-86.8% nucleotide identity with that of the reference isolate from passionfruit (MH379332). The presence of PeSV in pomegranate was confirmed by specific RT-PCR assays targeting either the coat protein (CP) or Nla-Pro genes in 37 cultivated and one ornamental pomegranate out of 133 samples collected from the Eastern Mediterranean region of Turkey. To our knowledge, this is the first application of HTS to assess virus occurrence in pomegranate and the first recognition of pomegranate as a new host for PeSV.Öğe Incidence and genetic diversity of grapevine leafroll-associated virus 3 (GLRaV-3) isolates in Turkey(Academic Press Ltd- Elsevier Science Ltd, 2022) Gazel, Mona; Tunc, Bahar; Elci, Eminur; Caglayan, KadriyeGrapevine leafroll-associated virus 3 (GLRaV-3) is the most important virus species within the grapevine leafroll complex. It causes significant losses to growers and vineries because of its effect on grape and wine quality. A survey was conducted in the major grape-growing provinces of Turkey in 2018 to investigate distribution and the genetic diversity of GLRaV-3 in local and foreign grapevine cultivars. The genetic diversity of GLRaV-3 isolates based on partial heat-shock protein 70 homologue (Hsp70 h), partial coat protein (CP) and partial RNA-dependent RNA polymerase (RdRp) genes were determined by RT-PCR and sequencing. The infection rate of GLRaV-3 in 141 tested grapevine samples was 13.47% by DAS-ELISA and 28.36% by RT-PCR analysis. Totally, 17 amplicons from Hsp70 h, 22 isolates from RdRp and 16 isolates from CP genes were sequenced in both directions. The sequence analysis of three genes revealed that the Turkish GLRaV-3 isolates shared 91-100% nucleotide identities with the sequences of GLRaV-3 isolated deposited in the GenBank from other parts of the world without any correlation between the distribution and geographical origin.
