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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 raspberry bushy dwarf virus (RBDV) in Rubus spp. in Turkey(Wiley, 2023) Caglayan, Kadriye; Ordek, Kivilcim; Gazel, Mona; Elci, Eminur; Roumi, Vahid; Lamovsek, Janja; Plesko, Irena MavricRaspberry bushy dwarf virus (RBDV), recently renamed to Idaeovirus rubi, is one of the most common viruses infecting Rubus species worldwide but there is still a limited number of genome sequences available in the GenBank database and the majority of the sequences include partial sequences of RNA-1 and RNA-2. The distribution and incidence of RBDV in main raspberry and blackberry growing provinces in Turkey were monitored during 2015-2019 and 537 Rubus spp. samples were tested by both DAS-ELISA and RT-PCR. Among the tested samples, 36 samples tested positive for RBDV by DAS-ELISA and 67 samples by RT-PCR. There was relatively low nucleotide diversity among the Turkish isolates. Turkish isolates shared 93%-97.7%, 84.3%-98.9%, and 85%-99.2% nucleotide sequence identities with available sequences in the GenBank, in partial RNA-1, movement protein (MP) and coat protein (CP) genes, respectively. In the phylogenetic tree constructed for RNA-1, MP, and CP sequences, all Turkish raspberry isolates were clustered in a distinct clade. However, the blackberry isolates showed considerable variation in nucleotide sequences and were placed in three distinct groups. The divergent blackberry isolates showed high variability in MP (84.5%-89.3%) and CP (85.5%-89.7%) regions and were placed in a distinct group. The rest of blackberry isolates clustered together with sweet cherry RBDV isolates adjacent to the grapevine clade or together with raspberry isolates. The comparative analysis conducted on three RNA segments of RBDV highlighted the high sequence diversity of Turkish RBDV isolates. This study also emphasizes the importance of regular monitoring of RBDV infections in Turkey, with special regard to those Rubus spp. and grapevine accessions employed in conservation and selection programmes. In particular, the presence of new RBDV genetic variants and infection of Rubus species must be taken into account to choose a correct detection protocol and management strategy.Öğe Incidence, distribution and limited genetic variability among Turkish isolates of Grapevine Pinot gris virus from different grapevine cultivars(Springer Heidelberg, 2018) Elci, Eminur; Gazel, Mona; Roumi, Vahid; Caglayan, KadriyeGrapevine Pinot gris virus (GPGV) was firstly identified in northern Italy by deep sequencing from grapevine cv. Pinot gris, exhibiting mottling and deformation of the leaves. The objective of this study was to investigate the prevalence and genetic variability of GPGV isolates obtained from different local and imported grapevine cultivars in Turkey based on partial coat protein, movement protein and RNA-dependent RNA polymerase (RdRp) domain of the replicase (Rep) gene. Two hundred and one grapevine samples from different provinces were tested by RT-PCR assays, approximately 25% of which were found to be infected by GPGV. The PCR products were sequenced and based on the phylogenetic analysis, RdRp gene was found to be most conserved region. The phylograms of three genomic regions revealed correlation between geography and genetic structure. Furthermore, nucleotide diversity studies revealed a low divergence from the homologous sequences from GenBank and some variations within the groups were detected. The results presented in this study provide a better understanding of genetic variation and phylogenetic of GPGV isolates worldwide.Öğe Occurrence of Hop stunt viroid in apple orchards of the Northwest Iran(Tarbiat Modares University, 2020) Roumi, Vahid; Gazel, Mona; Caglayan, KadriyeWe investigated the presence of Hop stunt viroid (HSVd) in apple samples, showing dappling fruit symptoms, in the Maragheh area (Northwest Iran) by means of RT-PCR. The viroid was detected only in leaves collected from symptomatic trees and a 298bp amplicon (IR-Gala) was directly sequenced in both directions. Multiple sequence alignment and Blast analyzes revealed that IR-Gala isolate shares the highest identity with grapevine isolates from Brazil and China. Amongst Iranian isolates of HSVd available in the GenBank, this isolate had the highest identity with grapevine isolate of HSVd from Maragheh region. In Phylogenetic analysis by MrBayes, IR-Gala was clustered with grapevine isolates from Brazil, China and Iran and may suggest that HSVd-apple isolate could be originated from grapevine. © 2020, Tarbiat Modares University. All rights reserved.Öğe Pomegranate(Elsevier, 2023) Çağlayan, Kadriye; Roumi, Vahid; Gazel, MonaPomegranate (Punica granatum L.), a deciduous shrub, belongs to the family Punicaceae, originated from Iran, and has been cultivated since ancient times throughout the Mediterranean parts of Asia, Africa, and Europe as a medicinal and ornamental plant as well as a fruit tree. The main pomegranate production occurs in Asian countries such as Iran, India, China, and Turkey. These studies revealed the presence of grapevine leafroll virus 1 and Passiflora edulis symptomless virus in cultivated pomegranates in Turkey and rose leaf curl virus in ornamental pomegranates in Pakistan. Although these viruses have been detected in mostly symptomatic pomegranates, the correlation between symptoms and viruses, their epidemiology, and economic impact are still unknown. © 2024 Elsevier Inc. All rights reserved.Öğe Sweet cherry, a new host of raspberry bushy dwarf virus(Springer, 2023) Caglayan, Kadriye; Gazel, Mona; Roumi, Vahid; Lamovsek, Janja; Beber, Aljosa; Plesko, Irena MavricRaspberry bushy dwarf virus (RBDV) is one of the most important pathogens of raspberries worldwide. In this study, we detected RBDV from 8 out of 50 cherry samples collected from Bursa, Turkey by DAS-ELISA and/or RT-PCR. We also determined the nearly full genome sequences of RBDV RNA2 from two cherry (Prunus avium) trees. The genomes were identical and shared 87.2 to 97.2% similarity to the RBDV RNA2 sequences from Rubus spp. and grapevine isolates available in GenBank, respectively. Phylogenetic analyses of RNA2 and MP gene sequences grouped cherry sequences in a clade more closely related to the grapevine clade (75 and 86% bootstrap value) while the topology based on the CP gene resulted in three separate clusters according host plant identity. Although host-dependent differentiations were confirmed in this study, no obvious geographical differentiation was observed from phylogenetic analysis, and no recombination events were detected. RBDV is found in raspberry and blackberry in many countries, including Turkey, however, here we report the first natural RBDV infection of cherry worldwide.
