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    Balıkesir ve Uşak İlleri Tütün Ekim AlanlarındaPotyvirus İzolatlarının Belirlenmesi ve Karakterizasyonu
    (2022) Zelyüt, Filiz Randa; Karanfil, Ali; Korkmaz, Savaş
    Tütünlerde enfeksiyona neden olan çok sayıda viral etmen mevcuttur. Bunlar arasından potyvirüsler oldukça yaygın olup, tütünlerde enfeksiyonlar meydana getiren en önemli üyelerinden bir tanesi de Patato virus Y (PVY)’dir. Ülkemizde ise potyvirus ve PVY izolatlarının tütün üretim alanlarındaki enfeksiyonuna yönelik çalışmalar oldukça sınırlıdır. Gerçekleştirilen bu çalışma kapsamında Balıkesir ve Uşak illeri tütün üretim alanlarından simptomatik 71 örnek alınmıştır. Alınan örnekler potyvirus dejenere primerleri kullanırak RT-PCR yöntemi ile testlenmiştir. Testlemeler sonucunda 10 örnekte potyvirus enfeksiyonu tespit edilmiştir. Elde edilen potyvirus izolatlarının tür düzeyinde tanılanması amacı ile yapılan dizileme çalışmaları sonucunda 9 PVY izolatı belirlenmiştir. Bir izolat ise tam olarak tür düzeyinde tanılanamamakla birlikte Leek yellow stripe virus (LYSV) izolatları ile % 75’e kadar benzerlik göstermiştir. PVY İzolatlarının benzerlik analizleri sonucunda genel olarak kendi içlerinde yüksek oranda dizi homolojisi gösterdiği belirlenmiştir. Filogenetik analizler sonucunda 7 izolat N streynleri ile kümelenirken, 2 izolat ise rekombinasyon göstermeyen izolatların dışında kaldığı saptanmıştır.
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    ‘Candidatus Phytoplasma solani’ (Subgroup 16SrXII-A) Associated with Nicotiana tabacum Leaf Abnormality in Turkey
    (Namik Kemal University - Agricultural Faculty, 2022) Zelyüt, Filiz Randa; Santosa, Adyatma Irawan; Karanfil, Ali
    Tobacco (Nicotiana tabacum) is among the agricultural products with the highest added value in Turkey. Although frequently associated with its negative effects on human health, it also provides important contributions to the Turkish economy with the employment it creates in rural areas and continues to be a strategic product. Many postgraduate theses and studies related to the sociological and economic importance of the production of this plant, which is of great importance for our country, have been carried out. However, there are very limited studies on plant diseases in tobacco production areas in Turkey. Phytoplasma is one of the important plant pathogens that cause yield loss in tobacco. Since available data on phytoplasma diseases on tobacco was very scarce worldwide, field surveys to collect samples showing phytoplasma infection-like symptoms such as yellowish color changes, leaf blisters, proliferation, dwarfism, and other physical abnormalities were carried out in Çanakkale and Balıkesir provinces of Turkey from June to August 2021. The presence of phytoplasmas in six samples was confirmed by 16S ribosomal DNA amplification by nested-PCR using universal phytoplasma primer sets, which also suggested the pathogen associated with the symptoms on tobacco. According to phylogenetic study and virtual-RFLP analysis using AluI and MseI endonuclease enzymes, the six Turkish tobacco phytoplasma strains all belong to group 16SrXII and have more than 99% nucleotide sequence identity with some members of ‘Candidatus Phytoplasma solani’ of the taxonomic subgroup ‘stolbur’ (16SrXII-A). Genetic distances analysis indicated that group 16SrI was more closely related to 16SrXII than 16SrVI, in agreement with the groups clustering in the phylogenetic tree. Neutrality tests found that 16SrI and 16SrXII groups are experiencing expanding or bottleneck selections, probably due to new mutations in the 16S rRNA gene fragment. Meanwhile, 16SrVI populations are shown to be undergoing balancing selections, indicating that its isolates have evolved for a long time. © Bu çalışma Tekirdağ Namık Kemal Üniversitesi tarafından Creative Commons Lisansı.
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    Detection of Cucumismeloendornavirus Infection in South Marmara Region of Turkey and Molecular Characterization of Isolates
    (Mevlüt AKÇURA, 2023) Karanfil, Ali; Zelyüt, Filiz Randa; Korkmaz, Savaş
    Cucumis melo endornavirus (CmEV) is one of the viral diseases that cause infection in cucurbits in recent years. The virus has been detected in a limited area in Turkey, and no study has been conducted on the causal agent's presence and genetic diversity in other production regions. This study was conducted in this context to find out the presence of CmEV infection in the Southern Marmara region, as well as their genetic diversity. Seventy-one samples showing virus and virus-like symptoms were collected from the cucurbit cultivation fields in the provinces forming the Southern Marmara region. Reverse transcription-polymerase chain reaction (RT-PCR) was used to analyze the samples using a gene-specific primer. The testing revealed that CmEV was present in 31 of the samples that were collected. Melon, zucchini, watermelon, cucumber, and gherkins are among the cucurbit species where the infection has been found. CmEV infection detected in cucumber and zucchini plants is a new host report for Turkey, and CmEV infection detected in watermelon plants is a new host report for the world. As a result of the molecular characterization of 6 isolates selected from among the isolates obtained, it was determined that the isolates generally showed sequence similarity of 91% and above at the nucleotide and amino acid levels. As a result of the phylogenetic analysis, it was seen that most of the Turkish isolates were in a different phylogenetic group from the world isolates. With this study, it was determined that the areas and cucurbit species in which CmEV detected increased in Turkey
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    Evaluation of genetic diversity of tomato spotted wilt virus (TSWV) NSs gene region isolates at geographical level
    (Muhammet DOĞAN, 2024) Zelyüt, Filiz Randa; Karanfil, Ali
    One of the most significant plant protection problems that adversely affect agricultural production is diseases caused by viruses, as there are no direct and rapid control methods. Tomato spotted wilt virus (TSWV), which is known to cause major losses in vegetable production and is quite common in the Mediterranean basin, is one of these viruses. In reducing the prevalence of the agent, control of vector insects and use of resistant varieties are the primary parameters. In this study, the genetic diversity of the partial Non-Structural NSs gene, which produces a putative silencing suppressor protein of TSWV, was investigated at the level of geographical populations. A total of 325 isolates were clustered from Eastern European, European Mediterranean, Asian, African, and American populations and geographic genetic diversity analyses were performed. Phylogenetic analyses revealed 2 major phylogroups (Clade I and II). Isolates reported from Asia and Africa were clustered only in Clade II, while other isolates were distributed in both groups. Haplotype network analyses revealed that the isolates had genotypes partially related to their geography. In support of these results, molecular variance analyses (AMOVA) showed that there were significant results for both proposals when applied between and within geographic groups. The findings highlight that TSWV has experienced different evolutionary processes in geographical regions, that the virus spreads along different genetic lines in regions, that local genotypes may dominate in regions and potentially adapt more quickly, and that local plant health institutions should increase regional quarantine measures and isolation strategies, and that it is important to take these genetic differences into account in order for the control to be more effective and targeted.
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    Full-genome characterization of Turkish Rose Yellow Vein Virus (RYVV) Isolates
    (2024) Karanfil, Ali; Zelyüt, Filiz Randa; Korkmaz, Savaş
    Rose yellow vein virus (RYVV) is a viral agent that has been identified in roses in recent years and is known to exist in a very limited area in the world. However, in studies conducted in our country, the presence of the agent has been detected in different regions and provinces. Since direct chemical control of viral diseases is not possible as in other biotic diseases, molecular characterization of the agent forms the basis for possible resistance or gene silencing studies to be conducted in the coming years. Thus, 44 RYVV isolates previously identified in our country were used for full genome studies. In full genome studies, overlapping PCR method was used with 7 different species-specific primer pairs. The full genomes of 3 of these isolates were obtained. The full genomes of the other isolates could not be obtained. It was determined that the genome size of the 3 RYVV isolates whose full genomes were obtained was 9314 nucleotides. It was determined that the only RYVV isolate found in the GenBank and the Türkiye isolates also showed a high level of nucleotide sequence similarity. However, the fact that the entire genome of the other isolates could not be obtained and the ones obtained were amplified with primer pairs designed according to the single isolate in the GenBank database may be due to the presence of different strains of RYVV isolates. For this reason, it is thought that next-generation sequencing studies should be prioritized to obtain complete genome information in future studies.
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    Investigation of viruses and phytoplasma infections in tomato plantations in Bilecik province, Türkiye
    (Gültekin ÖZDEMİR, 2024) Zelyüt, Filiz Randa; Karanfil, Ali; Santosa, Adyatma Irawan
    In this study, the status of infections caused by viruses and phytoplasmas in tomato production areas of Bilecik province was determined using conventional molecular methods. During the 2022 tomato production season, 93 plants exhibiting symptoms such as mosaic, leaf and fruit deformations, flower anomalies, and necrotic spots were collected. Viral agents such as tomato spotted wilt virus (TSWV), cucumber mosaic virus (CMV), southern tomato virus (STV), tobamoviruses, and potyviruses were screened by RT-PCR, while phytoplasmas were detected by nested-PCR. Single, double, and triple infections were detected in 50 of the 93 plants. 17, 5, and 21 plants were infected by a single pathogen for TSWV, STV, and phytoplasmas, respectively. 1, 3, and 2 plants were infected by two pathogens for STV+TSWV, STV+phytoplasma, and TSWV+phytoplasma, respectively. Only one plant detected a triple infection caused by STV, TSWV, and phytoplasmas. The phytoplasma genetic group was determined as 16Sr XII-A by PCR RFLP in-silico and in-vitro methods. Sequencing studies revealed that TSWV had high nucleotide sequence similarity with other Türkiye isolates for the NSs partial gene and STV entire CP gene region. For phytoplasmas, sequencing studies showed that the obtained tomato strains overlapped one-to-one with stolbur strains. Phylogenetic analyses applied with global isolates for TSWV NSs and STV CP gene regions showed the existence of 2 main groups (Clade I and Clade II). TSWV and STV isolates obtained from this study clustered in large main branches (Clade I).
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    Ülkemiz Tütün Üretim Alanlarında Cucumber mosaic virus (CMV) Enfeksiyonunun Belirlenmesi ve Türk CMV izolatlarının Popülasyon Yapısı
    (Mevlüt AKÇURA, 2023) Karanfil, Ali; Zelyüt, Filiz Randa; Korkmaz, Savaş
    Cucumber mosaic virus (CMV) bitki virüs hastalıkları arasında muhtemelen en fazla konukçu genişliğine sahip bir viral hastalık etmenidir. CMV enfeksiyonu Türkiye’de birçok farklı bitki türünde tespit edilmiştir. Etmenin Türkiye’deki konukçu aralığı oldukça fazla olmasına rağmen, Türkiye tütün üretim alanlarının çok büyük bir kısmını oluşturan Marmara ve Ege Bölgeleri tütün üretim alanlarındaki enfeksiyonu ve Türk CMV izolatlarının popülasyon yapıları ile ilgili yapılmış detaylı bir çalışma bulunmamaktadır. Bu çalışma kapsamında belirtilen alanlardan 300 simptomatik tütün bitkisi toplanmış ve 12 tanesinin CMV ile enfekteli olduğu belirlenmiştir. Bu sonuçla CMV’nin tütün üretim alanlarında ana viral patojen olmadığı görülmüştür. Türk CMV izolatlarının moleküler karakterizasyonu amacı ile yürütülen sekans ve biyoinformatik analizler sonucunda izolatların birbirleri ile nükleotit ve aminoasit düzeyinde %91-100 arasında benzerlik gösterdiği belirlenmiştir. Filogenetik analizler ile Türk CMV izolatlarının Ia ve Ib olmak üzere iki altgruba dağılım gösterdiği görülmüştür. Bu altgruplardan Ib’de bulunan CMV izolatlarının Ia’ya göre genetik açıdan oldukça polimorfik olduğu belirlenmiştir. Ayrıca konukçu ve coğrafik orijinin Türk CMV izolatlarının filogenetik ilişkilerinde rol oynamadığı belirlenmiştir