Yazar "Santosa, Adyatma Irawan" seçeneğine göre listele

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    'Candidatus Phytoplasma solani' (Subgroup 16SrXII-A) Associated with Nicotiana tabacum Leaf Abnormality in Turkey
    (Univ Namik Kemal, 2022) Zelyut, 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 canakkale and Balikesir 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.
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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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    First Insight into Genetic Variation and Population Structure of The Emerging Citrus chlorotic dwarf-associated virus (CCDaV, genus Citlodavirus)
    (Centenary University, 2022) Randa Zelyüt, Filiz; Santosa, Adyatma Irawan; Karanfil, Ali; Silva, Jose Cleydson Ferreira
    Citrus spp. is widely planted in tropical and subtropical regions, including in Turkey and other Mediterranean countries. Due to its widespread vector and climate change, Citrus chlorotic dwarf-associated virus (CCDaV), a member of the newly formed genus Citlodavirus, is one of the emerging viruses that can be a serious constraint to Citrus crops production in the coming years. Therefore, in-silico analysis on all available isolates in NCBI GenBank was performed to provide the first insight into the genetic population and evolution of CCDaV, which may contribute to its control. CCDaV phylogroups based on full genome, complete movement protein, and complete coat protein sequences were found to be not associated with isolate origins or host species, and all isolates also shared a high genetic identity among them. However, neutrality tests indicated that the current populations are expanding, driven by new mutations. Low Fixation index (FST) values (0.00000-0.36207) confirmed no genetic separation among different ORFs of isolates from three countries. The constructed TimeTree suggested that CCDaV emergence was very recent compared to the other three members of the genus Citlodavirus. Therefore, the obtained results of this study could also expand our knowledge on other even more obscure citladovirus and even other plant DNA viruses, which are still less studied than RNA viruses. © 2022, Centenary University. All rights reserved.
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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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    Phylogenetic and diversity analyses revealed that leek yellow stripe virus population consists of three types: S, L, and N
    (Springer, 2023) Santosa, Adyatma Irawan; Randa-Zelyut, Filiz; Karanfil, Ali; Korkmaz, Savaş; Hartono, Sedyo; Ertunç, Filiz
    Phylogenetic and evolutionary analyses were performed on the P1 and CP genes of global isolates to clarify the phylogrouping of leek yellow stripe virus (LYSV, genus Potyvirus), a pathogen affecting Allium spp. worldwide, into different types based on genetic variation and host species. The constructed phylogenetic trees divided the isolates into three major groups: S, L, and N. Low nucleotide (nt) and amino acid (aa) percent identities among the three groups were observed on full ORF (75.4–99.0 and 79.1–99.0), P1 (59.1–98.3 and 36.8–98.3), and CP (76.6–100 and 75.7–100) coding regions. The dN/dS values of P1 and CP confirmed that both genes are under strong negative (purifying) selection pressure. Neutrality tests on Eastern Asian isolates suggested that the ancestors of current LYSV isolates evolved with garlic while they were in Asia before spreading to other world regions through garlic propagative materials. Genetic differentiation and gene flow analysis showed extremely frequent gene flow from S group to L and N groups, and these phylogroups differentiated from each other over time. Host differences, inconsistent serological test results, substantial nt and aa variation, and phylogenetic and diversity analyses in this study supported previous reports that LYSV can be separated into three major evolutionary lineages: S, L, and N types.