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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 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 Molecular detection of ‘Candidatus Phytoplasma mali’ associated with virescence in Narcissus tazetta in Turkey(Technology Society of Basic and Applied Sciences, 2023) Boztas, Kadir; Kocabag, Hamide Deniz; Derecik, Kayhan; Gazel, Mona; Sipahioglu, Hikmet Murat; Caglayan, Kadriye; Tulum, IsilIn the winter 2019 virescence, flower sterility, and stunting symptoms were observed in daffodil plants in Mersin province of Turkey. To detect the presence of phytoplasmas ten plants showing symptoms and ten asymptomatic plants were assayed by PCR analysis. The nested-PCR analysis of extracted DNA with universal primer pairs amplifying 16S phytoplasma ribosomal gene were positive for 9 out of the 10 symptomatic daffodil samples. BLAST analysis of the 16S rDNA sequences, virtual restriction fragment length polymorphism (RFLP) and RFLP analyses confirmed the presence of ‘Candidatus Phytoplasma mali’ in Narcissus tazetta plants. The detected strains of ‘Ca. P. mali’ were sequenced and compared in multiple alignments using sequences in NCBI GenBank. The nucleotide identity among the 16S rDNA gene fragments ranged between 99.26 and 99.91% to ‘Ca. P. mali’, ribosomal subgroup 16SrX-A. Although phytoplasmas in this subgroup have been reported frequently from woody plants, this is the first report of a ‘Ca. P. mali’ strain infecting daffodil plants. © 2023, Technology Society of Basic and Applied Sciences. All rights reserved.Öğe Molecular identification of phytoplasmas in ornamental pomegranates in Turkey(Technology Society of Basic and Applied Sciences, 2019) Çaglayan, Kadriye; Gazel, Mona; Acioglu, Mehtap; Kocabag, Hamide Deniz; Sipahioglu, Hikmet MuratLeaves, flowers and shoots of ornamental pomegranates showing yellowing and leaf deformation were collected from symptomatic and non-symptomatic plants between 2015 and 2017 from Hatay, Sanliurfa and Gebze provinces of Turkey. Among the 20 tested pomegranate samples, 10 were positive for phytoplasmas using 16R758f/16R1232r and U5/U3 primers amplifying 16S ribosomal RNA gene. The sequences of 8 strains shared the closest nucleotide identity (99%) with phytoplasmas in group 16SrIX and the remaining 2 strains had 98% identity with the ‘Candidatus Phytoplasma solani’ (subgroup 16SrXII-A). The present study represents the first evidence of phytoplasma association with yellowing symptoms in ornamental pomegranates in Turkey. © 2019, Technology Society of Basic and Applied Sciences. All rights reserved.Öğe Whole-genome sequencing of extended-spectrum ?-lactamase (ESBL)-producing Enterobacteriaceae from retail raw milk(Wiley, 2022) Aslantas, Ozkan; Yilmaz, Ebru Sebnem; Buyukaltay, Kaan; Kocabag, Hamide DenizThe contaminated products of food-producing animals have been proposed to lead the transmission of resistant bacteria to consumers. Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae, which were isolated from raw milk samples, were characterised using whole-genome sequencing in this study. Three confirmed ESBL and one plasmid-mediated AmpC beta-lactamase (pAmpC)-producing isolate were obtained. All of the ESBL-producing isolates showed a multidrug-resistant (MDR) phenotype, but the pAmpC-producing isolate was only resistant to beta-lactams. This study showed that raw milk can contain MDR bacteria that have several resistance determinants and highlighted the necessity of efficiently and routinely screening the products of food-producing animals.
