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    First Detection and Molecular Characterization of Peach latent mosaic viroid in a New Natural Host: Walnut (Juglans regia L.)
    (2020) Tuncel, Feyza; Tekkaş, Nazlı; Türk, Gökay; Oksal, Hatice Diğdem; Sipahioğlu, Hikmet Murat
    Peach latent mosaic viroid (PLMVd) occurs naturally in peach and nectarines worldwide including North and South America, Europe, Asia and Australia with high infection frequencies. Here, our experimental findings revealed for the first time PLMVd infections in walnut (Juglans regia L.) in the world. Twelve walnut leaves, all from symptomless plants, were obtained from a nearby walnut germplasm collection in Malatya (Turkey). Genomic RNAs were extracted using a commercial RNA isolation kit and the complete viroid genome was amplified by reverse transcriptase polymerase chain reaction (RT-PCR) assay using end to end primer pair. The PCR amplicons of expected size (approx. 0.34-kb DNA fragments) were cloned into pGEM-T Easy vector and transformed into competent Escherichia coli strain JM109. Purified plasmids were sequenced bidirectionally. Of the 12 walnut specimens tested by RT-PCR, 4 were found infected by PLMVd detected in mid-summer of 2018 and in autumn of 2019. Analysis of nucleotide sequence of two walnut isolates (Acces. no: MN857143- MN857144) confirmed the presence of PLMVd and shared 96.6-98.8% similarity (Acces. no: MN857143) and %97-98.8% similarity (Acces. no: MN857144) with peach, nectarine and cherry isolates of the world. By identifying walnut as an alternate host, we confirm that PLMVd potentially may infect other fruit trees cultivated worldwide. Here, we also report molecular features of these two distinct PLMVd-walnut isolates detected in Malatya (Turkey).
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    Natural phytoplasma infections on fruit, vegetable and weed plants at the same agroecosystem and their molecular properties
    (AcademicPres, 2020) Oksal, Hatice Diğdem
    The phytoplasma associated diseases are an emerging threat to fruit and vegetable crops leading severe yield losses worldwide. Pear (Pyrus communis L.) trees, with symptoms of severe reddening, dwarfing and shoot proliferation were observed in pear orchards of Malatya province of Turkey. Tomato (Solanum lycopersicum L.) plants grown nearby the symptomatic pear orchard displaying leaf rolling, severe flower sterility and purple leaves were observed at the same agroecosystem. To verify the presence and diversity of phytoplasmas, symptomatic pears and tomatoes were sampled and weeds nearby the symptomatic plants were collected. Total plant DNA was purified from midrib of collected leaves using a commercial kit. The DNA samples were analyzed by nested polymerase chain reaction (PCR) using universal primer pairs to amplify 16S rDNA fragments. The phytoplasmas detected in collected samples were differed according to the host. Here we detected and characterized ‘Candidatus Phytoplasma pyri’ belonging to apple proliferation group (subgroup 16SrX-C) from a pear tree, ‘Candidatus Phytoplasma trifolii’ belonging to clover proliferation group (subgroup 16SrVI-A) from a weed (Amaranthus retroflexus) and ‘Candidatus Phytoplasma solani’ belonging to the stolbur phytoplasma group (subgroup 16SrXII-A) from a tomato plant. Direct sequencing of PCR products verified the phytoplasmal nature of the infections. The occurrence of ‘Ca. P. trifolii’ on A. retroflexus is the first report for the world. The irregular presence of the phytoplasmas in fruit and vegetable crops and weeds indicates continuous spread of the phytoplasmas threatening the new crops and new horizons.
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    Occurrence and Molecular Characterization of Some Economically Relevant Cucurbit Viruses in Malatya, Turkey
    (Adem Yavuz Sönmez, 2020) Örs, Fatih; Oksal, Hatice Diğdem; Sipahioğlu, Hikmet Murat
    Field surveys were conducted from 2016 to 2017 to detect and determine the prevalence of viruses in the major cucurbit growing areas of Malatya. A total of 162, namely 110 melon, 25 pumpkin and 27 watermelon leaf samples were collected from Arapgir, Arguvan and Battalgazi districts from symptomatic and non-symptomatic cucurbit plants. Using molecular methods, the plant samples were tested against four viruses, including Cucumber mosaic cucumovirus (CMV), Zucchini yellow mosaic potyvirus (ZYMV), Watermelon mosaic potyvirus (WMV) and Squash mosaic comovirus (SqMV). Results of RT-PCR tests revealed that none of the samples collected from Arapgir and Arguvan reacted positive against surveyed viruses. However, CMV infection was found in 1 cucumber, ZYMV in 5 pumpkin and WMV in 6 watermelon samples in Battalgazi district. The nucleotide sequences of partial coat protein (CP) genes of ZYMV-Malatya and WMV-Malatya isolates were determined. Nucleotide sequence comparisons revealed 95-100% similarity of ZYMV-Malatya isolate with other isolates of ZYMV reported worldwide with no mutation site on CP gene. However, WMV-Malatya isolate exhibited 94-99% similarity with other WMV sequences reported worldwide consisting a unique mutation site on CP gene sequence. These isolates are recorded to the Gene Bank with the accession numbers MT186266 (Zucchini yellow mosaic virus isolate, Malatya ZYMV1) and MT186267 (Watermelon mosaic virus isolate Malatya WMV1).