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    Assessment of susceptibility of different rootstock/variety combinations of pear to Candidatus Phytoplasma pyri and experimental transmission studies by Cacopsylla pyri
    (Springer, 2022) Caglayan, Kadriye; Gazel, Mona; Serce, Cigdem Ulubas; Kaya, Kamuran
    In this study, efficient transmission ways of 'Ca. P. pyri' which causes Pear Decline (PD) disease and response of different rootstock-scion combinations to this pathogen were evaluated. For graft transmission trials, fifty BA29 clonal rootstocks were grafted with buds taken from a 'Ca. P. pyri' infected pear tree, cv. Deveci, and the transmission rate was found to be 8% according to PCR/RFLP analyses. Growth retardation was detected in some grafted plants but the specific reddening symptoms for PD were not observed during the 2 years of observation. Cacopsylla pyri L., playing important role for the transmission of pear decline phytoplasma in open field, was used for experimental transmission trials. It has been shown that it can acquire phytoplasma (in 1 day) and transmit it (in 2 weeks to healthy pear saplings). Therefore it was revealed that C. pyri plays an important role in pear decline epidemiology. When the response of several rootstock-scion combinations to 'Ca. P. pyri'was evaluated over two vegetative periods by visual monitoring of symptom development and by PCR analyses, two Santa Maria and one Williams plants grafted on OHF333 and one Deveci plant grafted on P. communis were found infected by 'Ca. P. pyri', but no infection was detected in a local cv. Ankara grafted on any rootstocks. Among the commercial cultivars, our local cv. Deveci was found the most sensitive and cv. Ankara was the most tolerant. The use of healthy plant materials, as well as the appropriate control of the vector will play an important role in disease control.
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    Detection and partial characterization of grapevine leafroll-associated virus 1 in pomegranate trees in Turkey
    (SPRINGER, 2016) Caglayan, Kadriye; Elci, Eminur; Gazel, Mona
    Foliar virus-like symptoms consisting of yellowing, chlorotic spots, oak-leaf and vein clearing were observed on pomegranate cultivar Hicaz in Hatay province of Turkey in 2013. Three symptomatic out of 23 pomegranate samples reacted to Grapevine leafroll-associated virus 1 (GLRaV-1) antibodies in DAS-ELISA. In order to confirm the presence of GLRaV-1 in pomegranate, total RNA extracted from petiole samples was used in RT-PCR using specific primers designed on sequences of the heat-shock protein 70 homolog (HSP70h), coat protein (CP), coat protein duplicate 2 (CPd2) and open reading frame 9 (p24) genes of GLRaV-1. Amplicons were only obtained from symptomatic pomegranate samples for the CP, CPd2, and p24 genes but, unlike for GLRaV-1 isolates from grapevine, no amplicon was obtained for the HSP70h gene of GLRaV-1 isolates from pomegranate. The CP, CPd2 and p24 genes of GLRaV-1 from pomegranate (accession no. KP411914-KP411922) had 91-94 % nucleotide sequence identity with GLRaV-1 isolates from grapevine. Phylogenetic analyses reconstructed using the neighbor joining method showed a clustering of GLRaV-1 isolates from pomegranate and grapevine. These results suggest that pomegranate could be an alternate host for GLRaV-1.
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    Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies
    (Peerj Inc, 2023) Rollin, Johan; Bester, Rachelle; Brostaux, Yves; Caglayan, Kadriye; De Jonghe, Kris; Eichmeier, Ales; Foucart, Yoika
    Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area. For this purpose, HTS has greatly facilitated the sequencing of new genomes of detected viruses and their comparison. However, bioinformatics analyses allowing reconstruction of genome sequences and detection of single nucleotide polymorphisms (SNPs) can potentially create bias and has not been widely addressed so far. Therefore, more knowledge is required on the limitations of predicting SNPs based on HTS-generated sequence samples. To address this issue, we compared the ability of 14 plant virology laboratories, each employing a different bioinformatics pipeline, to detect 21 variants of pepino mosaic virus (PepMV) in three samples through large-scale performance testing (PT) using three artificially designed datasets. To evaluate the impact of bioinformatics analyses, they were divided into three key steps: reads pre-processing, virus-isolate identification, and variant calling. Each step was evaluated independently through an original, PT design including discussion and validation between participants at each step. Overall, this work underlines key parameters influencing SNPs detection and proposes recommendations for reliable variant calling for plant viruses. The identification of the closest reference, mapping parameters and manual validation of the detection were recognized as the most impactful analysis steps for the success of the SNPs detections. Strategies to improve the prediction of SNPs are also discussed.
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    Incidence and genetic diversity of grapevine leafroll-associated virus 3 (GLRaV-3) isolates in Turkey
    (Academic Press Ltd- Elsevier Science Ltd, 2022) Gazel, Mona; Tunc, Bahar; Elci, Eminur; Caglayan, Kadriye
    Grapevine leafroll-associated virus 3 (GLRaV-3) is the most important virus species within the grapevine leafroll complex. It causes significant losses to growers and vineries because of its effect on grape and wine quality. A survey was conducted in the major grape-growing provinces of Turkey in 2018 to investigate distribution and the genetic diversity of GLRaV-3 in local and foreign grapevine cultivars. The genetic diversity of GLRaV-3 isolates based on partial heat-shock protein 70 homologue (Hsp70 h), partial coat protein (CP) and partial RNA-dependent RNA polymerase (RdRp) genes were determined by RT-PCR and sequencing. The infection rate of GLRaV-3 in 141 tested grapevine samples was 13.47% by DAS-ELISA and 28.36% by RT-PCR analysis. Totally, 17 amplicons from Hsp70 h, 22 isolates from RdRp and 16 isolates from CP genes were sequenced in both directions. The sequence analysis of three genes revealed that the Turkish GLRaV-3 isolates shared 91-100% nucleotide identities with the sequences of GLRaV-3 isolated deposited in the GenBank from other parts of the world without any correlation between the distribution and geographical origin.
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    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 Mavric
    Raspberry 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.
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    Molecular Identification of Fig Cryptic Virus and Fig Fleck-Associated Virus in Turkey
    (Ars Docendi, 2017) Elci, Eminur; Hancer, Tugce; Caglayan, Kadriye
    Recently, several new viruses infecting fig trees were identified. To assess the presence, distribution and genetic diversity of Fig cryptic virus (FCV) and Fig fleck-associated virus (FFkaV) in fig trees of Turkey, a total of 65 fig samples, which show yellowing, chlorotic, necrotic spots and vein clearing symptoms, were collected from Aegean and Mediterranean regions, which are the most important fig growing regions of Turkey, in spring 2014 and tested by molecular analysis. After cDNA synthesis, FCV and FFkaV specific primer sets of RNA dependent RNA polymerase (RdRp) regions were used for reverse transcription-polymerase chain reaction (RT-PCR) analysis and the PCR products were directly sequenced. The obtained sequences were analyzed and nucleotide sequence analysis confirmed the FCV and FFkaV infections. According to the results, some of the fig trees are infected in Turkey by FCV and FFkaV with an incidence of 20 % and 9.2 %, respectively. BLAST analysis of both FCV and FFkaV has shown high identity with Italian isolates (FCV\ref\NC015494.1 and FFkaV\ref\NC015229.1). For FFkaV, the phylogenetic analysis, constructed from partial RdRp nucleotide sequences, clustered the isolates based on their geographical origin. While the correlation between FFkaV isolates and regions was very high, no correlation between collection regions and FCV isolates was observed. It can be concluded that, fig trees from the most important fig growing regions of Turkey are infected by FCV and FFkaV and it is instrumental to overview of the viral control strategies for fig plantations in Turkey.
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    POTENTIAL PSYLLID VECTORS OF CANDIDATUS PHYTOPLASMA MALI AND CANDIDATUS PHYTOPLASMA PYRI IN TURKEY
    (Univ Agriculture, Fac Veterinary Science, 2016) Kaya, Kamuran; Serce, Cigdem Ulubas; Gazel, Mona; Caglayan, Kadriye; Sauvion, Nicolas
    Psyllids are vectors of phytoplasma, which cause important diseases of pome fruit trees. Psyllid species reported as phytoplasma vectors were captured during 2010-2011 in several pome fruit growing regions in Turkey. Potential psyllid vectors of 'Candidatus Phytoplasma mali' were collected from Malus spp. (apple), Cydonia oblonga (quince), Crataegus spp. (hawthorn) and also from the overwintering hosts, whereas those of 'Candidatus Phytoplasma pyri' were collected from wild and cultured forms of Pyrus spp. (pear) trees. The psyllids were identified morphologically as Cacopsylla picta, C. melanoneura-C. affinis complex, C. crataegi, C. pyrisuga, C. pyri, C. pyricola and other Cacopsylla species. The highest natural phytoplasma infection rate was found in C. picta followed by C. pyri, C. melanoneura-C. affinis complex and C. crataegi with rates of 4.36, 3.84, 2.77 and 1.67%, respectively. No phytoplasma were detected in C. pyrisuga, C. pyricola, or the other Cacopsylla spp. 'Ca. P. mali' was detected in C. picta, C. melanoneura-C. affinis complex and C. pyri; 'Ca. P. pyri' was detected in C. picta, C. crataegi, C. melanoneura-C. affinis complex and C. pyri individuals. To our knowledge, this is the first report on the possible psyllid vectors of 'Ca. P. mali' in Turkey.