Search

Cestrum species are being used as hedge and ornamental plants in Turkey. In this study, a Cestrum elegans plant showing chlorotic spots, rings and reddening was subjected to high throughput sequencing of small RNAs, in order to clarify its etiology. Results suggested the presence of tomato chlorosis virus (ToCV), which was further confirmed by RT-PCR using two specific primers amplifying RNA-dependent RNA polymerase (RdRp) and coat protein (CP) of the virus. When 25 Cestrum samples were tested using CP primers, one symptomatic C. elegans and four symptomless C. nocturnum were infected by ToCV. The obtained sequences shared 83–99.9% nucleotide identity with ToCV isolates available in the GenBank. Phylogenetic relationship among Turkish tomato isolates of ToCV and those available in the GenBank showed that two Cestrum spp. isolates of ToCV were closely related to Turkish tomato isolates, while the other three clustered with isolates from different countries.

Pomegranate 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&ndash, 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.

WOS: 000373994100018, 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.

Grapevine Pinot gris virus (GPGV) was firstly identified in northern Italy by deep sequencing from grapevine cv. Pinot gris, exhibiting mottling and deformation of the leaves. The objective of this study was to investigate the prevalence and genetic variability of GPGV isolates obtained from different local and imported grapevine cultivars in Turkey based on partial coat protein, movement protein and RNA-dependent RNA polymerase (RdRp) domain of the replicase (Rep) gene. Two hundred and one grapevine samples from different provinces were tested by RT-PCR assays, approximately 25% of which were found to be infected by GPGV. The PCR products were sequenced and based on the phylogenetic analysis, RdRp gene was found to be most conserved region. The phylograms of three genomic regions revealed correlation between geography and genetic structure. Furthermore, nucleotide diversity studies revealed a low divergence from the homologous sequences from GenBank and some variations within the groups were detected. The results presented in this study provide a better understanding of genetic variation and phylogenetic of GPGV isolates worldwide. © 2018, Deutsche Phytomedizinische Gesellschaft.

Fruit tree diseases caused by phytoplasma have great economic effects on fruit production, especially in Europe. A major phytoplasma is ‘Candidatus Phytoplasma mali’, which causes apple proliferation (AP) disease mainly in cultured and wild forms of apple trees (Seemuller et al., 2011a); however, there has been a report of different hosts, including Prunus avium (L.) L., P. armeniaca L., and P.domestica L. (Mehle et al., 2007). ‘Ca. Phytoplasma pyri’ causes pear decline (PD) disease that is found mainly in cultured and wild forms of pear (Pyrus spp.) and quince (Cydonia oblonga Mill.) (Seemuller et al., 2011b). These phytoplasma are taxonomically classified into the 16SrX group (or AP-group) of phytoplasmas and constitute closely related subgroups (Seemuller and Schneider, 2004). Phytoplasmas are mainly spread by vegetative propagation or the grafting of infected plant material and phloem feeding insects, primarily leafhoppers, planthoppers and psyllids (Weintraub and Beanland, 2006). Only one genus of this last one, Cacopsylla spp., transmit AP-group phytoplasmas to pome and stone fruit trees. In apple orchards, ‘Ca. P. mali’ can be transmitted by two psyllid species. Cacopsylla (Thamnopsylla) picta (Foerster, 1848) (syn. C. costalis) has been reported main vector in Germany (Jarausch et al., 2003, 2011) and northern Italy (Frisinghelli et al., 2000; Carraro et al., 2008), while Cacopsylla (Thamnopsylla) melanoneura (Foerster, 1848) was identified as main vector in Aosta Valley (Tedeschi et al., 2002). C. picta is monophagous on Malus spp. and until now this species have been described only in Europe (Burckhardt, 1994; Ossiannilsson, 1992; Ouvrard, 2014) and Turkey (Klimaszewski and Lodos, 1977, 1979; Drohojowska and Burckhardt, 2014). C. melanoneura has a Palaearctic distribution and is oligophagous on Rosaceae, its principal host plant being a common shrub, hawthorn (Crataegus monogyna L.) (Ouvrard, 2014). In most of studied cases, both psyllid species are present in apple orchards (Jarausch et al., 2003; Delic et al., 2005; Carraro et al., 2008; Mattedi et al., 2008). Two others species living on hawthorn, Cacopsylla peregrina (Foerster, 1848) and Cacopsylla (Thamnopsylla) affinis (Low, 1880), were found able to harbor the phytoplasmas of the AP-group, in particular ‘Ca. P. mali’ (Tedeschi et al., 2009). Their transmission ability was not proven but this result highlights the potential role as vector of these psyllid species. In pear orchards, until recently, two psyllid species were known as vector of ‘Ca. P. pyri’. Cacopsylla (Hepatopsylla) pyricola (Foerster, 1848) has been reported for Great Britain (Davies et al., 1992) and North America (Jensen et al., 1964), while Cacopsylla (Hepatopsylla) pyri (Linne, 1758) was described as the vector in France (Lemoine 1984), Italy (Carraro et al., 1998a) and Spain (Garcia-Chapa et al., 2005). C. pyri is widespread in Europe, in the Caucasus, Georgia, the Middle Asia, including Turkey (Klimaszewski and Lodos, 1979; Burckhardt and Pak. J. Agri. Sci., Vol. 53(2), 383-392; 2016 ISSN (Print) 0552-9034, ISSN (Online) 2076-0906 DOI: 10.21162/PAKJAS/16.3804 http://www.pakjas.com.pk

Symptoms resembling those associated with phytoplasma presence were observed in pomegranate (Punica granatum L.) trees in June 2012 in the Aegean Region of Turkey (Aydin province). The trees exhibiting yellowing, reduced vigour, deformations and reddening of the leaves and die-back symptoms were analysed to verify phytoplasma presence. Total nucleic acids were extracted from fresh leaf midribs and phloem tissue from young branches of ten symptomatic and five asymptomatic plants. Nested polymerase chain reaction assays using universal phytoplasma-specific 16S rRNA and tuf gene primers were performed. Amplicons were digested with Tru1I, Tsp509I and HhaI restriction enzymes, according to the primer pair employed. The phytoplasma profiles were identical to each other and to aster yellows (16SrI-B) strain when digestion was carried out on 16Sr(I)F1/R1 amplicons. However, one of the samples showed mixed profiles indicating that 16SrI-B and 16SrXII-A phytoplasmas were present when M1/M2 amplicons were digested, the reamplification of this sample with tuf cocktail primers allowed to verify the presence of a 16SrXII-A profile. One pomegranate aster yellows strain AY-PG from 16S rRNA gene and the 16SrXII-A amplicon from tuf gene designed strain STOL-PG were directly sequenced and deposited in GenBank under the Accession Numbers KJ818293 and KP161063, respectively. To our knowledge, this is the first report of 16SrI-B and 16SrXII-A phytoplasmas in pomegranate trees.

Sixteen Plum pox virus (PPV) isolates collected in the Ankara region of Turkey were analyzed using available serological and molecular typing assays. Surprisingly, despite the fact that all isolates except one, which was a mix infection, were typed as belonging to the PPV-M strain in four independent molecular assays, nine of them (60%) reacted with both PPV-M specific and PPV-D specific monoclonal antibodies. Partial 5' and 3' genomic sequence analysis on four isolates demonstrated that irrespective of their reactivity towards the PPV-D specific monoclonal antibody, they were all closely related to a recombinant PPV isolate from Turkey, Ab-Tk. All three isolates for which the relevant genomic sequence was obtained showed the same recombination event as Ab-Tk in the HC-Pro gene, around position 1566 of the genome. Complete genomic sequencing of Ab-Tk did not provide evidence for additional recombination events in its evolutionary history. Taken together, these results indicate that a group of closely related PPV isolates characterized by a unique recombination in the HC-Pro gene is prevalent under field conditions in the Ankara region of Turkey. Similar to the situation with the PPV-Rec strain, we propose that these isolates represent a novel strain of PPV, for which the name PPV-T (Turkey) is proposed. Given that PPV-T isolates cannot be identified by currently available typing techniques, it is possible that their presence has been overlooked in other situations. Further efforts should allow a precise description of their prevalence and of their geographical distribution in Turkey and, possibly, in other countries. (C) 2009 Elsevier B.V. All rights reserved.