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    Identification and Characterization of a Novel Robigovirus Species from Sweet Cherry in Turkey
    (Mdpi, 2019) Caglayan, Kadriye; Roumi, Vahid; Gazel, Mona; Elci, Eminur; Acioglu, Mehtap; Plesko, Irena Mavric; Reynard, Jean-Sebastien
    High throughput sequencing of total RNA isolated from symptomatic leaves of a sweet cherry tree (Prunus avium cv. 0900 Ziraat) from Turkey identified a new member of the genus Robigovirus designated cherry virus Turkey (CVTR). The presence of the virus was confirmed by electron microscopy and overlapping RT-PCR for sequencing its whole-genome. The virus has a ssRNA genome of 8464 nucleotides which encodes five open reading frames (ORFs) and comprises two non-coding regions, 5 ' UTR and 3 ' UTR of 97 and 296 nt, respectively. Compared to the five most closely related robigoviruses, RdRp, TGB1, TGB2, TGB3 and CP share amino acid identities ranging from 43-53%, 44-60%, 39-43%, 38-44% and 45-50%, respectively. Unlike the four cherry robigoviruses, CVTR lacks ORFs 2a and 5a. Its genome organization is therefore more similar to African oil palm ringspot virus (AOPRV). Using specific primers, the presence of CVTR was confirmed in 15 sweet cherries and two sour cherries out of 156 tested samples collected from three regions in Turkey. Among them, five samples were showing slight chlorotic symptoms on the leaves. It seems that CVTR infects cherry trees with or without eliciting obvious symptoms, but these data should be confirmed by bioassays in woody and possible herbaceous hosts in future studies.
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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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    Sweet cherry, a new host of raspberry bushy dwarf virus
    (Springer, 2023) Caglayan, Kadriye; Gazel, Mona; Roumi, Vahid; Lamovsek, Janja; Beber, Aljosa; Plesko, Irena Mavric
    Raspberry bushy dwarf virus (RBDV) is one of the most important pathogens of raspberries worldwide. In this study, we detected RBDV from 8 out of 50 cherry samples collected from Bursa, Turkey by DAS-ELISA and/or RT-PCR. We also determined the nearly full genome sequences of RBDV RNA2 from two cherry (Prunus avium) trees. The genomes were identical and shared 87.2 to 97.2% similarity to the RBDV RNA2 sequences from Rubus spp. and grapevine isolates available in GenBank, respectively. Phylogenetic analyses of RNA2 and MP gene sequences grouped cherry sequences in a clade more closely related to the grapevine clade (75 and 86% bootstrap value) while the topology based on the CP gene resulted in three separate clusters according host plant identity. Although host-dependent differentiations were confirmed in this study, no obvious geographical differentiation was observed from phylogenetic analysis, and no recombination events were detected. RBDV is found in raspberry and blackberry in many countries, including Turkey, however, here we report the first natural RBDV infection of cherry worldwide.