Screening of Known and New Emerging Viruses in Rubus Species by RT-PCR and Whole Genome Analysis of Idaeovirus rubi (Raspberry Bushy Dwarf Virus) by High-Throughput Sequencing in Turkiye

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Ördek K., Roumı V., Çağlayan K.

Uluslararası Katılımlı IX. Bitki Koruma Kongresine, Ankara, Turkey, 3 - 05 September 2025, pp.61, (Summary Text)

  • Publication Type: Conference Paper / Summary Text
  • City: Ankara
  • Country: Turkey
  • Page Numbers: pp.61
  • Open Archive Collection: AVESIS Open Access Collection
  • Hatay Mustafa Kemal University Affiliated: Yes

Abstract

Although more than 40 viruses infect Rubus spp., the most common one in Turkiye is Idaeovirus rubi (raspberry bushy dwarf virus) (RBDV). Besides raspberries, RBDV can infect blackberries and some hybrid berry fruits, causing stunting, yellowing of leaves, crumbly fruits, and sometimes latent infections. The first aim of this study was screening of 303 randomly selected Rubus plants for the presence of new emerging viruses such as strawberry necrotic shock virus (SNSV: Ilarvirus), blackberry chlorotic ringspot virus) (BCRV: Ilarvirus), black raspberry necrosis virus (Sadwavirus rubi: BRNV), blackberry yellow vein associated virus (Crinivirus rubi: BYVaV), raspberry leaf mottle virus (Closterovirus macularubi: RLMV) and already known viruses such as tomato ringspot virus (Nepovirus lycopersici: ToRSV) and tobacco ringspot virus (Nepovirus  nicotianae :TRSV) by RT-PCR analysis. Second aim is  whole genome analysis of Turkish RBDVisolates using high-throughput sequencing (HTS) and Sanger sequencing techniques.The survey results showed  26.7 percent of the plants were infected by RBDV, while none of the other viruses were detected. Nine RBDV-positive blackberry samples from Hatay province were pooled and subjected to VANA-HTS (virion-associated nucleic acid HTS) method. Following HTS analysis, the complete genomes of Turkish RBDV isolates were determined. Several specific primer pairs were designed according to HTS results and the amlpicons were directly sequenced. Consequently , the complete genomes of 7 blackberry and 13 raspberry RBDV isolates were obtained. In the phylogenetic trees drawn for the RNA1, RNA2 and RNA3 nucleotide sequences of Turkish RBDV isolates, all raspberry isolates (including global isolates) clustered together while blackberries isolates placed in a separate group. Among blackberry isolates, Hatay isolates were placed in a separate clade in both phylogenetic trees together with more variant RBDV isolates obtained from grapevine and cherry, which have recently been reported as natural hosts of RBDV. The findings shows that the genetic diversity of RBDV is much broader than previously documented and there is no host-based grouping.