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چکیده
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Cherry trees are affected by many viral agents, but the detection of these viruses using traditional detection methods remains limited. High-throughput sequencing (HTS) technology has become a powerful tool for identifying known and unknown viruses. In this study, 26 cherry (Prunus avium L.) samples collected from Osmaniye province were mixed, and virions were purified using the VANA (Virion-Associated Nucleic Acid) method. cDNA libraries were prepared from viral RNAs and HTS analysis was performed on the Illumina NovaSeq (2×150 bp) platform.A total of 386,742 raw reads were obtained, and after quality control, 154,008 high-quality reads were de novo assembled into contigs ranging from 101 to 7300 nt in length. As a result of BLASTn/x analyses, sequences belonging to cherry green ring mottle virus (Robigovirus viridiavii, CGRMV) (99% coverage and 97.27% nucleotide identity), Cherry necrotic rusty mottle virus (Robigovirus necroavii, CNRMV) (98% coverage and 98.39% nucleotide identity), cherry virus Trakiya (CVT) (86% coverage, 94.70% nucleotide identity), and Cherry latent virus 1 (CLV-1) (99% coverage, 81.08% nucleotide identity). Another contig that provides 100% coverage with CVT but only shows 60.7% nucleotide identity indicates the presence of a potential new isolate. Additionally, contigs belonging to Cherry virus A (Capillovirus alphavii, CVA) (75.1% nucleotide identity) and prune dwarf virus (Ilarvirus PDV, PDV) (62.1% coverage and 67.2% nucleotide identity) indicate that both viruses may be present in the samples at low levels.The presence of all viruses detected by HTS analysis was also confirmed by RT-PCR/Sanger sequencing analysis using species specific primers. The findings revealed the presence of known and genetically diverse new virus species in Turkish cherry samples. VANA-based HTS analysis, by specific sequencing of viral nucleic acids and enabling the detection of multiple viruses, can be used for cost-effective, precise, and rapid virus diagnosis.
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