Investigation of viral agents in walnut (Juglandis spp) trees byhigh throughput sequencing

The virus-like symptoms observed in walnuts may be linked to known and/or unknown viral agents. The current research on walnut-related diseases has not utilized high-throughput sequencing technologies to investigate virus-like symptoms. To explore this further, symptomatic walnut trees were surveyed in walnut orchards and home gardens in Niğde province in October 2023. Double strand RNA (dsRNA) extraction was performed, dsRNAs were converted into cDNA and PCR was performed with random primers. The PCR products of samples B13, B22, B23 and B21+5 were sequenced using the Illumina Novaseq 6000 sequencing platform. The data were subjected to bioinformatics analysis using Geneious Prime and CLC Workbench. In the comparison, more contigs were constructed in CLC Workbench and precise results were obtained with Blastx. As a result of the map to reference analyses, the cherry leaf roll virus (CLRV) (Nepovirus avii) is matched with the sample B21+5 sample reads, and cucumber mosaic virus (CMV) (Cucumovirus CMV) is matched with the sample B23 reads. The matching viruses were tested with the virus specific primers in walnut total RNAs by PCR. Only CLRV was detected in B21 sample. It is recommended that in particular, nucleic acid extraction methods need to be improved for the detection of viral agents with high throughput sequencing.