High-throughput sequencing (HTS) has become a method that enables the rapid, cost-effective, and high-resolution analysis of plant virus and viroid genomes over the past 10 years. In this study, total RNA extracted from leaf and fruit tissues of four different lemon varieties (Alata, Gülsen, Kütdiken, and Uzun) grown in Turkey was sequenced using the Illumina HiSeq2000 instrument in a paired-end (90 nt) mode. Quality control, alignment, de novo assembly, and contig filtering of the raw reads were performed using Geneious Prime 2023.2.1 software. Subsequently, the relationship between the contigs and viruses/viroids was investigated using the Blastn/x algorithm. The study identified three viruses (Citrus chlorotic dwarf-associated virus - CCDaV, Citrusvirus A - CiVA, and Citrus endogenous pararetrovirus - CitPRV) and five viroids (Hop stunt viroid - HSVd, Citrus dwarfing viroid - CDVd, Citrus bent leaf viroid - CBLVd, Citrus bark cracking viroid - CBCVd, and Citrus exocortis viroid - CEVd) were identified. The presence of all detected viruses and viroids was confirmed by RT-PCR using specific primers. To determine the prevalence of viruses and viroids in the provinces of Mersin and Adana, 162 lemon samples were screened by RT-PCR. According to RT-PCR results, CitPRV was the most prevalent pathogen with a rate of 98.7%, while the prevalence of other pathogens varied depending on geographical region, tissue type, and collection time.
