Hop plants serve as a vital agricultural crop primarily used in beer production. However, its susceptibility to various pathogens, including viroids, poses significant challenges. Viroids are small, circular, single-stranded RNAs capable of infecting diverse plant species, which develop disease symptoms that can translate into substantial economic losses. To mitigate the detrimental effects of viroids on hop cultivation, growers employ a range of preventive measures. While considerable research efforts have focused on elucidating the pathology of viroids, the underlying molecular mechanisms remain largely elusive. In this PhD thesis, we aimed to investigate two key aspects: viroid replication and alterations in DNA methylation patterns in infected hop plants. Notably, we employed the Nanopore sequencing technology, which enabled direct RNA sequencing, making it a suitable tool for analyzing viroid replication intermediates. In addition, we observed that viroids can affect DNA methylation in hop plants. Our investigation of DNA methylation patterns yielded significant outcomes, offering promising directions for future research on plant immunity, and viroid pathogenesis. Our research has unveiled differential DNA methylation patterns associated with viroid presence, implicating their role in plant hypersensitive responses, defensive mechanisms, hormonal signaling, and ribosomal processes. Specifically, CBCVd displayed a strong likelihood of impacting RNA-dependent DNA methylation pathway, corroborating findings from previous studies on viroids and methylation.
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