UC Riverside

The full genome of citrus tatter leaf virus (CTLV) and citrus vein enation virus (CVEV) preserved at Citrus Clonal Protection Program were characterized through next generation sequencing. The sequence analysis showed that CTLV is a strain of Apple stem grooving virus, a type species belongs to Capillovirus, Betaflexiviridae, based on its genome structure and sequence identity. The phylogenetic analysis highlighted that CTLV is originated from Asia where the virus spillover to different plant species and then introduced to USA in a variety introduction. On the other hand, CVEV is a relatively newly characterized Enamovirus belongs to Luteoviridae family. High sequence identities were found among isolates from different geographic locations. Phylogenetic analysis displayed that the isolates from Spain, Korea and Japan were clustered together while Australia and USA isolates were in another. A China isolate stands by itself suggested that it has its own niche in evolution process. Through genome-wise analysis, detection assays of CTLV and CVEV were designed at the most conserve area instead of focus only on a certain gene and validated with different parameters including specificity, sensitivity, transferability and robustness by using multiple virus isolates. The virus-host interactions were also characterized by identifying the viral suppressors of RNA silencing (VSRs) in Nicotiana benthamiana. Both viruses have two VSRs. CTLV uses movement protein as a VSR to interact with double-stranded RNA (dsRNA) and presumably prevent dsRNA to be processed by the Dicer proteins. Meanwhile, CVEV P0 suppresses host antiviral RNA silencing by mimicking host F-box proteins, forming E3 ubiquitin ligase complex with host components and further guiding Argonautes, the core unit of RNA-induced silencing complex, to their degradation. Both CTLV coat protein and CVEV open reading frame 3 are also VSRs, especially in the systemic tissue, and use indirect mechanisms to suppress host antiviral RNA silencing. In summary, the present dissertation provides in-depth information of CTLV and CVEV in different aspects including genomic, phylogenetic, diagnostic and virus-host interaction. These studies lead to the development of detection assays and provide information to disease management strategies which can be applied to the high-value germplasm program and the citrus industry around the world.