REPOSITORY > RESULTS

Abstract

Viruses, satellite viruses, viroids, virusoids, and satellite nucleic acids (herewith, referred to collectively or in part as ‘viruses’) comprise the virosphere and are perhaps the most diverse and abundant, yet still under-sampled, microbes on Earth. They are primarily regarded as pathogens or parasites of their eukaryotic or prokaryotic hosts. In agroecosystems, viruses are particularly well known for their devastating effects on crops, and thus research on their diversity, biology, ecology, epidemiology, and evolution focuses primarily on pathogenic viruses. In recent years, the availability of cost effective high-throughput sequencing technologies (HTS), improved experimental approaches and computational tools has gradually shifted virology towards non-targeted studies on virus sequences in metagenomic data (i.e., viromics). In this doctoral research, we focused on tomato (Solanum lycopersicum L.) agroecosystems, including surrounding weeds, as a model to demonstrate the use of HTS for uncovering portions of the vast virome diversity, and to describe aspects of virus biology, epidemiology, and ecology. First, we gained a strong foundation by conducting a meta-analysis on tomato viruses worldwide by searching through the literature and databases. We found and curated 312 tomato-associated viruses, and showed that this number was underestimated in previous publications, and is still growing based on very recent reports. We showed that HTS accelerated the discovery and post-discovery characterization of tomato viruses. We synthesized pertinent information on economically important tomato viruses, and presented insights that HTS can bring forth. We then used this informational foundation to efficiently investigate the viromes of tomato and weeds in an agroecosystem setting. We detected and characterized the genomes of 125 known and novel viruses in 293 tomato samples and 143 weed plant samples (representing 59 different plant species). We did phylogenetic and diversity analyses to classify the viruses in known taxa, and found that the vast majority of novel viruses were detected in weeds. Ten viruses with probable wide host range were detected in both tomato and weeds. We demonstrated an association between plant rhabdoviruses and their taxonomically-related hosts, which provided hints to possible co-evolutionary relationships. We further characterized and showed infectivity of a novel Tobamovirus species in host plants from family Solanaceae. We determined the diversity of novel and previously undetected tomato viruses wherein we observed high genome-wide diversity for populations of two novel tomato viruses due to presence of two divergent lineages, while populations of other known tomato viruses showed variable diversities. Lastly, we demonstrated that HTS can be used to reveal previously undetected viruses circulating in crops, such as the case of Ranunculus white mottle ophiovirus (RWMV). We showed variable diversity of RWMV isolates from several localities in Slovenia collected since 2017, which is also the first time it was detected in tomato and pepper crops. Overall, our studies reported for the first time four known viruses in Slovenia and discovered ten novel viruses associated with tomato. We also report known or novel members of Albetovirus, Vitivirus, Picornaviridae, and Lispiviridae for the first time in tomato. Our HTS-based viromic studies and in-depth analyses, revealed vast undiscovered portions of the virosphere of tomato agroecosystems, predominantly present in weed plants, which has important implications in weed management decisions. Finally, it is pertinent to further characterize these viruses to aid in uncovering possible emergences and their influence on tomato health.