Endogenous viral elements: role in virus evolution and functions in plants – EVENTS

EVENTS aims to investigate both the positive and negative impacts of endogenous viral elements (EVEs) on plant metabolism. EVEs are viral sequences that are integrated in the genomes of their hosts. In plants, most characterized EVEs originate from viruses in the families Caulimoviridae and Geminiviridae, which have DNA genomes, following passive horizontal gene transfer (HGT).
Members of the project team recently showed that DNA from ancestral viruses in the family Caulimoviridae were captured within the genomes of a wide range of angiosperms, including economically important crops (rice, sorghum, citrus, grape, apple, pear, strawberry, eucalyptus, poplar, tomato, potato, cucumber, cotton). A new genus, tentatively named Florendovirus, was proposed to accommodate these viruses. Several endogenous florendoviruses could potentially be replication competent and, therefore, infective, although this hypothesis has not yet been tested. Different members of the project team have also discovered new geminivirus-like elements (EGVs) in the genome of yams and demonstrated that these EGVs represent transcriptionally active endogenous geminiviral sequences that may be functionally expressed in their respective host plants. Building on this pioneering work, EVENTS focuses on the role of caulimovirid and geminivirid EVEs in virus evolution and their functions in plants.
EVENTS will create automated computational tools to search for these EVEs in plant genomes and will implement these tools in a large-scale plant EVE discovery program, providing access to viral sequences that were integrated millions to tens of millions of years ago. These EVEs will be used to reconstruct accurate time-scaled evolutionary histories of entire viral lineages across unprecedented time-spans, helping to refine predictive models of viral emergence.
EVENTS will investigate the contributions of caulimovirid and geminivirid EVEs to viral diversity. A range of antigenic and molecular detection tools will be created and used to screen germplasm collections and collected samples for viral particles and infective genomes of as yet undescribed geminiviruses and florendoviruses with EVE counterparts. Graft experiments will be carried out to confirm infective status. The project will also explore synergistic interactions between endogenous viruses and exogenous viruses encoding suppressors of silencing, in order to investigate the role of silencing in the regulation of EVE gene expression in plants.
The contribution of caulimovirid and geminivirid EVEs to genetic and epigenetic regulation of plant gene expression will be investigated in silico through the systematic search for fused (viral/plant) open reading frames, alternative promoters, intron splicing sites and premature terminations of transcription. Immunological and molecular approaches will be designed and used to search for and characterize EVE-derived proteins and/or RNAs expressed in host plants. Experimental approaches using recombinant infective viral clones expressing EVE sequences will be designed and implemented to evaluate potential antiviral resistance in plants conferred by EVEs acting as natural viral transgenes.
By developing novel integrated and multidisciplinary approaches to illuminate the diversity of EVEs in plant genomes, their roles in viral evolution, their functions and potentially beneficial roles within their host plants, EVENTS stands at the forefront of an emerging research field. We anticipate that the project will contribute significantly to societal issues such as the control of viral diseases and the advancement of plant biotechnology. EVENTS brings together leading groups with complementary expertise in virology, bioinformatics and molecular systematics working in France, South Africa and Australia. Partners have a proven record of collaboration and joint publications that demonstrate their ability to meet project goals and deliver results in ground-breaking research domains.