Activity of novel endogenous pararetroviruses and their associations with S. lycopersicum ripening

Abstract

Endogenous pararetroviruses (EPRVs), integrated viral elements from the Caulimoviridae family, are increasingly recognized as dynamic regulators of plant development. This study investigates the activity and functional impact of EPRVs on the ripening process of Solanum lycopersicum (tomato). Using genomic and transcriptomic datasets, we identified 16,012 EPRV sequences in the tomato genome via Hidden Markov Models, with 134 sequences showing differential expression during ripening stages. Co-expression analysis revealed 28 EPRVs that are linked with 259 tomato genes, highlighting their possible regulatory roles. These tomato genes participate in pathways associated with ethylene signaling, pigment biosynthesis, and stress responses. The role of EPRV-derived small RNAs (sRNAs) was also explored, identifying these sRNAs as potential mediators of ripening-related gene expression. These findings reveal the regulatory significance of EPRVs in tomato ripening and establish a foundation for leveraging these elements in crop improvement strategies.