Discovery of a new konkovirus species in Lachenalia plants reveals possible co-evolution between 5′ and 3′ RNA sequence motifs

This study reports the discovery of a new konkovirus species, named <i>Lachenalia konkovirus</i> 1 (LaKoV1), from <i>Lachenalia</i> plants in an urban botanic garden in Amsterdam. Using a combination of RNA sequencing (RNA-seq), small RNA-seq and advanced bioinformatics, we identified a segmented, negative-strand RNA virus belonging to the family <i>Konkoviridae</i>. Our findings show significant divergence between this novel virus and known members of the family <i>Konkoviridae</i>, such as tulip streak virus (TuSV) and <i>Lactuca</i> big vein-associated <i>Phlebovirus</i> (LBVaPV), supporting its classification as a distinct species. Notably, the sequence differences found in the conserved 5' and 3' ends of these segments suggest potential co-evolution. Despite the observed genomic distances, there is significant conservation in the RNA-dependent RNA polymerase subdomain, underscoring evolutionary relationships among LaKoV1, TuSV and LBVaPV. Our findings expand the known global virome and highlight the importance of exploring plant viromes in diverse ecological settings to better understand virus evolution and diversity.