Computational evidence that the Ugandan Passiflora virus likely evolved from the Bean common mosaic necrosis virus primarily through recombination

Abstract

The Ugandan Passiflora virus (UPV) is an economically devastating virus affecting passion fruit (Passiflora edulis Sims), and a close relative of the Bean common mosaic necrosis virus (BCMNV). Using publicly available sequences, we studied the evolutionary relationship between the two viral species to understand UPV’s viral origin and evolutionary pressures associated with its emergence. Seven UPV virus sequences obtained from our previous study were used to identify 59 complete genome sequences with at least 70% similarity with our query and sequence coverage through batch-BLASTn on the NCBI website. Eleven recombination breakpoints (RBP) were revealed evidencing several recombination events within the viral sequences, including UPV as a recombinant of BCMNV (major parent) and a strain of the Watermelon mosaic virus (minor parent). Intensified selection and episodic selection, as well as the existence of positively selected sites and several selective sweep events were detected around the RBPs, indicating that the high recombination rates could have maintained genetic diversity within the viruses in the presence of positive selection. Besides, some of the viruses, including UPV, harbored unique conserved protein domains, suggesting that their emergence could have been through function gains, allowing colonization of new environments and hosts. This is the first computational report that elucidates the viral evolutionary origin of UPV and provides hypothetical evidence that it likely evolved from BCMNV, mainly through recombination. The results we present, however, need to be further investigated with the discovery and inclusion of more UPV isolate sequences to confirm its evolutionary relationship with other potyviruses.