Detection of RNA viruses in Cape gooseberry (Physalis peruviana L.) by RNAseq using total RNA and dsRNA inputs

Abstract

Physalis peruviana L. is a herbaceous solanaceous plant native to the South American Andes that produces a small yellow fruit of about 1-2 cm in diameter with high demand in the international markets. Currently, Colombia is the largest worldwide exporter of this fruit crop but, due to the emergence of several phytosanitary problems, yields have experienced a steady declined in recent years. Viruses are not included in current disease management programs of P. peruviana but, evidence suggest that viruses might play an important role in decreasing the productivity of this crop. High-throughput sequencing (HTS) has allowed a deeper understanding of the P. peruviana genome and promises to become a routine technique in future integrated disease management programs. Here, we evaluate the influence of the RNA input (total RNA vs dsRNA) on the sensitivity of HTS as a virus detection tool. Our results suggest that, total RNA can produce a high number of viral sequences but fails to detect viruses present at low concentrations and detectable using dsRNA. In particular, infection by potato mop-top virus (PMTV) was detected using both inputs. In addition to PMTV, dsRNA also allowed the assembly of a complete Potato yellow vein virus (PYVV) genome and scaffolds of Potato yellowing virus (PYV), Southern tomato virus (STV) and Potato virus S (PVS). Evidence for the presence of Potato virus X (PVX), Potato virus V (PVV), Potato virus Y (PVY), Bell pepper alphaendornavirus (BPEV) and a putative mycovirus was also obtained from the dsRNA dataset.