Detection of RNA viruses in Solanum quitoense by high-throughput sequencing (HTS) using total and double stranded RNA inputs

Solanum quitoense Lam. is a solanaceous fruit shrub native to South America that produces a tomato-sized fruit popular in the preparation of fresh juice, fermented beverages, nectars, ice cream and fruit concentrates. Unfortunately, this crop is highly susceptible to insects, nematodes, fungi, oomycetes, bacteria, and a wide range of viral diseases. With the arrival of High-Throughput Sequencing (HTS) methods, our understanding of the viruses affecting this crop has increased at a steady pace. In this work, we investigate the virome of S. quitoense in Antioquia (Colombia) using the Illumina HTS platform and analyze the effect of using ribosomal RNA depleted total RNA and dsRNA templates. Our results suggest that total RNA outputs a larger amount of viral sequences but fails to detect viruses present at lower loads. Both templates allowed detection and assembly of Potato leafroll virus (PLRV), Potato yellow vein virus (PYVV), and Potato mop-top virus (PMTV); however, the dsRNA input was more sensitive for detection of Potato virus Y (PVY), Potato virus X (PVX), Potato virus S (PVS), and Bell pepper alphaendornavirus (BPEV). These results suggest that the combination of different RNA inputs in HTS studies of plant viromes can give a more complete picture of the real virus diversity. •Different RNA inputs in HTS studies of plant viromes improve virus detection.•Total RNA gives higher coverage for viruses present at high levels.•dsRNA allows detection of viruses present a low titers and persistent viruses.•Using HTS, seven RNA viruses were found in S. quitoense in Colombia.