VIRUS DETECTION
For virus identification, RNA was extracted from the samples using phenol-chloroform-isoamylalcohol extraction (Chang et al. 1993). The small RNA (sRNA) was sequenced using Illumina Hiseq (2009). After quality check and adaptor removal, the obtained reads were analysed using the VirusDetect pipeline (Zheng et al. 2017) to obtain Operational Taxonomical Units (OTUs). The OTUs were classified according to their host range and plant associated OTUs were selected for our analysis (Hulo et al. 2011). The OTUs were named at the virus family level and are henceforward referred to as “viruses”. We compiled a presence-absence matrix describing the virus community in each host individual and host population.