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.