Wageningen University Wageningen, Gelderland, Netherlands
Next Generation Sequencing has further expanded our knowledge about the insect virome in pest species damaging agricultural production and human health. However, the bioinformatic pipelines that are used to analyze this data, greatly influence the reliability of virus detection and discovery of unknown viruses in insects. In our research, we selected different pipelines to unravel the virome of the beet armyworm (Spodoptera exigua) with WGS and RNAseq data. The WGS data was retrieved from a single female pupa and the RNAseq data from a selection of different life stages.Although some pipelines had some constraints, two pipelines could be implemented and detected an interesting set of viruses. Both Spodoptera exigua iflavirus 1 (SeIV-1) and Spodoptera exigua iflavirus 2 (SeIV-2) were noticed and their presence was confirmed in the S. exigua population by qPCR. The detection of Spodoptera exigua multicapsid nucleopolyhedrovirus (SeMNPV) was not straight-forward and dependent on the bioinformatic pipeline used. When the reads were first mapped on the insect host genome, one pipeline could not retrieve viral reads of SeMNPV. When this step was skipped, a number of viral SeMNPV reads were detected. Furthermore, other viruses originating from other lepidopteran species and wasp parasitoids were also retrieved and requier further research. In conclusion, a reliable and user-friendly bioinformatic pipeline is essential to unravel the diverse virome of the beet armyworm.
