The metagenomic analysis of viral diversity in Colorado potato beetle public NGS data

The Colorado potato beetle (CPB) is one of the most serious insect pests with high ecological plasticity and ability to rapidly develop resistance to insecticides. The use of biological insecticides based on viruses is a promising approach to control insect pests, but the information on viruses, which infect leaf feeding beetles, is scarce. We performed the metagenomic analysis of 297 CPB genomic and transcriptomic samples from public NBCI SRA database. The reads that were not aligned to the reference genome were assembled with metaSPAdes and 13314 selected contigs were analyzed with BLAST tools. The contigs and non-aligned reads were also analyzed with Kraken2 software. 3137 virus-positive contigs were attributed to different viruses belonging to 6 types, 17 orders and 32 families, matching over 97 viral species. The annotated sequences can be divided into several groups: homologous to genetic sequences of insect viruses (Adintoviridae, Ascoviridae, Baculoviridae, Dicistroviridae, Chuviridae, Hytrosaviridae, Iflaviridae, Iridoviridae, Nimaviridae, Nudiviridae, Phasmaviridae, Picornaviridae, Polydnaviriformidae, Xinmoviridae etc.), plant viruses (Betaflexiviridae, Bromoviridae, Kitaviridae, Potyviridae), and endogenous retroviral elements (Retroviridae, Metaviridae). Also, the full-length genomes and near-full length genome sequences of several viruses were assembled. We have also found the sequences belonging to Bracoviriform viruses and for the first time experimentally validated the presence of bracoviral genetic fragments in CPB genome. Our work is the first attempt to discover the viral genetic material in CPB samples and we hope that further studies will help to identify new viruses to extend the arsenal of biopesticides against CPB. The analytical pipeline and additional materials are available at https://github.com/starchevskaya-maria17/uncoVir