Data from: Re-assessing the diversity of negative strand RNA viruses in insects

The spectrum of viruses in insects is important for subjects as diverse as
public health, veterinary medicine, food production, and biodiversity
conservation. The traditional interest in vector-borne diseases of humans
and livestock has drawn the attention of virus studies to hematophagous
insect species. However, these represent only a tiny fraction of the broad
diversity of Hexapoda, the most speciose group of animals. Here, we
systematically probed the diversity of negative strand RNA viruses in the
largest and most representative collection of insect transcriptomes from
samples representing all 34 extant orders of Hexapoda and 3 orders of
Entognatha, as well as outgroups, altogether representing 1243 species.
Based on profile hidden Markov models we detected 488 viral RNA-directed
RNA polymerase (RdRp) sequences with similarity to negative strand RNA
viruses. These were identified in members of 324
arthropod species. Selection for length, quality, and uniqueness
left 234 sequences for analyses, showing similarity to genomes of viruses
classified in Bunyavirales (n=86), Articulavirales (n=54), and several
orders within Haploviricotina (n=94). Coding-complete genomes or
nearly-complete subgenomic assemblies were obtained in 61 cases. Based on
phylogenetic topology and the availability of coding complete genomes we
estimate that at least 20 novel viral genera in seven families need to be
defined, only two of them monospecific. Seven additional viral clades
emerge when adding sequences from the present study to formerly
monospecific lineages, potentially requiring up to seven additional
genera. One long sequence may indicate a novel family. For segmented
viruses, cophylogenies between genome segments were generally improved by
the inclusion of viruses from the present study, suggesting that in silico
misassembly of segmented genomes is rare or absent. Contrary to previous
assessments, significant virus-host codivergence was identified in major
phylogenetic lineages based on two different approaches of codivergence
analysis in a hypotheses testing framework. In spite of these additions to
the known spectrum of viruses in insects, we caution that basing taxonomic
decisions on genome information alone is challenging due to technical
uncertainties, such as the inability to prove integrity of complete genome
assemblies of segmented viruses.