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 sp...
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Zusammenfassung: | 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. |
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DOI: | 10.5061/dryad.87vt6hm |