This is a Preprint and has not been peer reviewed. This is version 3 of this Preprint.
RNA Virus Discovery from Daphnia meta-transcriptomes: A novel Tombunoda-like virus based on RNA dependent RNA polymerase identification
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Abstract
The discovery of RNA viruses from meta-transcriptomes has led to an explosion in viral diversity and identified many novel host-virus associations. To date, no studies have examined the RNA virome of the model zooplankter Daphnia. From which only four viruses are known, with only one being well understood. Here, I assemble and annotate RNA-dependent RNA polymerase (RdRp) containing contigs from Daphnia meta-transcriptomes. Homology searches and phylogenetic inference show that the RdRp genes are related to another crustacean RNA virus identified as order Tolivirales, family Tombusviridae. A second open reading frame encodes for a protein associated with Nodaviruses, also discovered in crustaceans. Taken together, this suggests that Daphnia pulex virus 1 is part of a growing set of tombunodaviruses, which are commonly found in invertebrate viromes.
DOI
https://doi.org/10.32942/X2DW8B
Subjects
Bioinformatics, Life Sciences, Virology
Keywords
RNA Virus, Daphnia, metatranscriptomes, Tombusviridae, RNA-dependent RNA Polymerase, RdRp
Dates
Published: 2025-11-21 21:03
Last Updated: 2025-11-21 21:03
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License
CC-BY Attribution-NonCommercial 4.0 International
Additional Metadata
Conflict of interest statement:
None
Data and Code Availability Statement:
I analyzed the RNA sequencing libraries (SRX14976444-SRX14976451) accessioned under BioProject (PRJNA830892). Viral genome sequences have been submitted to NCBI Genbank under submission ID 3021179. Once stable identifiers are provided, I will update this section. Scripts and data are provided on GitHub at: https://github.com/mwersebe/DaphniaRNAvirus.
Language:
English
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