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A Needle in A Haystack: Tracing Bivalve-Associated Viruses in High-Throughput Transcriptomic Data.

Umberto Rosani1, Maxwell Shapiro2, Paola Venier3

  • 1Department of Biology, University of Padua, 35121 Padua, Italy. umberto.rosani@unipd.it.

Viruses
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Summary

This study reveals the vast diversity of RNA viruses in bivalve mollusks, reconstructing numerous viral genomes. Findings highlight novel viruses and provide insights into virus-host interactions through RNA modifications.

Keywords:
ADARRNA virusesRNA-seqRNAibivalvesncRNAvirome

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Area of Science:

  • Marine biology
  • Virology
  • Genomics

Background:

  • Bivalve mollusks inhabit microbial-rich waters and accumulate diverse particles, including viruses.
  • Existing research on mollusk viruses primarily focuses on a few pathogens, leaving bivalve-associated viromes largely unexplored.

Purpose of the Study:

  • To investigate the abundance and diversity of viruses within bivalve mollusks.
  • To reconstruct viral genomes from transcriptomic data and explore virus-host interactions.

Main Methods:

  • Analysis of RNA-sequencing (RNA-seq) data from 58 bivalve species.
  • Reconstruction of nearly complete and partial RNA virus genomes.
  • Investigation of short non-coding RNAs (sncRNA) and Single Nucleotide Polymorphism (SNP) analysis for virus host-assignment.

Main Results:

  • Reconstruction of 26 nearly complete and over 413 partial RNA virus genomes.
  • Identification of novel viruses, with 96.4% of predicted viral proteins belonging to new viral sequences.
  • Discovery of 938 A-to-G substitutions on viral RNA, preferentially impacting the AA di-nucleotide motif, which was found to be under-represented.

Conclusions:

  • This study significantly expands the understanding of bivalve viromes, revealing extensive viral diversity.
  • The findings establish a foundation for future research into the specificity and dynamics of newly identified bivalve-associated viruses.