The evolutionary success of viruses is supported by highly dynamic genomes, which can undergo punctual changes or integration events that enable the circumvention of host immune defenses, the capture of new genes, and even host switching, among other events. The only constraint that viruses have is the need for a host for their replication, either to take advantage of the host replication machinery, or to hijack the genome to freely replicate as selfish genetic elements. Viruses are the most abundant biological entity on the Earth, likely outnumbering bacteria and eukaryotic cells, with the oceans being the most likely richest reservoir of virus biodiversity. These findings improve our understanding of bivalve viromes, and set the stage for targeted investigations on the specificity and dynamics of identified viruses. Under-representation analysis revealed that the AA motif is under-represented in these bivalve-associated viruses. Single Nucleotide Polymorphism (SNP) analysis revealed 938 A-to-G substitutions occurring on the 26 identified RNA viruses, preferentially impacting the AA di-nucleotide motif. We could not identify virus-derived small RNAs in sncRNA reads obtained from the oyster sample richest in viral reads. We considered short non-coding RNAs (sncRNA) and post-transcriptional modifications occurring specifically on viral RNAs as tools for virus host-assignment. Although 96.4% of the predicted viral proteins refer to new viruses, some sequences belong to viruses associated with bivalve species or other marine invertebrates.
From analyzing RNA-seq data of 58 bivalve species, we have reconstructed 26 nearly complete and over 413 partial RNA virus genomes. This study was designed to explore the viral abundance and diversity in bivalve mollusks using transcriptomic datasets. However, the current knowledge on mollusk viruses is mainly centered on few pathogenic viruses, whereas a general view of bivalve-associated viromes is lacking. Bivalve mollusks thrive in environments rich in microorganisms, such as estuarine and coastal waters, and they tend to accumulate various particles, including viruses.
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