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

Abstract

Bivalve mollusks thrive in environments rich in microorganisms, such as estuarine and coastal waters, and they tend to accumulate various particles, including viruses. However, the current knowledge on mollusk viruses is mainly centered on few pathogenic viruses, whereas a general view of bivalve-associated viromes is lacking. This study was designed to explore the viral abundance and diversity in bivalve mollusks using transcriptomic datasets. From analyzing RNA-seq data of 58 bivalve species, we have reconstructed 26 nearly complete and over 413 partial RNA virus genomes. 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. We considered short non-coding RNAs (sncRNA) and post-transcriptional modifications occurring specifically on viral RNAs as tools for virus host-assignment. We could not identify virus-derived small RNAs in sncRNA reads obtained from the oyster sample richest in viral reads. 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. Under-representation analysis revealed that the AA motif is under-represented in these bivalve-associated viruses. These findings improve our understanding of bivalve viromes, and set the stage for targeted investigations on the specificity and dynamics of identified viruses.

Parallel analysis of miRNAs and mRNAs suggests distinct regulatory networks in Crassostrea gigas infected by Ostreid herpesvirus 1

“…Also, the size profile of OsHV-1 sncRNA reads suggested that RNAi is not active against OsHV-1 in oyster, since a size-bias would be expected in case of RNAi-mediated RNA degradation [64]. RNAi was reported during WSSV infection in shrimp [35] as well as in other arthropod species [65], but this study rather supports previous findings indicative of a marginal role for RNA interference in the antiviral response of bivalve species [66,67].…”

A-to-I editing of Malacoherpesviridae RNAs supports the antiviral role of ADAR1 in mollusks

“…As a result, all cellular organisms have developed antiviral defense mechanisms [2] and the arms race between viruses and their hosts has contributed to shape both their genomes over millions of years [3]. Virus abundances are especially noticeable in marine coastal ecosystems [4] and viruses of different origin are often found in filter-feeding invertebrates such as bivalve mollusks [5–9]. Among the variety of potential pathogens, dsDNA viruses of the Malacoherpesviridae family represent a major issue for a number of bivalve and gastropod species, as they have greatly challenged the abalone and oyster aquaculture in the last decades [10–13].…”

Viromes in Marine Ecosystems Reveal Remarkable Invertebrate RNA Virus Diversity

“…However, to date, aquatic viromic studies tended to study phages but already showed enormous genetic diversity and ecological distributions (Roux, et al 2016; Vlok, et al 2019; Guajardo-Leiva, et al 2020; Gulino, et al 2020; Moon, et al 2020; Zhang, et al 2020). Although some studies included aquatic invertebrates (Magbanua, et al 2000; Thakur, et al 2002; Shi, et al 2016; Rosani, et al 2019), there is a lack of systematic study of these animals in a whole.…”