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Open AccessArticle

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

1
Department of Biology, University of Padua, 35121 Padua, Italy
2
Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11794-5000, USA
3
School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA
*
Author to whom correspondence should be addressed.
Viruses 2019, 11(3), 205; https://doi.org/10.3390/v11030205
Received: 1 February 2019 / Revised: 25 February 2019 / Accepted: 25 February 2019 / Published: 1 March 2019
(This article belongs to the Special Issue Virus Bioinformatics)
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. View Full-Text
Keywords: bivalve; virome; RNA-seq; RNA viruses; sncRNA; ADAR; RNAi bivalve; virome; RNA-seq; RNA viruses; sncRNA; ADAR; RNAi
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Rosani, U.; Shapiro, M.; Venier, P.; Allam, B. A Needle in A Haystack: Tracing Bivalve-Associated Viruses in High-Throughput Transcriptomic Data. Viruses 2019, 11, 205.

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