A needle in a haystack: tracing bivalve-associated viruses in high-throughput transcriptomic data
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-as...
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ftunivpadovairis:oai:www.research.unipd.it:11577/3290108 2024-02-27T08:39:54+00:00 A needle in a haystack: tracing bivalve-associated viruses in high-throughput transcriptomic data Umberto Rosani Maxwell Shapiro Paola Venier ALLAM, BASSEM Rosani, Umberto Maxwell, Shapiro Venier, Paola Allam, Bassem 2019 ELETTRONICO http://hdl.handle.net/11577/3290108 https://doi.org/10.3390/v11030205 https://www.mdpi.com/1999-4915/11/3/205 eng eng MDPI (Switzerland) info:eu-repo/semantics/altIdentifier/pmid/30832203 info:eu-repo/semantics/altIdentifier/wos/WOS:000464401900002 volume:11 issue:3 firstpage:1 lastpage:21 numberofpages:21 journal:VIRUSES info:eu-repo/grantAgreement/EC/H2020/678589 http://hdl.handle.net/11577/3290108 doi:10.3390/v11030205 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85062399529 https://www.mdpi.com/1999-4915/11/3/205 OsHV-1 Crassostrea gigas omics info:eu-repo/semantics/article 2019 ftunivpadovairis https://doi.org/10.3390/v11030205 2024-01-31T17:57:04Z 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 viral abundance and diversity in bivalve mollusks using transcriptomic datasets. 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 to 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. 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. Article in Journal/Newspaper Crassostrea gigas Padua Research Archive (IRIS - Università degli Studi di Padova) Haystack ENVELOPE(-19.392,-19.392,75.726,75.726) Viruses 11 3 205 |
institution |
Open Polar |
collection |
Padua Research Archive (IRIS - Università degli Studi di Padova) |
op_collection_id |
ftunivpadovairis |
language |
English |
topic |
OsHV-1 Crassostrea gigas omics |
spellingShingle |
OsHV-1 Crassostrea gigas omics Umberto Rosani Maxwell Shapiro Paola Venier ALLAM, BASSEM A needle in a haystack: tracing bivalve-associated viruses in high-throughput transcriptomic data |
topic_facet |
OsHV-1 Crassostrea gigas omics |
description |
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 viral abundance and diversity in bivalve mollusks using transcriptomic datasets. 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 to 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. 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. |
author2 |
Rosani, Umberto Maxwell, Shapiro Venier, Paola Allam, Bassem |
format |
Article in Journal/Newspaper |
author |
Umberto Rosani Maxwell Shapiro Paola Venier ALLAM, BASSEM |
author_facet |
Umberto Rosani Maxwell Shapiro Paola Venier ALLAM, BASSEM |
author_sort |
Umberto Rosani |
title |
A needle in a haystack: tracing bivalve-associated viruses in high-throughput transcriptomic data |
title_short |
A needle in a haystack: tracing bivalve-associated viruses in high-throughput transcriptomic data |
title_full |
A needle in a haystack: tracing bivalve-associated viruses in high-throughput transcriptomic data |
title_fullStr |
A needle in a haystack: tracing bivalve-associated viruses in high-throughput transcriptomic data |
title_full_unstemmed |
A needle in a haystack: tracing bivalve-associated viruses in high-throughput transcriptomic data |
title_sort |
needle in a haystack: tracing bivalve-associated viruses in high-throughput transcriptomic data |
publisher |
MDPI (Switzerland) |
publishDate |
2019 |
url |
http://hdl.handle.net/11577/3290108 https://doi.org/10.3390/v11030205 https://www.mdpi.com/1999-4915/11/3/205 |
long_lat |
ENVELOPE(-19.392,-19.392,75.726,75.726) |
geographic |
Haystack |
geographic_facet |
Haystack |
genre |
Crassostrea gigas |
genre_facet |
Crassostrea gigas |
op_relation |
info:eu-repo/semantics/altIdentifier/pmid/30832203 info:eu-repo/semantics/altIdentifier/wos/WOS:000464401900002 volume:11 issue:3 firstpage:1 lastpage:21 numberofpages:21 journal:VIRUSES info:eu-repo/grantAgreement/EC/H2020/678589 http://hdl.handle.net/11577/3290108 doi:10.3390/v11030205 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85062399529 https://www.mdpi.com/1999-4915/11/3/205 |
op_doi |
https://doi.org/10.3390/v11030205 |
container_title |
Viruses |
container_volume |
11 |
container_issue |
3 |
container_start_page |
205 |
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1792046968276516864 |