Oyster RNA-seq Data Support the Development of Malacoherpesviridae Genomics
The family of double-stranded DNA (dsDNA) Malacoherpesviridae includes viruses able to infect marine mollusks and detrimental for worldwide aquaculture production. Due to fast-occurring mortality and a lack of permissive cell lines, the available data on the few known Malacoherpesviridae provide onl...
Published in: | Frontiers in Microbiology |
---|---|
Main Authors: | , |
Format: | Text |
Language: | English |
Published: |
Frontiers Media S.A.
2017
|
Subjects: | |
Online Access: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552708/ http://www.ncbi.nlm.nih.gov/pubmed/28848525 https://doi.org/10.3389/fmicb.2017.01515 |
id |
ftpubmed:oai:pubmedcentral.nih.gov:5552708 |
---|---|
record_format |
openpolar |
spelling |
ftpubmed:oai:pubmedcentral.nih.gov:5552708 2023-05-15T15:58:44+02:00 Oyster RNA-seq Data Support the Development of Malacoherpesviridae Genomics Rosani, Umberto Venier, Paola 2017-08-09 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552708/ http://www.ncbi.nlm.nih.gov/pubmed/28848525 https://doi.org/10.3389/fmicb.2017.01515 en eng Frontiers Media S.A. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552708/ http://www.ncbi.nlm.nih.gov/pubmed/28848525 http://dx.doi.org/10.3389/fmicb.2017.01515 Copyright © 2017 Rosani and Venier. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. CC-BY Microbiology Text 2017 ftpubmed https://doi.org/10.3389/fmicb.2017.01515 2017-09-03T00:18:42Z The family of double-stranded DNA (dsDNA) Malacoherpesviridae includes viruses able to infect marine mollusks and detrimental for worldwide aquaculture production. Due to fast-occurring mortality and a lack of permissive cell lines, the available data on the few known Malacoherpesviridae provide only partial support for the study of molecular virus features, life cycle, and evolutionary history. Following thorough data mining of bivalve and gastropod RNA-seq experiments, we used more than five million Malacoherpesviridae reads to improve the annotation of viral genomes and to characterize viral InDels, nucleotide stretches, and SNPs. Both genome and protein domain analyses confirmed the evolutionary diversification and gene uniqueness of known Malacoherpesviridae. However, the presence of Malacoherpesviridae-like sequences integrated within genomes of phylogenetically distant invertebrates indicates broad diffusion of these viruses and indicates the need for confirmatory investigations. The manifest co-occurrence of OsHV-1 genotype variants in single RNA-seq samples of Crassostrea gigas provide further support for the Malacoherpesviridae diversification. In addition to simple sequence motifs inter-punctuating viral ORFs, recombination-inducing sequences were found to be enriched in the OsHV-1 and AbHV1-AUS genomes. Finally, the highly correlated expression of most viral ORFs in multiple oyster samples is consistent with the burst of viral proteins during the lytic phase. Text Crassostrea gigas PubMed Central (PMC) Frontiers in Microbiology 8 |
institution |
Open Polar |
collection |
PubMed Central (PMC) |
op_collection_id |
ftpubmed |
language |
English |
topic |
Microbiology |
spellingShingle |
Microbiology Rosani, Umberto Venier, Paola Oyster RNA-seq Data Support the Development of Malacoherpesviridae Genomics |
topic_facet |
Microbiology |
description |
The family of double-stranded DNA (dsDNA) Malacoherpesviridae includes viruses able to infect marine mollusks and detrimental for worldwide aquaculture production. Due to fast-occurring mortality and a lack of permissive cell lines, the available data on the few known Malacoherpesviridae provide only partial support for the study of molecular virus features, life cycle, and evolutionary history. Following thorough data mining of bivalve and gastropod RNA-seq experiments, we used more than five million Malacoherpesviridae reads to improve the annotation of viral genomes and to characterize viral InDels, nucleotide stretches, and SNPs. Both genome and protein domain analyses confirmed the evolutionary diversification and gene uniqueness of known Malacoherpesviridae. However, the presence of Malacoherpesviridae-like sequences integrated within genomes of phylogenetically distant invertebrates indicates broad diffusion of these viruses and indicates the need for confirmatory investigations. The manifest co-occurrence of OsHV-1 genotype variants in single RNA-seq samples of Crassostrea gigas provide further support for the Malacoherpesviridae diversification. In addition to simple sequence motifs inter-punctuating viral ORFs, recombination-inducing sequences were found to be enriched in the OsHV-1 and AbHV1-AUS genomes. Finally, the highly correlated expression of most viral ORFs in multiple oyster samples is consistent with the burst of viral proteins during the lytic phase. |
format |
Text |
author |
Rosani, Umberto Venier, Paola |
author_facet |
Rosani, Umberto Venier, Paola |
author_sort |
Rosani, Umberto |
title |
Oyster RNA-seq Data Support the Development of Malacoherpesviridae Genomics |
title_short |
Oyster RNA-seq Data Support the Development of Malacoherpesviridae Genomics |
title_full |
Oyster RNA-seq Data Support the Development of Malacoherpesviridae Genomics |
title_fullStr |
Oyster RNA-seq Data Support the Development of Malacoherpesviridae Genomics |
title_full_unstemmed |
Oyster RNA-seq Data Support the Development of Malacoherpesviridae Genomics |
title_sort |
oyster rna-seq data support the development of malacoherpesviridae genomics |
publisher |
Frontiers Media S.A. |
publishDate |
2017 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552708/ http://www.ncbi.nlm.nih.gov/pubmed/28848525 https://doi.org/10.3389/fmicb.2017.01515 |
genre |
Crassostrea gigas |
genre_facet |
Crassostrea gigas |
op_relation |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5552708/ http://www.ncbi.nlm.nih.gov/pubmed/28848525 http://dx.doi.org/10.3389/fmicb.2017.01515 |
op_rights |
Copyright © 2017 Rosani and Venier. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.3389/fmicb.2017.01515 |
container_title |
Frontiers in Microbiology |
container_volume |
8 |
_version_ |
1766394505700835328 |