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 |
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Frontiers Media S.A.
2017
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Online Access: | http://hdl.handle.net/11577/3240289 https://doi.org/10.3389/fmicb.2017.01515 https://fjfsdata01prod.blob.core.windows.net/articles/files/276363/pubmed-zip/.versions/1/.package-entries/fmicb-08-01515/fmicb-08-01515.pdf |
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ftunivpadovairis:oai:www.research.unipd.it:11577/3240289 2024-04-14T08:10:43+00:00 Oyster RNA-seq data support the development of Malacoherpesviridae genomics ROSANI, UMBERTO VENIER, PAOLA Rosani, Umberto Venier, Paola 2017 ELETTRONICO http://hdl.handle.net/11577/3240289 https://doi.org/10.3389/fmicb.2017.01515 https://fjfsdata01prod.blob.core.windows.net/articles/files/276363/pubmed-zip/.versions/1/.package-entries/fmicb-08-01515/fmicb-08-01515.pdf eng eng Frontiers Media S.A. info:eu-repo/semantics/altIdentifier/pmid/28848525 info:eu-repo/semantics/altIdentifier/wos/WOS:000407430500004 volume:8 issue:AUG firstpage:1 lastpage:17 numberofpages:17 journal:FRONTIERS IN MICROBIOLOGY info:eu-repo/grantAgreement/EC/H2020/678589 http://hdl.handle.net/11577/3240289 doi:10.3389/fmicb.2017.01515 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85027108358 https://fjfsdata01prod.blob.core.windows.net/articles/files/276363/pubmed-zip/.versions/1/.package-entries/fmicb-08-01515/fmicb-08-01515.pdf info:eu-repo/semantics/openAccess Bivalve Herpesvirale Malacoherpesviridae OsHV-1 RNA-seq Virome Microbiology Microbiology (medical) info:eu-repo/semantics/article 2017 ftunivpadovairis https://doi.org/10.3389/fmicb.2017.01515 2024-03-21T19:27:14Z 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. Article in Journal/Newspaper Crassostrea gigas Padua Research Archive (IRIS - Università degli Studi di Padova) Frontiers in Microbiology 8 |
institution |
Open Polar |
collection |
Padua Research Archive (IRIS - Università degli Studi di Padova) |
op_collection_id |
ftunivpadovairis |
language |
English |
topic |
Bivalve Herpesvirale Malacoherpesviridae OsHV-1 RNA-seq Virome Microbiology Microbiology (medical) |
spellingShingle |
Bivalve Herpesvirale Malacoherpesviridae OsHV-1 RNA-seq Virome Microbiology Microbiology (medical) ROSANI, UMBERTO VENIER, PAOLA Oyster RNA-seq data support the development of Malacoherpesviridae genomics |
topic_facet |
Bivalve Herpesvirale Malacoherpesviridae OsHV-1 RNA-seq Virome Microbiology Microbiology (medical) |
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. |
author2 |
Rosani, Umberto Venier, Paola |
format |
Article in Journal/Newspaper |
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://hdl.handle.net/11577/3240289 https://doi.org/10.3389/fmicb.2017.01515 https://fjfsdata01prod.blob.core.windows.net/articles/files/276363/pubmed-zip/.versions/1/.package-entries/fmicb-08-01515/fmicb-08-01515.pdf |
genre |
Crassostrea gigas |
genre_facet |
Crassostrea gigas |
op_relation |
info:eu-repo/semantics/altIdentifier/pmid/28848525 info:eu-repo/semantics/altIdentifier/wos/WOS:000407430500004 volume:8 issue:AUG firstpage:1 lastpage:17 numberofpages:17 journal:FRONTIERS IN MICROBIOLOGY info:eu-repo/grantAgreement/EC/H2020/678589 http://hdl.handle.net/11577/3240289 doi:10.3389/fmicb.2017.01515 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85027108358 https://fjfsdata01prod.blob.core.windows.net/articles/files/276363/pubmed-zip/.versions/1/.package-entries/fmicb-08-01515/fmicb-08-01515.pdf |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.3389/fmicb.2017.01515 |
container_title |
Frontiers in Microbiology |
container_volume |
8 |
_version_ |
1796308367230107648 |