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RNA Phage Biology in a Metagenomic Era

The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the “viral dark matter”). Also, these sequences...

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Autores principales: Callanan, Julie, Stockdale, Stephen R., Shkoporov, Andrey, Draper, Lorraine A., Ross, R. Paul, Hill, Colin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6071253/
https://www.ncbi.nlm.nih.gov/pubmed/30037084
http://dx.doi.org/10.3390/v10070386
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author Callanan, Julie
Stockdale, Stephen R.
Shkoporov, Andrey
Draper, Lorraine A.
Ross, R. Paul
Hill, Colin
author_facet Callanan, Julie
Stockdale, Stephen R.
Shkoporov, Andrey
Draper, Lorraine A.
Ross, R. Paul
Hill, Colin
author_sort Callanan, Julie
collection PubMed
description The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the “viral dark matter”). Also, these sequences are primarily derived from DNA-encoded bacteriophages (phages) with few RNA phages included. Despite the rapid advancements in high-throughput sequencing, few studies enrich for RNA viruses, i.e., target viral rather than cellular fraction and/or RNA rather than DNA via a reverse transcriptase step, in an attempt to capture the RNA viruses present in a microbial communities. It is timely to compile existing and relevant information about RNA phages to provide an insight into many of their important biological features, which should aid in sequence-based discovery and in their subsequent annotation. Without comprehensive studies, the biological significance of RNA phages has been largely ignored. Future bacteriophage studies should be adapted to ensure they are properly represented in phageomic studies.
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spelling pubmed-60712532018-08-09 RNA Phage Biology in a Metagenomic Era Callanan, Julie Stockdale, Stephen R. Shkoporov, Andrey Draper, Lorraine A. Ross, R. Paul Hill, Colin Viruses Review The number of novel bacteriophage sequences has expanded significantly as a result of many metagenomic studies of phage populations in diverse environments. Most of these novel sequences bear little or no homology to existing databases (referred to as the “viral dark matter”). Also, these sequences are primarily derived from DNA-encoded bacteriophages (phages) with few RNA phages included. Despite the rapid advancements in high-throughput sequencing, few studies enrich for RNA viruses, i.e., target viral rather than cellular fraction and/or RNA rather than DNA via a reverse transcriptase step, in an attempt to capture the RNA viruses present in a microbial communities. It is timely to compile existing and relevant information about RNA phages to provide an insight into many of their important biological features, which should aid in sequence-based discovery and in their subsequent annotation. Without comprehensive studies, the biological significance of RNA phages has been largely ignored. Future bacteriophage studies should be adapted to ensure they are properly represented in phageomic studies. MDPI 2018-07-21 /pmc/articles/PMC6071253/ /pubmed/30037084 http://dx.doi.org/10.3390/v10070386 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
Callanan, Julie
Stockdale, Stephen R.
Shkoporov, Andrey
Draper, Lorraine A.
Ross, R. Paul
Hill, Colin
RNA Phage Biology in a Metagenomic Era
title RNA Phage Biology in a Metagenomic Era
title_full RNA Phage Biology in a Metagenomic Era
title_fullStr RNA Phage Biology in a Metagenomic Era
title_full_unstemmed RNA Phage Biology in a Metagenomic Era
title_short RNA Phage Biology in a Metagenomic Era
title_sort rna phage biology in a metagenomic era
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6071253/
https://www.ncbi.nlm.nih.gov/pubmed/30037084
http://dx.doi.org/10.3390/v10070386
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