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Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes

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Chan, Jacqueline, Millard, Andrew D., Mann, Nicholas H. and Schäfer, Hendrik (2014) Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes. Frontiers in Microbiology, Volume 5 . Article number 506. doi:10.3389/fmicb.2014.00506 ISSN 1664-302X.

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Official URL: http://dx.doi.org/10.3389/fmicb.2014.00506

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Abstract

Two bacteriophages, RPP1 and RLP1, infecting members of the marine Roseobacter clade were isolated from seawater. Their linear genomes are 74.7 and 74.6 kb and encode 91 and 92 coding DNA sequences, respectively. Around 30% of these are homologous to genes found in Enterobacter phage N4. Comparative genomics of these two new Roseobacter phages and 23 other sequenced N4-like phages (three infecting members of the Roseobacter lineage and 20 infecting other Gammaproteobacteria) revealed that N4-like phages share a core genome of 14 genes responsible for control of gene expression, replication and virion proteins. Phylogenetic analysis of these genes placed the five N4-like roseophages (RN4) into a distinct subclade. Analysis of the RN4 phage genomes revealed they share a further 19 genes of which nine are found exclusively in RN4 phages and four appear to have been acquired from their bacterial hosts. Proteomic analysis of the RPP1 and RLP1 virions identified a second structural module present in the RN4 phages similar to that found in the Pseudomonas N4-like phage LIT1. Searches of various metagenomic databases, including the GOS database, using CDS sequences from RPP1 suggests these phages are widely distributed in marine environments in particular in the open ocean environment.

Item Type: Journal Article
Subjects: Q Science > QH Natural history > QH426 Genetics
Q Science > QR Microbiology
Q Science > QR Microbiology > QR355 Virology
Divisions: Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- )
Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School > Biomedical Sciences > Microbiology & Infection
Faculty of Science, Engineering and Medicine > Medicine > Warwick Medical School
Library of Congress Subject Headings (LCSH): Bacteriophages, Comparative genomics , Genes
Journal or Publication Title: Frontiers in Microbiology
Publisher: Frontiers Research Foundation
ISSN: 1664-302X
Official Date: 10 October 2014
Dates:
DateEvent
10 October 2014Published
8 September 2014Accepted
6 June 2014Submitted
Volume: Volume 5
Article Number: Article number 506
DOI: 10.3389/fmicb.2014.00506
Status: Peer Reviewed
Publication Status: Published
Date of first compliant deposit: 28 July 2016
Date of first compliant Open Access: 28 July 2016
Funder: Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Natural Environment Research Council (Great Britain) (NERC)
Grant number: NE/E01333/1 (NERC), NE/F010044/1 (NERC)

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