Staphylococci phages display vast genomic diversity and evolutionary relationships
BACKGROUND: Bacteriophages are the most abundant and diverse entities in the biosphere, and this diversity is driven by constant predator–prey evolutionary dynamics and horizontal gene transfer. Phage genome sequences are under-sampled and therefore present an untapped and uncharacterized source of...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6507118/ https://www.ncbi.nlm.nih.gov/pubmed/31072320 http://dx.doi.org/10.1186/s12864-019-5647-8 |
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author | Oliveira, Hugo Sampaio, Marta Melo, Luís D. R. Dias, Oscar Pope, Welkin H. Hatfull, Graham F. Azeredo, Joana |
author_facet | Oliveira, Hugo Sampaio, Marta Melo, Luís D. R. Dias, Oscar Pope, Welkin H. Hatfull, Graham F. Azeredo, Joana |
author_sort | Oliveira, Hugo |
collection | PubMed |
description | BACKGROUND: Bacteriophages are the most abundant and diverse entities in the biosphere, and this diversity is driven by constant predator–prey evolutionary dynamics and horizontal gene transfer. Phage genome sequences are under-sampled and therefore present an untapped and uncharacterized source of genetic diversity, typically characterized by highly mosaic genomes and no universal genes. To better understand the diversity and relationships among phages infecting human pathogens, we have analysed the complete genome sequences of 205 phages of Staphylococcus sp. RESULTS: These are predicted to encode 20,579 proteins, which can be sorted into 2139 phamilies (phams) of related sequences; 745 of these are orphams and possess only a single gene. Based on shared gene content, these phages were grouped into four clusters (A, B, C and D), 27 subclusters (A1-A2, B1-B17, C1-C6 and D1-D2) and one singleton. However, the genomes have mosaic architectures and individual genes with common ancestors are positioned in distinct genomic contexts in different clusters. The staphylococcal Cluster B siphoviridae are predicted to be temperate, and the integration cassettes are often closely-linked to genes implicated in bacterial virulence determinants. There are four unusual endolysin organization strategies found in Staphylococcus phage genomes, with endolysins predicted to be encoded as single genes, two genes spliced, two genes adjacent and as a single gene with inter-lytic-domain secondary translational start site. Comparison of the endolysins reveals multi-domain modularity, with conservation of the SH3 cell wall binding domain. CONCLUSIONS: This study provides a high-resolution view of staphylococcal viral genetic diversity, and insights into their gene flux patterns within and across different phage groups (cluster and subclusters) providing insights into their evolution. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5647-8) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6507118 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-65071182019-05-13 Staphylococci phages display vast genomic diversity and evolutionary relationships Oliveira, Hugo Sampaio, Marta Melo, Luís D. R. Dias, Oscar Pope, Welkin H. Hatfull, Graham F. Azeredo, Joana BMC Genomics Research Article BACKGROUND: Bacteriophages are the most abundant and diverse entities in the biosphere, and this diversity is driven by constant predator–prey evolutionary dynamics and horizontal gene transfer. Phage genome sequences are under-sampled and therefore present an untapped and uncharacterized source of genetic diversity, typically characterized by highly mosaic genomes and no universal genes. To better understand the diversity and relationships among phages infecting human pathogens, we have analysed the complete genome sequences of 205 phages of Staphylococcus sp. RESULTS: These are predicted to encode 20,579 proteins, which can be sorted into 2139 phamilies (phams) of related sequences; 745 of these are orphams and possess only a single gene. Based on shared gene content, these phages were grouped into four clusters (A, B, C and D), 27 subclusters (A1-A2, B1-B17, C1-C6 and D1-D2) and one singleton. However, the genomes have mosaic architectures and individual genes with common ancestors are positioned in distinct genomic contexts in different clusters. The staphylococcal Cluster B siphoviridae are predicted to be temperate, and the integration cassettes are often closely-linked to genes implicated in bacterial virulence determinants. There are four unusual endolysin organization strategies found in Staphylococcus phage genomes, with endolysins predicted to be encoded as single genes, two genes spliced, two genes adjacent and as a single gene with inter-lytic-domain secondary translational start site. Comparison of the endolysins reveals multi-domain modularity, with conservation of the SH3 cell wall binding domain. CONCLUSIONS: This study provides a high-resolution view of staphylococcal viral genetic diversity, and insights into their gene flux patterns within and across different phage groups (cluster and subclusters) providing insights into their evolution. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-019-5647-8) contains supplementary material, which is available to authorized users. BioMed Central 2019-05-09 /pmc/articles/PMC6507118/ /pubmed/31072320 http://dx.doi.org/10.1186/s12864-019-5647-8 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Oliveira, Hugo Sampaio, Marta Melo, Luís D. R. Dias, Oscar Pope, Welkin H. Hatfull, Graham F. Azeredo, Joana Staphylococci phages display vast genomic diversity and evolutionary relationships |
title | Staphylococci phages display vast genomic diversity and evolutionary relationships |
title_full | Staphylococci phages display vast genomic diversity and evolutionary relationships |
title_fullStr | Staphylococci phages display vast genomic diversity and evolutionary relationships |
title_full_unstemmed | Staphylococci phages display vast genomic diversity and evolutionary relationships |
title_short | Staphylococci phages display vast genomic diversity and evolutionary relationships |
title_sort | staphylococci phages display vast genomic diversity and evolutionary relationships |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6507118/ https://www.ncbi.nlm.nih.gov/pubmed/31072320 http://dx.doi.org/10.1186/s12864-019-5647-8 |
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