Diversity of Environmental Single-Stranded DNA Phages Revealed by PCR Amplification of the Partial Major Capsid Protein
The small single-stranded DNA (ssDNA) bacteriophages of the subfamily Gokushovirinae were traditionally perceived as narrowly targeted, niche-specific viruses infecting obligate parasitic bacteria, such as Chlamydia. The advent of metagenomics revealed gokushoviruses to be widespread in global envir...
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Digital Commons @ University of South Florida
2014
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ftunisfloridatam:oai:digitalcommons.usf.edu:msc_facpub-1570 2023-05-15T13:34:05+02:00 Diversity of Environmental Single-Stranded DNA Phages Revealed by PCR Amplification of the Partial Major Capsid Protein Hopkins, Max S. Kailasan, Shweta Cohen, Allison Roux, Simon Shevenell, Amelia E. Agbandje-McKenna, Mavis Breitbart, Mya 2014-04-01T07:00:00Z application/pdf https://digitalcommons.usf.edu/msc_facpub/590 https://digitalcommons.usf.edu/cgi/viewcontent.cgi?article=1570&context=msc_facpub unknown Digital Commons @ University of South Florida https://digitalcommons.usf.edu/msc_facpub/590 https://digitalcommons.usf.edu/cgi/viewcontent.cgi?article=1570&context=msc_facpub http://creativecommons.org/licenses/by-nc-sa/3.0/ CC-BY-NC-SA Marine Science Faculty Publications single-stranded phage virus gokushovirus Microviridae Life Sciences article 2014 ftunisfloridatam 2021-10-09T07:50:02Z The small single-stranded DNA (ssDNA) bacteriophages of the subfamily Gokushovirinae were traditionally perceived as narrowly targeted, niche-specific viruses infecting obligate parasitic bacteria, such as Chlamydia. The advent of metagenomics revealed gokushoviruses to be widespread in global environmental samples. This study expands knowledge of gokushovirus diversity in the environment by developing a degenerate PCR assay to amplify a portion of the major capsid protein (MCP) gene of gokushoviruses. Over 500 amplicons were sequenced from 10 environmental samples (sediments, sewage, seawater and freshwater), revealing the ubiquity and high diversity of this understudied phage group. Residue-level conservation data generated from multiple alignments was combined with a predicted 3D structure, revealing a tendency for structurally internal residues to be more highly conserved than surface-presenting protein–protein or viral–host interaction domains. Aggregating this data set into a phylogenetic framework, many gokushovirus MCP clades contained samples from multiple environments, although distinct clades dominated the different samples. Antarctic sediment samples contained the most diverse gokushovirus communities, whereas freshwater springs from Florida were the least diverse. Whether the observed diversity is being driven by environmental factors or host-binding interactions remains an open question. The high environmental diversity of this previously overlooked ssDNA viral group necessitates further research elucidating their natural hosts and exploring their ecological roles. Article in Journal/Newspaper Antarc* Antarctic Digital Commons University of South Florida (USF) Antarctic |
institution |
Open Polar |
collection |
Digital Commons University of South Florida (USF) |
op_collection_id |
ftunisfloridatam |
language |
unknown |
topic |
single-stranded phage virus gokushovirus Microviridae Life Sciences |
spellingShingle |
single-stranded phage virus gokushovirus Microviridae Life Sciences Hopkins, Max S. Kailasan, Shweta Cohen, Allison Roux, Simon Shevenell, Amelia E. Agbandje-McKenna, Mavis Breitbart, Mya Diversity of Environmental Single-Stranded DNA Phages Revealed by PCR Amplification of the Partial Major Capsid Protein |
topic_facet |
single-stranded phage virus gokushovirus Microviridae Life Sciences |
description |
The small single-stranded DNA (ssDNA) bacteriophages of the subfamily Gokushovirinae were traditionally perceived as narrowly targeted, niche-specific viruses infecting obligate parasitic bacteria, such as Chlamydia. The advent of metagenomics revealed gokushoviruses to be widespread in global environmental samples. This study expands knowledge of gokushovirus diversity in the environment by developing a degenerate PCR assay to amplify a portion of the major capsid protein (MCP) gene of gokushoviruses. Over 500 amplicons were sequenced from 10 environmental samples (sediments, sewage, seawater and freshwater), revealing the ubiquity and high diversity of this understudied phage group. Residue-level conservation data generated from multiple alignments was combined with a predicted 3D structure, revealing a tendency for structurally internal residues to be more highly conserved than surface-presenting protein–protein or viral–host interaction domains. Aggregating this data set into a phylogenetic framework, many gokushovirus MCP clades contained samples from multiple environments, although distinct clades dominated the different samples. Antarctic sediment samples contained the most diverse gokushovirus communities, whereas freshwater springs from Florida were the least diverse. Whether the observed diversity is being driven by environmental factors or host-binding interactions remains an open question. The high environmental diversity of this previously overlooked ssDNA viral group necessitates further research elucidating their natural hosts and exploring their ecological roles. |
format |
Article in Journal/Newspaper |
author |
Hopkins, Max S. Kailasan, Shweta Cohen, Allison Roux, Simon Shevenell, Amelia E. Agbandje-McKenna, Mavis Breitbart, Mya |
author_facet |
Hopkins, Max S. Kailasan, Shweta Cohen, Allison Roux, Simon Shevenell, Amelia E. Agbandje-McKenna, Mavis Breitbart, Mya |
author_sort |
Hopkins, Max S. |
title |
Diversity of Environmental Single-Stranded DNA Phages Revealed by PCR Amplification of the Partial Major Capsid Protein |
title_short |
Diversity of Environmental Single-Stranded DNA Phages Revealed by PCR Amplification of the Partial Major Capsid Protein |
title_full |
Diversity of Environmental Single-Stranded DNA Phages Revealed by PCR Amplification of the Partial Major Capsid Protein |
title_fullStr |
Diversity of Environmental Single-Stranded DNA Phages Revealed by PCR Amplification of the Partial Major Capsid Protein |
title_full_unstemmed |
Diversity of Environmental Single-Stranded DNA Phages Revealed by PCR Amplification of the Partial Major Capsid Protein |
title_sort |
diversity of environmental single-stranded dna phages revealed by pcr amplification of the partial major capsid protein |
publisher |
Digital Commons @ University of South Florida |
publishDate |
2014 |
url |
https://digitalcommons.usf.edu/msc_facpub/590 https://digitalcommons.usf.edu/cgi/viewcontent.cgi?article=1570&context=msc_facpub |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic |
genre_facet |
Antarc* Antarctic |
op_source |
Marine Science Faculty Publications |
op_relation |
https://digitalcommons.usf.edu/msc_facpub/590 https://digitalcommons.usf.edu/cgi/viewcontent.cgi?article=1570&context=msc_facpub |
op_rights |
http://creativecommons.org/licenses/by-nc-sa/3.0/ |
op_rightsnorm |
CC-BY-NC-SA |
_version_ |
1766048703719669760 |