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BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE

Bacteriophages (phages) exhibit high genetic diversity, and the mosaic nature of the shared genetic pool makes quantifying phage relatedness a shifting target. Early parameters for clustering of related Mycobacteria and Arthrobacter phage genomes relied on nucleotide identity thresholds but, more re...

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Autores principales: Demo, Stephanie, Kapinos, Andrew, Bernardino, Aaron, Guardino, Kristina, Hobbs, Blake, Hoh, Kimberly, Lee, Edward, Vuong, Iphen, Reddi, Krisanavane, Freise, Amanda C., Moberg Parker, Jordan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7954295/
https://www.ncbi.nlm.nih.gov/pubmed/33711060
http://dx.doi.org/10.1371/journal.pone.0248418
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author Demo, Stephanie
Kapinos, Andrew
Bernardino, Aaron
Guardino, Kristina
Hobbs, Blake
Hoh, Kimberly
Lee, Edward
Vuong, Iphen
Reddi, Krisanavane
Freise, Amanda C.
Moberg Parker, Jordan
author_facet Demo, Stephanie
Kapinos, Andrew
Bernardino, Aaron
Guardino, Kristina
Hobbs, Blake
Hoh, Kimberly
Lee, Edward
Vuong, Iphen
Reddi, Krisanavane
Freise, Amanda C.
Moberg Parker, Jordan
author_sort Demo, Stephanie
collection PubMed
description Bacteriophages (phages) exhibit high genetic diversity, and the mosaic nature of the shared genetic pool makes quantifying phage relatedness a shifting target. Early parameters for clustering of related Mycobacteria and Arthrobacter phage genomes relied on nucleotide identity thresholds but, more recently, clustering of Gordonia and Microbacterium phages has been performed according to shared gene content. Singleton phages lack the nucleotide identity and/or shared gene content required for clustering newly sequenced genomes with known phages. Whole genome metrics of novel Arthrobacter phage BlueFeather, originally designated a putative singleton, showed low nucleotide identity but high amino acid and gene content similarity with Arthrobacter phages originally assigned to Clusters FE and FI. Gene content similarity revealed that BlueFeather shared genes with these phages in excess of the parameter for clustering Gordonia and Microbacterium phages. Single gene analyses revealed evidence of horizontal gene transfer between BlueFeather and phages in unique clusters that infect a variety of bacterial hosts. Our findings highlight the advantage of using shared gene content to study seemingly genetically isolated phages and have resulted in the reclustering of BlueFeather, a putative singleton, as well as former Cluster FI phages, into a newly expanded Cluster FE.
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spelling pubmed-79542952021-03-22 BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE Demo, Stephanie Kapinos, Andrew Bernardino, Aaron Guardino, Kristina Hobbs, Blake Hoh, Kimberly Lee, Edward Vuong, Iphen Reddi, Krisanavane Freise, Amanda C. Moberg Parker, Jordan PLoS One Research Article Bacteriophages (phages) exhibit high genetic diversity, and the mosaic nature of the shared genetic pool makes quantifying phage relatedness a shifting target. Early parameters for clustering of related Mycobacteria and Arthrobacter phage genomes relied on nucleotide identity thresholds but, more recently, clustering of Gordonia and Microbacterium phages has been performed according to shared gene content. Singleton phages lack the nucleotide identity and/or shared gene content required for clustering newly sequenced genomes with known phages. Whole genome metrics of novel Arthrobacter phage BlueFeather, originally designated a putative singleton, showed low nucleotide identity but high amino acid and gene content similarity with Arthrobacter phages originally assigned to Clusters FE and FI. Gene content similarity revealed that BlueFeather shared genes with these phages in excess of the parameter for clustering Gordonia and Microbacterium phages. Single gene analyses revealed evidence of horizontal gene transfer between BlueFeather and phages in unique clusters that infect a variety of bacterial hosts. Our findings highlight the advantage of using shared gene content to study seemingly genetically isolated phages and have resulted in the reclustering of BlueFeather, a putative singleton, as well as former Cluster FI phages, into a newly expanded Cluster FE. Public Library of Science 2021-03-12 /pmc/articles/PMC7954295/ /pubmed/33711060 http://dx.doi.org/10.1371/journal.pone.0248418 Text en © 2021 Demo et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Demo, Stephanie
Kapinos, Andrew
Bernardino, Aaron
Guardino, Kristina
Hobbs, Blake
Hoh, Kimberly
Lee, Edward
Vuong, Iphen
Reddi, Krisanavane
Freise, Amanda C.
Moberg Parker, Jordan
BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE
title BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE
title_full BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE
title_fullStr BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE
title_full_unstemmed BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE
title_short BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE
title_sort bluefeather, the singleton that wasn’t: shared gene content analysis supports expansion of arthrobacter phage cluster fe
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7954295/
https://www.ncbi.nlm.nih.gov/pubmed/33711060
http://dx.doi.org/10.1371/journal.pone.0248418
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