The use of genomic signature distance between bacteriophages and their hosts displays evolutionary relationships and phage growth cycle determination.

Virology Journal
Patrick DeschavanneChristophe Regeard

Abstract

Bacteriophage classification is mainly based on morphological traits and genome characteristics combined with host information and in some cases on phage growth lifestyle. A lack of molecular tools can impede more precise studies on phylogenetic relationships or even a taxonomic classification. The use of methods to analyze genome sequences without the requirement for homology has allowed advances in classification. Here, we proposed to use genome sequence signature to characterize bacteriophages and to compare them to their host genome signature in order to obtain host-phage relationships and information on their lifestyle. We analyze the host-phage relationships in the four most representative groups of Caudoviridae, the dsDNA group of phages. We demonstrate that the use of phage genomic signature and its comparison with that of the host allows a grouping of phages and is also able to predict the host-phage relationships (lytic vs. temperate). We can thus condense, in relatively simple figures, this phage information dispersed over many publications.

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Citations

Sep 17, 2013·Nature Communications·Lesley A OgilvieBrian V Jones
Jan 13, 2012·Bioinformatics·Katelyn McNairRobert A Edwards
Apr 24, 2013·Molecular Biology and Evolution·Thomas W SchoenfeldBrian P Hedlund
Apr 17, 2012·Applied and Environmental Microbiology·Omar Sepúlveda-RoblesGabriel Guarneros
Mar 4, 2014·Molecular Biology and Evolution·Shivapriya ChithambaramXuhua Xia
Aug 8, 2015·BMC Bioinformatics·Rallis KaramichalisSteffen Kopecki
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Aug 24, 2016·BMC Bioinformatics·Rallis KaramichalisStephen Solis-Reyes
Mar 1, 2019·Viruses·Cynthia Maria ChibaniHeiko Liesegang
Dec 4, 2016·Virology Journal·Leonardo Joaquim van ZylMarla Trindade
Jun 28, 2021·BMC Microbiology·Yousef NamiBahman Panahi

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