ArticleJournal of virology2013
Phylogenomic network and comparative genomics reveal a diverged member of the ΦKZ-related group, marine vibrio phage ΦJM-2012.
Article in Journal of virology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- The biology of jumbo phages.Nature communications · 2026Review
- Erwinia phage Asesino is a nucleus-forming phage that lacks PhuZ.Scientific reports · 2025Article
- The intricate organizational strategy of nucleus-forming phages.Current opinion in microbiology · 2024Review
- Asesino: a nucleus-forming phage that lacks PhuZ.bioRxiv : the preprint server for biology · 2024Article
- Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY.Cell reports · 2023Article
- Article
- Comparative genomic analysis of dwarf Vibrio myoviruses defines a conserved gene cluster for successful phage infection.Archives of virology · 2022Article
- Bacteriophage classification for assembled contigs using graph convolutional network.Bioinformatics (Oxford, England) · 2021Article
- Integrative omics analysis of Pseudomonas aeruginosa virus PA5oct highlights the molecular complexity of jumbo phages.Environmental microbiology · 2020Article
- Characterization and Genomic Analysis of ValSw3-3, a NewJournal of virology · 2020Article
- Global Proteomic Profiling ofJournal of virology · 2019Article
- Metavirome Sequencing of the Termite Gut Reveals the Presence of an Unexplored Bacteriophage Community.Frontiers in microbiology · 2017Article
- A network perspective on the virus world.Communicative & integrative biology · 2017Article
- Article
- Replications of Two Closely Related Groups of Jumbo Phages Show Different Level of Dependence on Host-encoded RNA Polymerase.Frontiers in microbiology · 2017Article
- To Be or Not To Be T4: Evidence of a Complex Evolutionary Pathway of Head Structure and Assembly in GiantFrontiers in microbiology · 2017Article
- Identification of Essential Genes in the Salmonella Phage SPN3US Reveals Novel Insights into Giant Phage Head Structure and Assembly.Journal of virology · 2016Article
- A proposed integrated approach for the preclinical evaluation of phage therapy in Pseudomonas infections.Scientific reports · 2016Article
- Characterization of Novel Bacteriophages for Biocontrol of Bacterial Blight in Leek Caused by Pseudomonas syringae pv. porri.Frontiers in microbiology · 2016Article
- Replicating phages in the epidermal mucosa of the eel (Anguilla anguilla).Frontiers in microbiology · 2015Article
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10 authors.
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Abstract
Bacteriophages are the largest reservoir of genetic diversity. Here we describe the novel phage ΦJM-2012. This natural isolate from marine Vibrio cyclitrophicus possesses very few gene contents relevant to other well-studied marine Vibrio phages. To better understand its evolutionary history, we built a mathematical model of pairwise relationships among 1,221 phage genomes, in which the genomes (nodes) are linked by edges representing the normalized number of shared orthologous protein families. This weighted network revealed that ΦJM-2012 was connected to only five members of the Pseudomonas ΦKZ-like phage family in an isolated network, strongly indicating that it belongs to this phage group. However, comparative genomic analyses highlighted an almost complete loss of colinearity with the ΦKZ-related genomes and little conservation of gene order, probably reflecting the action of distinct evolutionary forces on the genome of ΦJM-2012. In this phage, typical conserved core genes, including six RNA polymerase genes, were frequently displaced and the hyperplastic regions were rich in both unique genes and predicted unidirectional promoters with highly correlated orientations. Further, analysis of the ΦJM-2012 genome showed that segments of the conserved N-terminal parts of ΦKZ tail fiber paralogs exhibited evidence of combinatorial assortment, having switched transcriptional orientation, and there was recruitment and/or structural changes among phage endolysins and tail spike protein. Thus, this naturally occurring phage appears to have branched from a common ancestor of the ΦKZ-related groups, showing a distinct genomic architecture and unique genes that most likely reflect adaptation to its chosen host and environment.
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