Two different evolutionary lines of filamentous phages in Ralstonia solanacearum: their effects on bacterial virulence

Askora, Ahmed; Yamada, Takashi

doi:10.3389/fgene.2015.00217

Cited by 17 publications

(20 citation statements)

References 40 publications

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“…To estimate the number of true bases in the genome, we followed Warr et al (2015) to calculate GC-content-adjusted read depths in 1-kb windows across Hmel2 (details on commands and scripts used can be found in the Dryad and GitHub repositories). BED files containing scaffold positions and gap positions were constructed with Unix tools operating on the Hmel2 scaffold, and chromosome AGP files (in the Hmel2 distribution).…”

Section: Methodsmentioning

confidence: 99%

Major Improvements to theHeliconius melpomeneGenome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution

Davey

Chouteau

Barker

et al. 2016

G3 Genes|Genomes|Genetics

157

109

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The Heliconius butterflies are a widely studied adaptive radiation of 46 species spread across Central and South America, several of which are known to hybridize in the wild. Here, we present a substantially improved assembly of the Heliconius melpomene genome, developed using novel methods that should be applicable to improving other genome assemblies produced using short read sequencing. First, we whole-genome-sequenced a pedigree to produce a linkage map incorporating 99% of the genome. Second, we incorporated haplotype scaffolds extensively to produce a more complete haploid version of the draft genome. Third, we incorporated ∼20x coverage of Pacific Biosciences sequencing, and scaffolded the haploid genome using an assembly of this long-read sequence. These improvements result in a genome of 795 scaffolds, 275 Mb in length, with an N50 length of 2.1 Mb, an N50 number of 34, and with 99% of the genome placed, and 84% anchored on chromosomes. We use the new genome assembly to confirm that the Heliconius genome underwent 10 chromosome fusions since the split with its sister genus Eueides, over a period of about 6 million yr.

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Section: Methodsmentioning

confidence: 99%

Major Improvements to theHeliconius melpomeneGenome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution

Davey

Chouteau

Barker

et al. 2016

G3 Genes|Genomes|Genetics

157

109

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“…On the contrary, the proteins responsible for Pf phages replication initiation (PA0727) and stabilization of ssDNA (PA0720, G5P), as well as PA0719 and PA0721 are generally common for both lineages. Likewise, two distinct evolutionary lines of ﬁlamentous phages were also recognized in the plant pathogen R. solanacearum ( Askora and Yamada 2015 ).…”

Section: Discussionmentioning

confidence: 99%

“…In the first scenario, one phage plays a dominant role over a “recessive” one, assuming that mixing of their capsid proteins during virion assembly is undesirable, and this control may be released with cell population aging, as in the case of mature biofilms and production Pf-SI forms. Alternatively, formation of “hybrid” virions is acceptable and replication of both viruses may occur simultaneously ( Askora and Yamada 2015 ).…”

Section: Discussionmentioning

confidence: 99%

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Two Lineages of Pseudomonas aeruginosa Filamentous Phages: Structural Uniformity over Integration Preferences

Fiedoruk

Zakrzewska

Daniluk

et al. 2020

Genome Biology and Evolution

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Pseudomonas aeruginosa filamentous (Pf) bacteriophages are important factors contributing to the pathogenicity of this opportunistic bacterium, including biofilm formation and suppression of bacterial phagocytosis by macrophages. In addition, the capacity of Pf phages to form liquid crystal structures and their high negative charge density make them potent sequesters of cationic antibacterial agents, such as aminoglycoside antibiotics or host antimicrobial peptides. Therefore, Pf phages have been proposed as a potential biomarker for risk of antibiotic resistance development. The majority of studies describing biological functions of Pf viruses have been performed with only three of them: Pf1, Pf4 and Pf5. However, our analysis revealed that Pf phages exist as two evolutionary lineages (I and II), characterized by substantially different structural/morphogenesis properties, despite sharing the same integration sites in the host chromosomes. All aforementioned model Pf phages are members of the lineage I. Hence, it is reasonable to speculate that their interactions with P. aeruginosa and impact on its pathogenicity may be not completely extrapolated to the lineage II members. Furthermore, in order to organize the present numerical nomenclature of Pf phages, we propose a more informative approach based on the insertion sites, i.e. Pf-tRNA-Gly, -Met, -Sec, -tmRNA and -DR (direct repeats), which are fully compatible with one of five types of tyrosine integrases/recombinases XerC/D carried by these viruses. Finally, we discuss possible evolutionary mechanisms behind this division and consequences from the perspective of virus-virus, virus-bacterium and virus-human interactions.

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“…Infection by filamentous phages affects the fitness of their bacterial hosts, a feature that can be exploited for securing desired ecological benefits. Mostly, a phage infection enhances the host's ability to combat abiotic and biotic stress, to invade a new habitat, and to partake in the development of microbial communities (Askora & Yamada, 2015;Bille et al, 2005;Derbise & Carniel, 2014;Jian, Xiao, & Wang, 2013;Mai-Prochnow et al, 2015;Rice et al, 2009;Shapiro et al, 2016;Waldor & Mekalanos, 1996;Webb, Lau, & Kjelleberg, 2004;Yu et al, 2015). However, at times a phage infection lowers the fitness of the host bacterium, which is also F I G U R E 1 Ecosystem and other environmental challenges for ecological restoration of degraded lands, where current techniques face challenges but filamentous phage has potential to provide solutions.…”

Section: Introductionmentioning

confidence: 99%

Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration

Sharma

Karmakar

Kumar

et al. 2019

Ecology and Evolution

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Theories in soil biology, such as plant–microbe interactions and microbial cooperation and antagonism, have guided the practice of ecological restoration (ecorestoration). Below‐ground biodiversity (bacteria, fungi, invertebrates, etc.) influences the development of above‐ground biodiversity (vegetation structure). The role of rhizosphere bacteria in plant growth has been largely investigated but the role of phages (bacterial viruses) has received a little attention. Below the ground, phages govern the ecology and evolution of microbial communities by affecting genetic diversity, host fitness, population dynamics, community composition, and nutrient cycling. However, few restoration efforts take into account the interactions between bacteria and phages. Unlike other phages, filamentous phages are highly specific, nonlethal, and influence host fitness in several ways, which make them useful as target bacterial inocula. Also, the ease with which filamentous phages can be genetically manipulated to express a desired peptide to track and control pathogens and contaminants makes them useful in biosensing. Based on ecology and biology of filamentous phages, we developed a hypothesis on the application of phages in environment to derive benefits at different levels of biological organization ranging from individual bacteria to ecosystem for ecorestoration. We examined the potential applications of filamentous phages in improving bacterial inocula to restore vegetation and to monitor changes in habitat during ecorestoration and, based on our results, recommend a reorientation of the existing framework of using microbial inocula for such restoration and monitoring. Because bacterial inocula and biomonitoring tools based on filamentous phages are likely to prove useful in developing cost‐effective methods of restoring vegetation, we propose that filamentous phages be incorporated into nature‐based restoration efforts and that the tripartite relationship between phages, bacteria, and plants be explored further. Possible impacts of filamentous phages on native microflora are discussed and future areas of research are suggested to preclude any potential risks associated with such an approach.

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Two different evolutionary lines of filamentous phages in Ralstonia solanacearum: their effects on bacterial virulence

Cited by 17 publications

References 40 publications

Major Improvements to theHeliconius melpomeneGenome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution

Major Improvements to theHeliconius melpomeneGenome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution

Two Lineages of Pseudomonas aeruginosa Filamentous Phages: Structural Uniformity over Integration Preferences

Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration

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