Scrutinizing Virus Genome Termini by High-Throughput Sequencing

Li, Shasha; Fan, Hang; An, Xiaoping; Fan, Hao; Jiang, Huanhuan; Chen, Yubao; Tong, Yigang

doi:10.1371/journal.pone.0085806

Cited by 60 publications

(57 citation statements)

References 36 publications

(95 reference statements)

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“…The existence of terminal repeats was suggested during sequence analysis by the identification of a localized area in the genome which had twice the read depth compared with the rest of the genome. Identification of phage genome ends by this approach has been reported for other phages (Fouts et al, 2013; Li et al, 2014). The existence of the terminal repeats was verified by PFGE, which indicated that the size of genome obtained from sequencing is within the correct range (Figure 2).…”

Section: Resultsmentioning

confidence: 77%

Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB

et al. 2017

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Enterobacteria phage vB_PcaM_CBB is a “jumbo” phage belonging to the family Myoviridae. It possesses highly atypical whisker-like structures along the length of its contractile tail. It has a broad host range with the capability of infecting species of the genera Erwinia, Pectobacterium, and Cronobacter. With a genome of 355,922 bp, excluding a predicted terminal repeat of 22,456 bp, phage CBB is the third largest phage sequenced to date. Its genome was predicted to encode 554 ORFs with 33 tRNAs. Based on prediction and proteome analysis of the virions, 29% of its predicted ORFs could be functionally assigned. Protein comparison shows that CBB shares between 33–38% of its proteins with Cronobacter phage GAP32, coliphages PBECO4 and 121Q as well as Klebsiella phage vB_KleM_Rak2. This work presents a detailed and comparative analysis of vB_PcaM_CBB of a highly atypical jumbo myoviridae phage, contributing to a better understanding of phage diversity and biology.

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Section: Resultsmentioning

confidence: 77%

Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB

et al. 2017

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“…A total of 2,389,752 reads with an average length of 220 bp were obtained. Assembly was carried out using SOAPdenovo software (Li et al, 2014). One uncertain region with direct repeats was checked using the CLC genomics workbench (version 9) (Li et al, 2014) and by PCR analysis.…”

Section: Dna Extraction Genome Sequencing and Assemblymentioning

confidence: 99%

“…Assembly was carried out using SOAPdenovo software (Li et al, 2014). One uncertain region with direct repeats was checked using the CLC genomics workbench (version 9) (Li et al, 2014) and by PCR analysis. The genome sequence has been submitted to the GenBank database under accession no.…”

Section: Dna Extraction Genome Sequencing and Assemblymentioning

confidence: 99%

Novel phage–host interactions and evolution as revealed by a cyanomyovirus isolated from an estuarine environment

Zhang

Wang

et al. 2018

Environmental Microbiology

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Cyanophages are thought to affect the community structure, population dynamics, metabolic activity and evolution of picocyanobacteria and to impact the biogeochemical cycling in aquatic ecosystems. Here, we report an estuarine Synechococcus phage, S-CBWM1, which represents a novel viral lineage and exhibits interesting genetic features related to phage-host interactions and evolution. S-CBWM1 encapsidates four virion-associated proteins related to cellular metabolic regulation. Several novel auxiliary metabolic genes related to multidrug efflux, cell wall and capsule synthesis or modifications were also identified. In addition, the presence of the largest number of tRNA genes hitherto found in a phage genome may contribute to the translation efficiency of unique genes. These genomic and proteomic features of S-CBWM1 suggested phage-host interactions involved in adaptation to eutrophic estuarine environments. Phylogenetic and metagenomic analysis of the polγ gene in the S-CBWM1 genome provided new insights into the evolutionary path of mitochondrial DNA polymerase gamma. The S-CBWM1 psbA contains two group I introns, representing the first instance of multiple introns within psbA from phage. The isolation of S-CBWM1 reveals that estuarine ecosystems contain evolutionarily novel cyanophages that drive unique phage-host interactions.

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“…Software-based methods using raw next-generation sequencing data provide insight into physical ends and packaging strategies [23]. These data can guide, clarify, or potentially replace wet lab experiments, especially when working with large datasets.…”

Section: Introductionmentioning

confidence: 99%

Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies

et al. 2016

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BackgroundPhage genome analysis is a rapidly growing field. Recurrent obstacles include software access and usability, as well as genome sequences that vary in sequence orientation and/or start position. Here we describe modifications to the phage comparative genomics software program, Phamerator, provide public access to the code, and include instructions for creating custom Phamerator databases. We further report genomic analysis techniques to determine phage packaging strategies and identification of the physical ends of phage genomes.ResultsThe original Phamerator code can be successfully modified and custom databases can be generated using the instructions we provide. Results of genome map comparisons within a custom database reveal obstacles in performing the comparisons if a published genome has an incorrect complementarity or an incorrect location of the first base of the genome, which are common issues in GenBank-downloaded sequence files. To address these issues, we review phage packaging strategies and provide results that demonstrate identification of the genome start location and orientation using raw sequencing data and software programs such as PAUSE and Consed to establish the location of the physical ends of the genome. These results include determination of exact direct terminal repeats (DTRs) or cohesive ends, or whether phages may use a headful packaging strategy. Phylogenetic analysis using ClustalO and phamily circles in Phamerator demonstrate that the large terminase gene can be used to identify the phage packaging strategy and thereby aide in identifying the physical ends of the genome.ConclusionsUsing available online code, the Phamerator program can be customized and utilized to generate databases with individually selected genomes. These databases can then provide fruitful information in the comparative analysis of phages. Researchers can identify packaging strategies and physical ends of phage genomes using raw data from high-throughput sequencing in conjunction with phylogenetic analyses of large terminase proteins and the use of custom Phamerator databases. We promote publication of phage genomes in an orientation consistent with the physical structure of the phage chromosome and provide guidance for determining this structure.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3018-2) contains supplementary material, which is available to authorized users.

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Scrutinizing Virus Genome Termini by High-Throughput Sequencing

Cited by 60 publications

References 36 publications

Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB

Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB

Novel phage–host interactions and evolution as revealed by a cyanomyovirus isolated from an estuarine environment

Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies

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