CoreGenes3.5: a webserver for the determination of core genes from sets of viral and small bacterial genomes

Turner, Dann; Reynolds, Darren M.; Seto, Donald; Mahadevan, Padmanabhan

doi:10.1186/1756-0500-6-140

Cited by 68 publications

(49 citation statements)

References 20 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The online tool FrameD [25] was used to search for frameshift mutations. Core genes were identified using the program CoreGenes 3.5 [57, 58] with the default BLASTP threshold of 75.…”

Section: Methodsmentioning

confidence: 99%

Characterization of Paenibacillus larvae bacteriophages and their genomic relationships to firmicute bacteriophages

et al. 2014

View full text Add to dashboard Cite

BackgroundPaenibacillus larvae is a Firmicute bacterium that causes American Foulbrood, a lethal disease in honeybees and is a major source of global agricultural losses. Although P. larvae phages were isolated prior to 2013, no full genome sequences of P. larvae bacteriophages were published or analyzed. This report includes an in-depth analysis of the structure, genomes, and relatedness of P. larvae myoviruses Abouo, Davis, Emery, Jimmer1, Jimmer2, and siphovirus phiIBB_Pl23 to each other and to other known phages.ResultsP. larvae phages Abouo, Davies, Emery, Jimmer1, and Jimmer2 are myoviruses with ~50 kbp genomes. The six P. larvae phages form three distinct groups by dotplot analysis. An annotated linear genome map of these six phages displays important identifiable genes and demonstrates the relationship between phages. Sixty phage assembly or structural protein genes and 133 regulatory or other non-structural protein genes were identifiable among the six P. larvae phages. Jimmer1, Jimmer2, and Davies formed stable lysogens resistant to superinfection by genetically similar phages. The correlation between tape measure protein gene length and phage tail length allowed identification of co-isolated phages Emery and Abouo in electron micrographs. A Phamerator database was assembled with the P. larvae phage genomes and 107 genomes of Firmicute-infecting phages, including 71 Bacillus phages. Phamerator identified conserved domains in 1,501 of 6,181 phamilies (only 24.3%) encoded by genes in the database and revealed that P. larvae phage genomes shared at least one phamily with 72 of the 107 other phages. The phamily relationship of large terminase proteins was used to indicate putative DNA packaging strategies. Analyses from CoreGenes, Phamerator, and electron micrograph measurements indicated Jimmer1, Jimmer2, Abouo and Davies were related to phages phiC2, EJ-1, KC5a, and AQ113, which are small-genome myoviruses that infect Streptococcus, Lactobacillus, and Clostridium, respectively.ConclusionsThis paper represents the first comparison of phage genomes in the Paenibacillus genus and the first organization of P. larvae phages based on sequence and structure. This analysis provides an important contribution to the field of bacteriophage genomics by serving as a foundation on which to build an understanding of the natural predators of P. larvae.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-745) contains supplementary material, which is available to authorized users.

show abstract

“…The online tool FrameD [25] was used to search for frameshift mutations. Core genes were identified using the program CoreGenes 3.5 [57, 58] with the default BLASTP threshold of 75.…”

Section: Methodsmentioning

confidence: 99%

Characterization of Paenibacillus larvae bacteriophages and their genomic relationships to firmicute bacteriophages

et al. 2014

View full text Add to dashboard Cite

show abstract

“…Since the results of homology searches indicate that the similarity between ArV1 and other Arthrobacter phages listed above is not limited to the head and tail morphogenesis genes, the CoreGenes3.5 comparison program (54), which proved to be …”

mentioning

confidence: 99%

Molecular Analysis of Arthrobacter Myovirus vB_ArtM-ArV1: We Blame It on the Tail

Kalinienė

Šimoliūnas

Truncaitė

et al. 2017

J Virol

View full text Add to dashboard Cite

This is the first report on a myophage that infects Arthrobacter. A novel virus, vB_ArtM-ArV1 (ArV1), was isolated from soil using Arthrobacter sp. strain 68b for phage propagation. Transmission electron microscopy showed its resemblance to members of the family Myoviridae: ArV1 has an isometric head (ϳ74 nm in diameter) and a contractile, nonflexible tail (ϳ192 nm). Phylogenetic and comparative sequence analyses, however, revealed that ArV1 has more genes in common with phages from the family Siphoviridae than it does with any myovirus characterized to date. The genome of ArV1 is a linear, circularly permuted, double-stranded DNA molecule (71,200 bp) with a GC content of 61.6%. The genome includes 101 open reading frames (ORFs) yet contains no tRNA genes. More than 50% of ArV1 genes encode unique proteins that either have no reliable identity to database entries or have homologues only in Arthrobacter phages, both sipho-and myoviruses. Using bioinformatics approaches, 13 ArV1 structural genes were identified, including those coding for head, tail, tail fiber, and baseplate proteins. A further 6 ArV1 ORFs were annotated as encoding putative structural proteins based on the results of proteomic analysis. Phylogenetic analysis based on the alignment of four conserved virion proteins revealed that Arthrobacter myophages form a discrete clade that seems to occupy a position somewhat intermediate between myo-and siphoviruses. Thus, the data presented here will help to advance our understanding of genetic diversity and evolution of phages that constitute the order Caudovirales. IMPORTANCE Bacteriophages, which likely originated in the early Precambrian Era, represent the most numerous population on the planet. Approximately 95% of known phages are tailed viruses that comprise three families: Podoviridae (with short tails), Siphoviridae (with long noncontractile tails), and Myoviridae (with contractile tails). Based on the current hypothesis, myophages, which may have evolved from siphophages, are thought to have first emerged among Gram-negative bacteria, whereas they emerged only later among Gram-positive bacteria. The results of the molecular characterization of myophage vB_ArtM-ArV1 presented here conform to the aforementioned hypothesis, since, at a glance, bacteriophage vB_ArtM-ArV1 appears to be a siphovirus that possesses a seemingly functional contractile tail. Our work demonstrates that such "chimeric" myophages are of cosmopolitan nature and are likely characteristic of the ecologically important soil bacterial genus Arthrobacter.KEYWORDS Arthrobacter, Myoviridae, Siphoviridae, bacterial viruses, bacteriophage evolution, tailed viruses, vB_ArtM-ArV1

show abstract

“…The relatedness of these two phages was further explored using progressiveMauve (Fig. 2) (58, 59), CoreGenes (60,61), which the Bacterial and Archaeal Virus Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) has used extensively to compare the proteomes of viruses, and phylogenetic analysis of their whole-genome sequences (see Fig. S6) and their large terminase subunit protein sequences (Fig.…”

Section: Resultsmentioning

confidence: 99%

Yersinia enterocolitica-Specific Infection by Bacteriophages TG1 and ϕR1-RT Is Dependent on Temperature-Regulated Expression of the Phage Host Receptor OmpF

León-Velarde

Happonen

Pajunen

et al. 2016

Appl Environ Microbiol

View full text Add to dashboard Cite

Bacteriophages present huge potential both as a resource for developing novel tools for bacterial diagnostics and for use in phage therapy. This potential is also valid for bacteriophages specific for Yersinia enterocolitica. To increase our knowledge of Y. enterocolitica-specific phages, we characterized two novel yersiniophages. The genomes of the bacteriophages vB_YenM_TG1 (TG1) and vB_YenM_R1-RT (R1-RT), isolated from pig manure in Canada and from sewage in Finland, consist of linear double-stranded DNA of 162,101 and 168,809 bp, respectively. Their genomes comprise 262 putative coding sequences and 4 tRNA genes and share 91% overall nucleotide identity. Based on phylogenetic analyses of their whole-genome sequences and large terminase subunit protein sequences, a genus named Tg1virus within the family Myoviridae is proposed, with TG1 and R1-RT (R1RT in the ICTV database) as member species. These bacteriophages exhibit a host range restricted to Y. enterocolitica and display lytic activity against the epidemiologically significant serotypes O:3, O:5,27, and O:9 at and below 25°C. Adsorption analyses of lipopolysaccharide (LPS) and OmpF mutants demonstrate that these phages use both the LPS inner core heptosyl residues and the outer membrane protein OmpF as phage receptors. Based on RNA sequencing and quantitative proteomics, we also demonstrate that temperature-dependent infection is due to strong repression of OmpF at 37°C. In addition, R1-RT was shown to be able to enter into a pseudolysogenic state. Together, this work provides further insight into phage-host cell interactions by highlighting the importance of understanding underlying factors which may affect the abundance of phage host receptors on the cell surface. IMPORTANCEOnly a small number of bacteriophages infecting Y. enterocolitica, the predominant causative agent of yersiniosis, have been previously described. Here, two newly isolated Y. enterocolitica phages were studied in detail, with the aim of elucidating the host cell receptors required for infection. Our research further expands the repertoire of phages available for consideration as potential antimicrobial agents or as diagnostic tools for this important bacterial pathogen.Y ersinia enterocolitica, a facultative anaerobic, Gram-negative, nonsporulating, short bacillus isolated frequently from soil, water, animals, and foods, is an important zoonotic pathogen leading to human and animal enteric infection (1). The main animal reservoir for Y. enterocolitica is pigs, and pork-derived products are thought to be the main source of human infections, in addition to the drinking of contaminated water and blood transfusions (1, 2). Symptoms of yersiniosis may include diarrhea, terminal ileitis, mesenteric lymphadenitis, and septicemia (3). Among the species within the genus Yersinia, Y. enterocolitica is highly heterogeneous and is grouped into six phylogroups (4). The widely used bioserotype groups form the basis of the phylogroups such that phylogroup 1 contains the biotype 1A strains,...

show abstract

CoreGenes3.5: a webserver for the determination of core genes from sets of viral and small bacterial genomes

Cited by 68 publications

References 20 publications

Characterization of Paenibacillus larvae bacteriophages and their genomic relationships to firmicute bacteriophages

Characterization of Paenibacillus larvae bacteriophages and their genomic relationships to firmicute bacteriophages

Molecular Analysis of Arthrobacter Myovirus vB_ArtM-ArV1: We Blame It on the Tail

Yersinia enterocolitica-Specific Infection by Bacteriophages TG1 and ϕR1-RT Is Dependent on Temperature-Regulated Expression of the Phage Host Receptor OmpF

Contact Info

Product

Resources

About