Which phage gene callers are people using?

We are curious how people annotate their phage genomes, and so we looked at both the genbank records and the literature.

According to the 169 GenBank records that report how the ORFs were identified, approximately 1/3 of the annotations that report a gene caller use Glimmer (44 of 169 records with this information), approximately 2/3 use prodigal (122/169) and three used GeneMarkS.

We also explored the recent literature, looking at phage genome papers from 2017 and 2018. As shown below, a lot of people use RAST (which uses Glimmer for phages, I believe), or Prodigal (often as a component of PROKKA).

 

Title	Gene Caller(s)	Reference
Biology and Genomics of an Historic Therapeutic Escherichia coli Bacteriophage Collection	Prodigal	(Baig et al., 2017)
Characterization and Complete Genome Sequence of a Novel Siphoviridae Bacteriophage BS5	RAST	(Meng et al., 2017)
Characterization and genome analysis of novel bacteriophages infecting the opportunistic human pathogens Klebsiella oxytoca and K. pneumoniae	Glimmer; GenemarkS; FgenesV	(Park et al., 2017)
Characterization of vB_SauM-fRuSau02, a Twort-Like Bacteriophage Isolated from a Therapeutic Phage Cocktail	RAST	(Leskinen et al., 2017)
Comparative genomics of Cp8viruses with special reference to Campylobacter phage vB_CjeM_los1, isolated from a slaughterhouse in Ireland.	Glimmer/Prodigal	(O’Sullivan et al., 2018)
Complete genome sequence of a novel virulent phage ST31 infecting Escherichia coli H21	PHASTER	(Liu et al., 2018)
Complete Genome Sequence of Escherichia coli Phage vB_EcoS Sa179lw, Isolated from Surface Water in a Produce-Growing Area in Northern California	Prodigal	(Liao et al., 2018)
Complete Genome Sequence of EtG, the First Phage Sequenced from Erwinia tracheiphila	RAST; PHAST	(Andrade-Domínguez et al., 2018)
Complete genome sequence of lytic bacteriophage RG-2014 that infects the multidrug resistant bacterium Delftia tsuruhatensis ARB-1	GeneMarkS	(Bhattacharjee et al., 2017)
Complete genome sequence of Pseudoalteromonas phage vB_PspS-H40/1 (formerly H40/1) that infects Pseudoalteromonas sp. strain H40 and is used as biological tracer in hydrological transport studies	RAST. Glimmer3, GeneMark.hmm	(Kallies et al., 2017)
Complete Genome Sequence of Sinorhizobium meliloti Bacteriophage HMSP1-Susan	GeneMark; DNAmaster	(Fleagle et al., 2018)
Complete Genome Sequence of Streptococcus pneumoniae Virulent Phage MS1	RASTtk	(Kot et al., 2017)
Complete Genome Sequences of 38 Gordonia sp. Bacteriophages	GeneMark; Glimmer	(Pope et al., 2017)
Complete nucleotide sequence of a new filamentous phage, Xf109, which integrates its genome into the chromosomal DNA of Xanthomonas oryzae	SerialCloner	(Yeh, 2017)
Discovery and Complete Genome Sequence of a Bacteriophage from an Obligate Intracellular Symbiont of a Cellulolytic Protist in the Termite Gut	RAST / Metavir	(Pramono et al., 2017)
Genome Analysis of a Novel Broad Host Range Proteobacteria Phage Isolated from a Bioreactor Treating Industrial Wastewater	Glimmer	(de Leeuw et al., 2017)
Genome characteristics and environmental distribution of the first phage that infects the LD28 clade, a freshwater methylotrophic bacterial group	RAST/GLIMMER/GENEMARK	(Moon et al., 2017)
Genome of a giant bacteriophage from a decaying Trichodesmium bloom	RAST	(Pfreundt et al., 2017)
Genome Sequence of a New Siphoviridae Phage Found in a Brazilian Bacillus thuringiensis Serovar israelensis Strain	Geneious	(Campos et al., 2018)
Genome Sequence of Escherichia coli Tailed Phage Utah	Geneious	(Leavitt et al., 2017)
Genome Sequence of Serratia marcescens Phage BF	Prodigal	(Casey et al., 2017)
Genome Sequence of the Pseudomonas protegens Phage ΦGP100	RAST; PHASTER	(Vacheron et al., 2018)
Genome Sequences of Chancellor, Mitti, and Wintermute, Three Subcluster K4 Phages Isolated Using Mycobacterium smegmatis mc2155	GeneMark; Glimmer	(Edgington et al., 2017)
Genomic analysis of WCP30 Phage of Weissella cibaria for Dairy Fermented Foods	NCBI ORF Finder	(Lee and Park, 2017)
Genomic Diversity of Type B3 Bacteriophages of Caulobacter crescentus	RAST	(Ash et al., 2017)
Isolation and Complete Genome Sequence of a Novel Pseudoalteromonas Phage PH357 from the Yangtze River Estuary	RAST	(Gong et al., 2017)
Large Preferred Region for Packaging of Bacterial DNA by phiC725A, a Novel Pseudomonas aeruginosa F116-Like Bacteriophage	Geneious	(Pourcel et al., 2017)
Phage-host interactions in Streptococcus thermophilus: Genome analysis of phages isolated in Uruguay and ectopic spacer acquisition in CRISPR array	NCBI ORF Finder	(Achigar et al., 2017)
Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades	RAST	(Kupczok et al., 2018)
Sequencing, genome analysis and host range of a novel Ralstonia phage, RsoP1EGY, isolated in Egypt	GeneMarkS	(Ahmad et al., 2018)
Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genom	GeneMark.hmm for prokaryotes; NCBI ORF Finder	(Johnson et al., 2017)
The genome sequence of Escherichia coli tailed phage D6 and the diversity of Enterobacteriales circular plasmid prophages	Snapgene; GenemarkS	(Gilcrease and Casjens, 2018)
The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile	Prodigal	(Ramírez-Vargas et al., 2018)
The smallest ssDNA phage infecting a marine bacterium	GeneMark.hmm; ;GeneMarkS; NCBI ORF Finder	(Zhan and Chen, 2018)
Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB	Glimmer; GenemarkS	(Buttimer et al., 2017)

References

Achigar,R. et al. (2017) Phage-host interactions in Streptococcus thermophilus: Genome analysis of phages isolated in Uruguay and ectopic spacer acquisition in CRISPR array. Sci. Rep., 7, 43438.

Ahmad,A.A. et al. (2018) Sequencing, genome analysis and host range of a novel Ralstonia phage, RsoP1EGY, isolated in Egypt. Arch. Virol., 163, 2271–2274.

Andrade-Domínguez,A. et al. (2018) Complete Genome Sequence of EtG, the First Phage Sequenced from Erwinia tracheiphila. Genome Announc., 6.

Ash,K.T. et al. (2017) Genomic Diversity of Type B3 Bacteriophages of Caulobacter crescentus. Curr. Microbiol., 74, 779–786.

Baig,A. et al. (2017) Biology and Genomics of an Historic Therapeutic Escherichia coli Bacteriophage Collection. Front. Microbiol., 8, 1652.

Bhattacharjee,A.S. et al. (2017) Complete genome sequence of lytic bacteriophage RG-2014 that infects the multidrug resistant bacterium Delftia tsuruhatensis ARB-1. Stand. Genomic Sci., 12, 82.

Buttimer,C. et al. (2017) Things Are Getting Hairy: Enterobacteria Bacteriophage vB_PcaM_CBB. Front. Microbiol., 8, 44.

Campos,F.S. et al. (2018) Genome Sequence of a New Siphoviridae Phage Found in a Brazilian Bacillus thuringiensis Serovar israelensis Strain. Genome Announc., 6.

Casey,E. et al. (2017) Genome Sequence of Serratia marcescens Phage BF. Genome Announc., 5.

Edgington,N.P. et al. (2017) Genome Sequences of Chancellor, Mitti, and Wintermute, Three Subcluster K4 Phages Isolated Using Mycobacterium smegmatis mc2155. Genome Announc., 5.

Fleagle,B. et al. (2018) Complete Genome Sequence of Sinorhizobium meliloti Bacteriophage HMSP1-Susan. Genome Announc., 6.

Gilcrease,E.B. and Casjens,S.R. (2018) The genome sequence of Escherichia coli tailed phage D6 and the diversity of Enterobacteriales circular plasmid prophages. Virology, 515, 203–214.

Gong,Z. et al. (2017) Isolation and Complete Genome Sequence of a Novel Pseudoalteromonas Phage PH357 from the Yangtze River Estuary. Curr. Microbiol., 74, 832–839.

Johnson,M.C. et al. (2017) Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genome. J. Struct. Biol., 200, 343–359.

Kallies,R. et al. (2017) Complete genome sequence of Pseudoalteromonas phage vB_PspS-H40/1 (formerly H40/1) that infects Pseudoalteromonas sp. strain H40 and is used as biological tracer in hydrological transport studies. Stand. Genomic Sci., 12, 20.

Kot,W. et al. (2017) Complete Genome Sequence of Streptococcus pneumoniae Virulent Phage MS1. Genome Announc., 5.

Kupczok,A. et al. (2018) Rates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades. Mol. Biol. Evol., 35, 1147–1159.

Leavitt,J.C. et al. (2017) Genome Sequence of Escherichia coli Tailed Phage Utah. Genome Announc., 5.

de Leeuw,M. et al. (2017) Genome Analysis of a Novel Broad Host Range Proteobacteria Phage Isolated from a Bioreactor Treating Industrial Wastewater. Genes , 8.

Lee,Y.-D. and Park,J.-H. (2017) Genomic analysis of WCP30 Phage of Weissella cibaria for Dairy Fermented Foods. Korean J Food Sci Anim Resour, 37, 884–888.

Leskinen,K. et al. (2017) Characterization of vB_SauM-fRuSau02, a Twort-Like Bacteriophage Isolated from a Therapeutic Phage Cocktail. Viruses, 9.

Liao,Y.-T. et al. (2018) Complete Genome Sequence of Escherichia coli Phage vB_EcoS Sa179lw, Isolated from Surface Water in a Produce-Growing Area in Northern California. Genome Announc., 6.

Liu,H. et al. (2018) Complete genome sequence of a novel virulent phage ST31 infecting Escherichia coli H21. Arch. Virol., 163, 1993–1996.

Meng,X. et al. (2017) Characterization and Complete Genome Sequence of a Novel Siphoviridae Bacteriophage BS5. Curr. Microbiol., 74, 815–820.

Moon,K. et al. (2017) Genome characteristics and environmental distribution of the first phage that infects the LD28 clade, a freshwater methylotrophic bacterial group. Environ. Microbiol., 19, 4714–4727.

O’Sullivan,L. et al. (2018) Comparative genomics of Cp8viruses with special reference to Campylobacter phage vB_CjeM_los1, isolated from a slaughterhouse in Ireland. Arch. Virol., 163, 2139–2154.

Park,E.-A. et al. (2017) Characterization and genome analysis of novel bacteriophages infecting the opportunistic human pathogens Klebsiella oxytoca and K. pneumoniae. Arch. Virol., 162, 1129–1139.

Pfreundt,U. et al. (2017) Genome of a giant bacteriophage from a decaying Trichodesmium bloom. Mar. Genomics, 33, 21–25.

Pope,W.H. et al. (2017) Complete Genome Sequences of 38 Gordonia sp. Bacteriophages. Genome Announc., 5.

Pourcel,C. et al. (2017) Large Preferred Region for Packaging of Bacterial DNA by phiC725A, a Novel Pseudomonas aeruginosa F116-Like Bacteriophage. PLoS One, 12, e0169684.

Pramono,A.K. et al. (2017) Discovery and Complete Genome Sequence of a Bacteriophage from an Obligate Intracellular Symbiont of a Cellulolytic Protist in the Termite Gut. Microbes Environ., 32, 112–117.

Ramírez-Vargas,G. et al. (2018) The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile. Front. Microbiol., 9, 26.

Vacheron,J. et al. (2018) Genome Sequence of the Pseudomonas protegens Phage ΦGP100. Genome Announc., 6.

Yeh,T.Y. (2017) Complete nucleotide sequence of a new filamentous phage, Xf109, which integrates its genome into the chromosomal DNA of Xanthomonas oryzae. Arch. Virol., 162, 567–572.

Zhan,Y. and Chen,F. (2018) The smallest ssDNA phage infecting a marine bacterium: The smallest marine ssDNA bacteriophage. Environ. Microbiol.