We express our gratitude to the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science Program for its support in this work. Microbial strains used in this work were provided by the USDA-ARS Culture Collection (NRRL).
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R","lastName":"Seares","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":""},{"affiliations":["University of North Texas, Denton, Texas, United States"],"departments":["Biological Sciences"],"credit":["investigation","writing_originalDraft","writing_reviewEditing"],"email":"tiireoluwaleyithomas-eshokhai@my.unt.edu","firstName":"Tiireoluwaleyi E","lastName":"Thomas-Eshokhai","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":""},{"affiliations":["University of North Texas, Denton, Texas, United States"],"departments":["Biological Sciences"],"credit":["investigation","writing_originalDraft","writing_reviewEditing"],"email":"SnehaTony@my.unt.edu","firstName":"Sneha","lastName":"Tony","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":""},{"affiliations":["University of North Texas, Denton, Texas, United States"],"departments":["Biological 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","dataTable":{"url":"https://portal.micropublication.org/uploads/2adfa2421c41c2798542cd73b0b87717.csv"},"extendedData":[],"funding":"N/A
","image":{"url":"https://portal.micropublication.org/uploads/bd5b4a1bfd52cd048400c73eccb3e9ca.jpg"},"imageCaption":"Plaque morphology on lawns of Streptomyces bicolor for (A) Dexers, (B) Jhitchelle, (C) Kaine,(D) Marav, (E) Pavo, (F) Provolone, (G) SheRa, (H) Speedwell, and (I) Sudan shown on standard 100mm diameter plates. Table: Bacteriophage genome characteristics.
","imageTitle":"Plaque Morphology
","methods":"","reagents":"","patternDescription":"Over 400 Streptomyces phage genomes have been sequenced and grouped into 20 clusters (BA–BT), with additional unclustered phages, in the Actinobacteriophage database (https://phagesdb.org/). Contributing to this diversity, nine bacteriophages—Dexers, Jhitchelle, Kaine, Marav, Pavo, Provolone, SheRa, Speedwell, and Sudan—were isolated from soil samples collected in Texas and Georgia using Streptomyces bicolor NRRL B-3897 as the host (Table 1). These phages add to the growing catalog of actinobacteriophages and provide further insight into genomic diversity in phages infecting Streptomyces.
Isolation was performed using an enrichment method. Briefly, soil samples were suspended in nutrient broth, inoculated with S. bicolor, and the mixture incubated while shaking at 30°C for two days (Poxleitner et al., 2017; Zorawik et al., 2024). Following incubation, samples were centrifuged and filtered through 0.22-μm filters, then spread plated on nutrient agar supplemented with MgCl₂, Ca(NO₃)₂, and glucose. Individual plaques were purified through a minimum of three rounds of serial dilution and replating, and high-titer lysates (>1 × 10⁸ PFU/mL) were obtained through multi-plate amplification. All isolates produced clear, circular plaques. Plaque diameters ranged from 0.25 to 2 mm (Figure 1).
DNA extraction was performed using the Promega Wizard DNA Cleanup System. Genomic DNA was sequenced at the University of Pittsburgh Bacteriophage Institute (Dexers, Kaine, Marav, Pavo, Provolone, SheRa, Speedwell) or the University of North Texas Genomics Center (Jhitchelle, Sudan) using Illumina sequencing. Sequencing libraries were prepared with the NEB Ultra II Library Kit, and 75-base single-end reads (Jhitchelle, Sudan), 100-base single-end reads (Kaine, Pavo, Speedwell) or 150-base single-end reads (Dexers, Marav, Provolone, SheRa) were generated on an Illumina MiSeq instrument using v3 reagents. Reads were assembled into single contigs following the method described by Russell (2018) using Newbler v2.9 (Miller et al., 2010) and Consed v29 (Gordon et al., 1998). Sequencing outcomes and genome characteristics are summarized in Table 1. All nine phages possess linear genomes with 3′ sticky overhang ends. Marav has 11-base overhangs (CGCCACGTCTT); Dexers, Jhitchelle, Kaine, Pavo, Provolone, Speedwell, and Sudan have 11-base overhangs (CGGTACGTGAT); and SheRa has a 9-base overhangs (CGCCGCCCT).
Annotation was conducted using multiple bioinformatics tools with default settings used for all software. Tools included DNA Master (Pope & Jacobs-Sera, 2018) for genome visualization, auto-annotation, and manual annotation refinement, PECAAN (Rinehart et al., 2016) for evidence integration and guided annotation support, Glimmer v.3.02 (Delcher et al., 2007) and GeneMark v.2.5 (Besemer & Borodovsky, 2005) for predicting protein-coding genes, Phamerator (Actiono_draft database v578) (Cresawn et al., 2011) for comparing gene content and synteny among related phages, BLASTp and NCBI BLAST v.2.13 (Altschul et al., 1990) for identifying similarity to known genes, HHpred (using databases: PDB_mmCIF70, NCBI_Conserved_Domains, and Pfam- v.36) (Söding et al., 2005) for detecting remote protein homology and predicting function, Aragorn v.1.2.41 (Laslett & Canback, 2004) and tRNAscan-SE v. 2.0.12 (Lowe & Chan, 2016) for identifying tRNA genes, and DeepTMHMM v.1.0.44 (Hallgren et al., 2022) for predicting transmembrane domains.
Based on shared gene content similarity greater than 85%, Marav was assigned to subcluster BD2; Dexers, Jhitchelle, Kaine, Pavo, Provolone, Speedwell, and Sudan were assigned to subcluster BD3, and SheRa to subcluster BI2. The GC content for all nine phages was over 60%, consistent with other Streptomyces phages. Functionally, the cluster BD phages isolated in this study encode a putative serine integrase from a gene phamily commonly found in other cluster BD phages, suggesting a temperate life cycle. However, SheRa lacks an identifiable integrase and, like other BI2 phages, is likely lytic. Marav was the only genome in this study to contain a tRNA gene, encoding for phenylalanine [Phe(GAA)]. About a third of all annotated members of subcluster BD2 also contain a single tRNA. With the isolation of the phages in this study, S. bicolor becomes the fourteenth different species on which cluster BD phages have been isolated and the tenth species for BI phages. While these genomes show similarity with genomes isolated on other Streptomyces host species and fit within existing actinobacteriophage clusters, they also exhibit new genetic diversity. Six of the nine isolates contain genes that do not fit into existing gene phamilies (1 each in Jhitchelle [gp49], Kaine [gp51], Marav [gp7], Pavo [gp53], and Sudan [gp4]; 3 in Speedwell [gp9, gp10, gp12]).
Nucleotide Sequence Accession Numbers
The GenBank and SRA accession numbers for the phages in this study are: Dexers (Accession No. OQ995439, SRA No. SRX21368059), Jhitchelle (Accession No. PZ319869, SRA No. SRX33201634), Kaine (Accession No. PQ723753, SRA No. SRX28484020), Marav (Accession No. OQ995441, SRA No. SRX20165769), Pavo (Accession No. PQ723757, SRA No. SRX28484025), Provolone (Accession No. OQ995429, SRA No. SRX21368081), SheRa (Accession No. OQ995437, SRA No. SRX21368085), Speedwell (Accession No. PQ723754, SRA No. SRX28484031), and Sudan (Accession No. PZ319862, SRA No. SRX33201643).
","references":[{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: A Graphical Tool for Sequence Finishing. Genome Research 8: 195-202.
","pubmedId":"","doi":"10.1101/gr.8.3.195"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Chan PP. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Research 44: W54-W57.
","pubmedId":"","doi":"10.1093/nar/gkw413"},{"reference":"Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data. Genomics 95: 315-327.
","pubmedId":"","doi":"10.1016/j.ygeno.2010.03.001"},{"reference":"Pope WH, Jacobs-Sera D. 2017. Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview. Methods in Molecular Biology,Bacteriophages : 217-229.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Poxleitner M, Hughes, L, Pope W, Jacobs-Sera D, Sivanathan V, Hatfull, G. 2017. Phage discovery guide, Streptomyces spp. Howard Hughes Medical Institute, Chevy Chase, MD.
","pubmedId":"","doi":""},{"reference":"Rinehart CA, Gaffney B, Wood JD, Smith J. 2016. PECAAN, a phage evidence collection and annotation network. Available from: https://discover.kbrinsgd.org/login
","pubmedId":"","doi":""},{"reference":"Russell DA. 2017. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods in Molecular Biology,Bacteriophages : 109-125.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods in Molecular Biology,Phage Engineering and Analysis : 273-298.
","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Genome Sequences of Nine Bacteriophages Infecting Streptomyces bicolor: Dexers, Jhitchelle, Kaine, Marav, Pavo, Provolone, SheRa, Speedwell, and Sudan
","reviews":[{"reviewer":{"displayName":"Marie Fogarty"},"openAcknowledgement":true,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"45d91afc-68a0-42a0-b894-da35befd4898","decision":"accept","abstract":"Bacteriophages Dexers, Jhitchelle, Kaine, Marav, Pavo, Provolone, SheRa, Speedwell, and Sudan were isolated on Streptomyces bicolor NRRL B-3897. These bacteriophages have genomes sizes spanning 43–50 kbp with 59–82 genes and assigned to clusters BD2, BD3, and BI1. Only one, Marav, encodes a tRNA. These are the first bacteriophage isolates reported for this species of Streptomyces.
","acknowledgements":"We express our gratitude to the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science Program for its support in this work. Microbial strains used in this work were provided by the USDA-ARS Culture Collection (NRRL).
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","dataTable":{"url":"https://portal.micropublication.org/uploads/2adfa2421c41c2798542cd73b0b87717.csv"},"extendedData":[],"funding":"N/A
","image":{"url":"https://portal.micropublication.org/uploads/bd5b4a1bfd52cd048400c73eccb3e9ca.jpg"},"imageCaption":"Plaque morphology on lawns of Streptomyces bicolor for (A) Dexers, (B) Jhitchelle, (C) Kaine,(D) Marav, (E) Pavo, (F) Provolone, (G) SheRa, (H) Speedwell, and (I) Sudan shown on standard 100mm diameter plates. Table 1: Bacteriophage genome characteristics.
","imageTitle":"Plaque Morphology
","methods":"","reagents":"","patternDescription":"The genus Streptomyces is diverse, contains many industrially-important species, and is best known for the large number of antibiotics produced by its members. Over 400 Streptomyces bacteriophage genomes have been sequenced and grouped into 20 clusters (BA–BT), with additional unclustered bacteriophages, in the Actinobacteriophage database (https://phagesdb.org/). Contributing to this diversity, nine bacteriophages—Dexers, Jhitchelle, Kaine, Marav, Pavo, Provolone, SheRa, Speedwell, and Sudan—were isolated from soil samples collected in Texas and Georgia using Streptomyces bicolor NRRL B-3897 as the host (Table 1). These bacteriophages add to the growing catalog of actinobacteriophages and provide further insight into genomic diversity in bacteriophages infecting Streptomyces.
Isolation was performed using an enrichment method. Briefly, soil samples were suspended in nutrient broth, inoculated with S. bicolor, and the mixture incubated while shaking at 30°C for two days (Poxleitner et al., 2017; Zorawik et al., 2024). Following incubation, samples were centrifuged and filtered through 0.22-μm filters, then spread plated on nutrient agar supplemented with MgCl₂, Ca(NO₃)₂, and glucose. Individual plaques were purified through a minimum of three rounds of serial dilution and replating, and high-titer lysates (>1 × 10⁸ PFU/mL) were obtained through multi-plate amplification. All isolates produced clear, circular plaques. Plaque diameters ranged from 0.25 to 2 mm (Figure 1).
DNA extraction was performed using the Promega Wizard DNA Cleanup System. Genomic DNA was sequenced at the University of Pittsburgh Bacteriophage Institute (Dexers, Kaine, Marav, Pavo, Provolone, SheRa, Speedwell) or the University of North Texas Genomics Center (Jhitchelle, Sudan) using Illumina sequencing. Sequencing libraries were prepared with the NEB Ultra II Library Kit, and 75-base single-end reads (Jhitchelle, Sudan), 100-base single-end reads (Kaine, Pavo, Speedwell) or 150-base single-end reads (Dexers, Marav, Provolone, SheRa) were generated on an Illumina MiSeq instrument using v3 reagents. Reads were assembled into single contigs following the method described by Russell (2018) using Newbler v2.9 (Miller et al., 2010) and Consed v29 (Gordon et al., 1998). Sequencing outcomes and genome characteristics are summarized in Table 1. All nine bacteriophages possess linear genomes with 3′ sticky overhang ends. Marav has 11-base overhangs (CGCCACGTCTT); Dexers, Jhitchelle, Kaine, Pavo, Provolone, Speedwell, and Sudan have 11-base overhangs (CGGTACGTGAT); and SheRa has a 9-base overhangs (CGCCGCCCT).
Annotation was conducted using multiple bioinformatics tools with default settings used for all software. Tools included DNA Master (Pope & Jacobs-Sera, 2018) for genome visualization, auto-annotation, and manual annotation refinement, PECAAN (Rinehart et al., 2016) for evidence integration and guided annotation support, Glimmer v.3.02 (Delcher et al., 2007) and GeneMark v.2.5 (Besemer & Borodovsky, 2005) for predicting protein-coding genes, Phamerator (Actiono_draft database v578) (Cresawn et al., 2011) for comparing gene content and synteny among related phages, BLASTp and NCBI BLAST v.2.13 (Altschul et al., 1990) for identifying similarity to known genes, HHpred (using databases: PDB_mmCIF70, NCBI_Conserved_Domains, and Pfam- v.36) (Söding et al., 2005) for detecting remote protein homology and predicting function, Aragorn v.1.2.41 (Laslett & Canback, 2004) and tRNAscan-SE v. 2.0.12 (Lowe & Chan, 2016) for identifying tRNA genes, and DeepTMHMM v.1.0.44 (Hallgren et al., 2022) for predicting transmembrane domains.
Based on shared gene content similarity greater than 35%, Marav was assigned to subcluster BD2; Dexers, Jhitchelle, Kaine, Pavo, Provolone, Speedwell, and Sudan were assigned to subcluster BD3, and SheRa to subcluster BI2. The GC content for all nine bacteriophages was over 60%, consistent with other Streptomyces bacteriophages. Functionally, the cluster BD bacteriophages isolated in this study encode a putative serine integrase from a gene phamily commonly found in other cluster BD phages, suggesting a temperate life cycle. However, SheRa lacks an identifiable integrase and, like other BI2 phages, is likely lytic. Marav was the only genome in this study to contain a tRNA gene, encoding for phenylalanine [Phe(GAA)]. About a third of all annotated members of subcluster BD2 also contain a single tRNA. With the isolation of the bacteriophages in this study, S. bicolor becomes the fourteenth different species on which cluster BD bacteriophages have been isolated and the tenth species for BI bacteriophages. While these genomes show similarity with genomes isolated on other Streptomyces host species and fit within existing actinobacteriophage clusters, they also exhibit new genetic diversity. Six of the nine isolates contain genes that do not fit into existing gene phamilies (1 each in Jhitchelle [gp49], Kaine [gp51], Marav [gp7], Pavo [gp53], and Sudan [gp4]; 3 in Speedwell [gp9, gp10, gp12]).
Nucleotide Sequence Accession Numbers
The GenBank and SRA accession numbers for the phages in this study are: Dexers (Accession No. OQ995439, SRA No. SRX21368059), Jhitchelle (Accession No. PZ319869, SRA No. SRX33201634), Kaine (Accession No. PQ723753, SRA No. SRX28484020), Marav (Accession No. OQ995441, SRA No. SRX20165769), Pavo (Accession No. PQ723757, SRA No. SRX28484025), Provolone (Accession No. OQ995429, SRA No. SRX21368081), SheRa (Accession No. OQ995437, SRA No. SRX21368085), Speedwell (Accession No. PQ723754, SRA No. SRX28484031), and Sudan (Accession No. PZ319862, SRA No. SRX33201643).
","references":[{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: A Graphical Tool for Sequence Finishing. Genome Research 8: 195-202.
","pubmedId":"","doi":"10.1101/gr.8.3.195"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Chan PP. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Research 44: W54-W57.
","pubmedId":"","doi":"10.1093/nar/gkw413"},{"reference":"Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data. Genomics 95: 315-327.
","pubmedId":"","doi":"10.1016/j.ygeno.2010.03.001"},{"reference":"Pope WH, Jacobs-Sera D. 2017. Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview. Methods in Molecular Biology,Bacteriophages : 217-229.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Poxleitner M, Hughes, L, Pope W, Jacobs-Sera D, Sivanathan V, Hatfull, G. 2017. Phage discovery guide, Streptomyces spp. Howard Hughes Medical Institute, Chevy Chase, MD.
","pubmedId":"","doi":""},{"reference":"Rinehart CA, Gaffney B, Wood JD, Smith J. 2016. PECAAN, a phage evidence collection and annotation network. Available from: https://discover.kbrinsgd.org/login
","pubmedId":"","doi":""},{"reference":"Russell DA. 2017. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods in Molecular Biology,Bacteriophages : 109-125.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods in Molecular Biology,Phage Engineering and Analysis : 273-298.
","pubmedId":"","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Genome Sequences of Nine Bacteriophages Infecting Streptomyces bicolor: Dexers, Jhitchelle, Kaine, Marav, Pavo, Provolone, SheRa, Speedwell, and Sudan
","reviews":[],"curatorReviews":[]},{"id":"0b0872d1-a5f0-4879-b5bb-9b41b628b20f","decision":"publish","abstract":"Bacteriophages Dexers, Jhitchelle, Kaine, Marav, Pavo, Provolone, SheRa, Speedwell, and Sudan were isolated on Streptomyces bicolor NRRL B-3897. These bacteriophages have genomes sizes spanning 43–50 kbp with 59–82 genes and assigned to clusters BD2, BD3, and BI1. Only one, Marav, encodes a tRNA. These are the first bacteriophage isolates reported for this species of Streptomyces.
","acknowledgements":"We express our gratitude to the Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science Program for its support in this work. Microbial strains used in this work were provided by the USDA-ARS Culture Collection (NRRL).
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","dataTable":{"url":"https://portal.micropublication.org/uploads/2adfa2421c41c2798542cd73b0b87717.csv"},"extendedData":[],"funding":"N/A
","image":{"url":"https://portal.micropublication.org/uploads/bd5b4a1bfd52cd048400c73eccb3e9ca.jpg"},"imageCaption":"Plaque morphology on lawns of Streptomyces bicolor for (A) Dexers, (B) Jhitchelle, (C) Kaine,(D) Marav, (E) Pavo, (F) Provolone, (G) SheRa, (H) Speedwell, and (I) Sudan shown on standard 100mm diameter plates. Table 1: Bacteriophage genome characteristics.
","imageTitle":"Plaque Morphology
","methods":"","reagents":"","patternDescription":"The genus Streptomyces is diverse, contains many industrially-important species, and is best known for the large number of antibiotics produced by its members. Over 400 Streptomyces bacteriophage genomes have been sequenced and grouped into 21 clusters (BA–BT,JN), with additional unclustered bacteriophages, in the Actinobacteriophage database (https://phagesdb.org/). Contributing to this diversity, nine bacteriophages—Dexers, Jhitchelle, Kaine, Marav, Pavo, Provolone, SheRa, Speedwell, and Sudan—were isolated from soil samples collected in Texas and Georgia using Streptomyces bicolor NRRL B-3897 as the host (Table 1). These bacteriophages add to the growing catalog of actinobacteriophages and provide further insight into genomic diversity in bacteriophages infecting Streptomyces.
Isolation was performed using an enrichment method. Briefly, soil samples were suspended in nutrient broth, inoculated with S. bicolor, and the mixture incubated while shaking at 30°C for two days (Poxleitner et al., 2017; Zorawik et al., 2024). Following incubation, samples were centrifuged and filtered through 0.22-μm filters, then spread plated on nutrient agar supplemented with MgCl₂, Ca(NO₃)₂, and glucose. Individual plaques were purified through a minimum of three rounds of serial dilution and replating, and high-titer lysates (>1 × 10⁸ PFU/mL) were obtained through multi-plate amplification. All isolates produced clear, circular plaques. Plaque diameters ranged from 0.25 to 2 mm (Figure 1).
DNA extraction was performed using the Promega Wizard DNA Cleanup System. Genomic DNA was sequenced at the University of Pittsburgh Bacteriophage Institute (Dexers, Kaine, Marav, Pavo, Provolone, SheRa, Speedwell) or the University of North Texas Genomics Center (Jhitchelle, Sudan) using Illumina sequencing. Sequencing libraries were prepared with the NEB Ultra II Library Kit, and 75-base single-end reads (Jhitchelle, Sudan), 100-base single-end reads (Kaine, Pavo, Speedwell) or 150-base single-end reads (Dexers, Marav, Provolone, SheRa) were generated on an Illumina MiSeq instrument using v3 reagents. Reads were assembled into single contigs following the method described by Russell (2018) using Newbler v2.9 (Miller et al., 2010) and Consed v29 (Gordon et al., 1998). Sequencing outcomes and genome characteristics are summarized in Table 1. All nine bacteriophages possess linear genomes with 3′ sticky overhang ends. Marav has 11-base overhangs (CGCCACGTCTT); Dexers, Jhitchelle, Kaine, Pavo, Provolone, Speedwell, and Sudan have 11-base overhangs (CGGTACGTGAT); and SheRa has a 9-base overhangs (CGCCGCCCT).
Annotation was conducted using multiple bioinformatics tools with default settings used for all software. Tools included DNA Master (Pope & Jacobs-Sera, 2018) for genome visualization, auto-annotation, and manual annotation refinement, PECAAN (Rinehart et al., 2016) for evidence integration and guided annotation support, Glimmer v.3.02 (Delcher et al., 2007) and GeneMark v.2.5 (Besemer & Borodovsky, 2005) for predicting protein-coding genes, Phamerator (Actiono_draft database v578) (Cresawn et al., 2011) for comparing gene content and synteny among related phages, BLASTp and NCBI BLAST v.2.13 (Altschul et al., 1990) for identifying similarity to known genes, HHpred (using databases: PDB_mmCIF70, NCBI_Conserved_Domains, and Pfam- v.36) (Söding et al., 2005) for detecting remote protein homology and predicting function, Aragorn v.1.2.41 (Laslett & Canback, 2004) and tRNAscan-SE v. 2.0.12 (Lowe & Chan, 2016) for identifying tRNA genes, and DeepTMHMM v.1.0.44 (Hallgren et al., 2022) for predicting transmembrane domains.
Based on shared gene content similarity greater than 35%, Marav was assigned to subcluster BD2; Dexers, Jhitchelle, Kaine, Pavo, Provolone, Speedwell, and Sudan were assigned to subcluster BD3, and SheRa to subcluster BI2. The GC content for all nine bacteriophages was over 60%, consistent with other Streptomyces bacteriophages. Functionally, the cluster BD bacteriophages isolated in this study encode a putative serine integrase from a gene phamily commonly found in other cluster BD phages, suggesting a temperate life cycle. However, SheRa lacks an identifiable integrase and, like other BI2 phages, is likely lytic. Marav was the only genome in this study to contain a tRNA gene, encoding for phenylalanine [Phe(GAA)]. About a third of all annotated members of subcluster BD2 also contain a single tRNA. With the isolation of the bacteriophages in this study, S. bicolor becomes the fourteenth different species on which cluster BD bacteriophages have been isolated and the tenth species for BI bacteriophages. While these genomes show similarity with genomes isolated on other Streptomyces host species and fit within existing actinobacteriophage clusters, they also exhibit new genetic diversity. Six of the nine isolates contain genes that do not fit into existing gene phamilies (1 each in Jhitchelle [gp49], Kaine [gp51], Marav [gp7], Pavo [gp53], and Sudan [gp4]; 3 in Speedwell [gp9, gp10, gp12]).
Nucleotide Sequence Accession Numbers
The GenBank and SRA accession numbers for the phages in this study are: Dexers (Accession No. OQ995439, SRA No. SRX21368059), Jhitchelle (Accession No. PZ319869, SRA No. SRX33201634), Kaine (Accession No. PQ723753, SRA No. SRX28484020), Marav (Accession No. OQ995441, SRA No. SRX20165769), Pavo (Accession No. PQ723757, SRA No. SRX28484025), Provolone (Accession No. OQ995429, SRA No. SRX21368081), SheRa (Accession No. OQ995437, SRA No. SRX21368085), Speedwell (Accession No. PQ723754, SRA No. SRX28484031), and Sudan (Accession No. PZ319862, SRA No. SRX33201643).
","references":[{"reference":"Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
","pubmedId":"","doi":"10.1016/S0022-2836(05)80360-2"},{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 33: W451-W454.
","pubmedId":"","doi":"10.1093/nar/gki487"},{"reference":"Cresawn SG, Bogel M, Day N, Jacobs-Sera D, Hendrix RW, Hatfull GF. 2011. Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12: 10.1186/1471-2105-12-395.
","pubmedId":"","doi":"10.1186/1471-2105-12-395"},{"reference":"Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
","pubmedId":"","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: A Graphical Tool for Sequence Finishing. Genome Research 8: 195-202.
","pubmedId":"","doi":"10.1101/gr.8.3.195"},{"reference":"Hallgren J, Tsirigos KD, Pedersen MD, Almagro Armenteros JJ, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. : 10.1101/2022.04.08.487609.
","pubmedId":"","doi":"10.1101/2022.04.08.487609"},{"reference":"Laslett D. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Research 32: 11-16.
","pubmedId":"","doi":"10.1093/nar/gkh152"},{"reference":"Lowe TM, Chan PP. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Research 44: W54-W57.
","pubmedId":"","doi":"10.1093/nar/gkw413"},{"reference":"Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data. Genomics 95: 315-327.
","pubmedId":"","doi":"10.1016/j.ygeno.2010.03.001"},{"reference":"Pope WH, Jacobs-Sera D. 2017. Annotation of Bacteriophage Genome Sequences Using DNA Master: An Overview. Methods in Molecular Biology,Bacteriophages : 217-229.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_16"},{"reference":"Poxleitner M, Hughes, L, Pope W, Jacobs-Sera D, Sivanathan V, Hatfull, G. 2017. Phage discovery guide, Streptomyces spp. Howard Hughes Medical Institute, Chevy Chase, MD.
","pubmedId":"","doi":""},{"reference":"Rinehart CA, Gaffney B, Wood JD, Smith J. 2016. PECAAN, a phage evidence collection and annotation network. Available from: https://discover.kbrinsgd.org/login
","pubmedId":"","doi":""},{"reference":"Russell DA. 2017. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods in Molecular Biology,Bacteriophages : 109-125.
","pubmedId":"","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 33: W244-W248.
","pubmedId":"","doi":"10.1093/nar/gki408"},{"reference":"Zorawik M, Jacobs-Sera D, Freise AC, SEA-PHAGES, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods in Molecular Biology,Phage Engineering and Analysis : 273-298.
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