LastNadiia and Mireles are novel bacteriophages of Arthrobacter globiformis isolated from eastern Texas soil. Both exhibit siphoviral morphology and belong to the recently established cluster FR. Their genomes display the characteristic cluster FR organization, with predominantly forward-transcribed genes in the first half and reverse-transcribed genes in the second half. Neither genome contains identifiable lysogeny-associated genes, suggesting a lytic lifestyle.
","acknowledgements":"LastNadiia and Mireles were isolated and annotated at East Texas A&M University through the Science Education Alliance–Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program. This work was supported by the Howard Hughes Medical Institute (HHMI) SEA-PHAGES program and the School of Science and Engineering at East Texas A&M University. We thank the SEA-PHAGES Review-to-Improve Quality Control (QC) team for their guidance during genome annotation and review and gratefully acknowledge the MINT team for their assistance during manuscript revision. We are grateful to T. deCarvalho at the Keith R. Porter Imaging Facility, University of Maryland, Baltimore County, for generating the transmission electron micrographs. We also thank Graham F. Hatfull, Deborah Jacobs-Sera, and Daniel A. Russell at the University of Pittsburgh for genome sequencing and assembly.
","authors":[{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis"],"email":"kvoroshylo@leomail.tamuc.edu","firstName":"Kateryna","lastName":"Voroshylo","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration"],"email":"nfigueroa3@leomail.tamuc.edu","firstName":"Neyda","lastName":"Figueroa","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis"],"email":"ksantana@leomail.tamuc.edu","firstName":"Karina","lastName":"Santana","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis"],"email":"tbizzell@leomail.tamuc.edu","firstName":"Traniece","lastName":"Bizzell","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis"],"email":"gcerda1@leomail.tamuc.edu","firstName":"Gerardo","lastName":"Cerda","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis"],"email":"calixto@leomail.tamuc.edu","firstName":"Lesly","lastName":"Calixto","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis"],"email":"mhowell6@leomail.tamuc.edu","firstName":"Makayla","lastName":"Howell","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":""},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration"],"email":"pbelt1@leomail.tamuc.edu","firstName":"Payten","lastName":"Belt","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","project"],"email":"sfathima1@leomail.tamuc.edu","firstName":"Shabnam","lastName":"Fathima","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["conceptualization","project","formalAnalysis"],"email":"venu.cheriyath@etamu.edu","firstName":"Venugopalan","lastName":"Cheriyath","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-6424-2813"},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","investigation","project","supervision"],"email":"archana.srinivas@etamu.edu","firstName":"Archana","lastName":"Srinivas","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["formalAnalysis","project","supervision","validation","writing_originalDraft","writing_reviewEditing"],"email":"hyun-joo.nam@etamu.edu","firstName":"Hyun-Joo","lastName":"Nam","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":true,"WBId":null,"orcid":"0000-0002-0235-9311"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":"https://portal.micropublication.org/uploads/963733122b5a2d675cb5904ea307e1d9.csv"},"extendedData":[],"funding":"Funding was provided by the Department of Biological and Environmental Sciences, East Texas A&M University.
","image":{"url":"https://portal.micropublication.org/uploads/08a609a7f2b970c4dce815cefcffbfc1.png"},"imageCaption":"Transmission electron micrographs of LastNadiia (A) and Mireles (B) showing siphovirus morphology. The scale bar represents 200 nm, with tick marks indicating 20 nm intervals.
Table: Genome and Sequencing Characteristics of Bacteriophages LastNadiia and Mireles.
","imageTitle":"Transmission electron micrographs of LastNadiia and Mireles
","methods":"","reagents":"","patternDescription":"Continued efforts to isolate and characterize novel bacteriophages have expanded our understanding of phage diversity, evolution, and genome organization (Heller et al., 2024). Here, we report the isolation, morphological characterization, and genome sequencing and annotation of LastNadiia and Mireles, two novel bacteriophages with predicted lytic lifestyles that infect Arthrobacter globiformis B-2979.LastNadiia and Mireles were isolated from soil samples obtained in eastern Texas. The sample containing phage LastNadiia was collected on the East Texas A&M University campus near Charles S. Garvin Lake (33.24377° N, 95.91124° W), whereas phage Mireles was isolated from a sample collected from a natural storm water basin in Caddo Mills, Texas, USA (33.04428° N, 96.2313° W). The phages were isolated following the established protocol(Zorawik et al., 2024). Briefly, soil samples were suspended in PYCa medium, vortexed, and filtered through a 0.22-µm membrane. The filtrates were inoculated with Arthrobacter globiformis B-2979 and incubated at 30°C for 48 h. Following enrichment, the cultures were filtered and filtrates plated with A. globiformis B-2979 using the soft-agar overlay method. Initial plaques were small and heterogeneous; after three rounds of plaque purification, both LastNadiia and Mireles formed clear, well-defined plaques ranging in size between 1.5 to 3 mm in diameter. Transmission electron microscopy (TEM) of high-titer lysates performed using Hitachi HT7800 is 120 kV TEM equipped with an AMT Nanosprint15 B camera, and a brightfield STEM and an Oxford Xplore EDS detector revealed that both phages exhibit siphovirus morphology, characterized by an icosahedral capsid and a long, flexible, noncontractile tail (Fig. 1 A and B). TEM analyses showed that LastNadiia has a capsid diameter of approximately 60 nm and a tail length of 122 nm (n=1) while Mireles has 53-nm head and a 120-nm tail (n=1). Genomic DNA was extracted from high-titer lysates using the Promega Wizard DNA Clean-Up Kit. Sequencing libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit and sequenced on an Illumina NextSeq 1000 (XLEAP-P1 kit) at the Pittsburgh Bacteriophage Institute. Raw reads were trimmed with cutadapt 4.7 (using the option: –nextseq-trim 30) and filtered with skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly (Jiang et al., 2014; Martin, 2011; Wick et al., 2017). Illumina shotgun sequencing reads for both LastNadiia and Mireles were assembled using Newbler v2.9 (Miller et al., 2010), producing a single contig for each genome. Assembly completeness, accuracy, and genomic termini were verified using Consed v29 (Chung et al., 2017; Gordon et al., 1998; Russell, 2018). The LastNadiia and Mireles genomes are 41,591 bp and 41,147 bp, with GC contents of 58.5% and 58.6%, respectively. Both genomes contain identical 10-base 3′ cohesive ends (5′-TTTACGGCAT-3′). A summary of the sequencing results and genomic characteristics of LastNadiia and Mireles is provided in Table 1.Genome annotation of LastNadiia and Mireles began with automated gene prediction using Glimmer v3.02 (Delcher et al., 2007) and GeneMark v2.5 (Besemer and Borodovsky, 2005), followed by manual refinement in PECAAN v2.0 (http://discover.kbringsgd.org) which integrates multiple annotation tools. Gene start sites were evaluated using Phamerator (Actino_draft database v578) (Cresawn et al., 2011) and Starterator v627 (phages.wustl.edu/starterator/). Putative gene functions were assigned based on BLASTp v2.2.26 searches against the Actinobacteriophage and NCBI databases (Boratyn et al., 2013), and HHPred searches against the PDB_mmCIF70, pfam-A-v37.4, NCBI_Conserved_Domains (CD), and SCOPe70_2.08 and tRNAscan-SE databases (Soding et al., 2005). Membrane proteins were predicted with DeepTMHMM v1.0.42 (Hallgren et al., 2022). No tRNA genes were identified in either genome using Aragorn v1.2.38 (Chan and Lowe, 2019; Laslett and Canback, 2004). All software was run with default settings. The LastNadiia genome contains 66 predicted protein-coding genes were predicted, 35 of which were assigned putative functions. Of the remaining hypothetical genes, one was classified as an orpham. In Mireles, 68 protein-coding genes were predicted, including 33 with putative functional assignments. Among the remaining hypothetical genes, five were identified as orphams. No immunity-related genes were detected in either genome, consistent with the predicted lytic lifestyle of both phages.\n\nLastNadiia and Mireles were assigned to the cluster FR based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, phagesdb (Pope et al., 2017; Russell and Hatfull, 2017). The cluster FR is a recently established cluster, with its first members reported in 2024, and currently comprises 11 fully annotated bacteriophages (Robinson et al., 2025). All FR phages exhibit a conserved genome organization, with most forward-transcribed genes located in the first half of the genome and predominantly reverse-transcribed genes in the second half. A single forward-transcribed gene is embedded within the reverse-transcribed region, followed by a terminal forward-transcribed gene at the end of the genome. These findings expand our understanding of Arthrobacter phages in the recently established cluster FR by defining key genomic and morphological features of LastNadiia and Mireles.Discovery and Genome Annotation of Arthrobacter Bacteriophages LastNadiia and Mireles Isolated from Soil in Eastern Texas
","reviews":[],"curatorReviews":[]},{"id":"0476ba1a-3f0a-45bd-a1dd-d9127b132513","decision":"revise","abstract":"LastNadiia and Mireles are novel bacteriophages of Arthrobacter globiformis isolated from eastern Texas soil. Both exhibit siphoviral morphology and belong to the recently established cluster FR. Their genomes display the characteristic cluster FR organization, with predominantly forward-transcribed genes in the first half and reverse-transcribed genes in the second half. Neither genome contains identifiable lysogeny-associated genes, suggesting a lytic lifestyle.
","acknowledgements":"LastNadiia and Mireles were isolated and annotated at East Texas A&M University through the Science Education Alliance–Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program. This work was supported by the Howard Hughes Medical Institute (HHMI) SEA-PHAGES program and the School of Science and Engineering at East Texas A&M University. We thank the SEA-PHAGES Review-to-Improve Quality Control (QC) team for their guidance during genome annotation and review and gratefully acknowledge the MINT team for their assistance during manuscript revision. We are grateful to T. deCarvalho at the Keith R. Porter Imaging Facility, University of Maryland, Baltimore County, for generating the transmission electron micrographs. We also thank Graham F. Hatfull, Deborah Jacobs-Sera, and Daniel A. Russell at the University of Pittsburgh for genome sequencing and assembly.
","authors":[{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis"],"email":"kvoroshylo@leomail.tamuc.edu","firstName":"Kateryna","lastName":"Voroshylo","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration"],"email":"nfigueroa3@leomail.tamuc.edu","firstName":"Neyda","lastName":"Figueroa","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis"],"email":"ksantana@leomail.tamuc.edu","firstName":"Karina","lastName":"Santana","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis"],"email":"tbizzell@leomail.tamuc.edu","firstName":"Traniece","lastName":"Bizzell","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis"],"email":"gcerda1@leomail.tamuc.edu","firstName":"Gerardo","lastName":"Cerda","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis"],"email":"calixto@leomail.tamuc.edu","firstName":"Lesly","lastName":"Calixto","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis"],"email":"mhowell6@leomail.tamuc.edu","firstName":"Makayla","lastName":"Howell","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":""},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration"],"email":"pbelt1@leomail.tamuc.edu","firstName":"Payten","lastName":"Belt","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","project"],"email":"sfathima1@leomail.tamuc.edu","firstName":"Shabnam","lastName":"Fathima","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["conceptualization","project","formalAnalysis"],"email":"venu.cheriyath@etamu.edu","firstName":"Venugopalan","lastName":"Cheriyath","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-6424-2813"},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","investigation","project","supervision"],"email":"archana.srinivas@etamu.edu","firstName":"Archana","lastName":"Srinivas","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["formalAnalysis","project","supervision","validation","writing_originalDraft","writing_reviewEditing"],"email":"hyun-joo.nam@etamu.edu","firstName":"Hyun-Joo","lastName":"Nam","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":true,"WBId":null,"orcid":"0000-0002-0235-9311"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":"https://portal.micropublication.org/uploads/963733122b5a2d675cb5904ea307e1d9.csv"},"extendedData":[],"funding":"Funding was provided by the Department of Biological and Environmental Sciences, East Texas A&M University.
","image":{"url":"https://portal.micropublication.org/uploads/08a609a7f2b970c4dce815cefcffbfc1.png"},"imageCaption":"Transmission electron micrographs of LastNadiia (A) and Mireles (B) showing siphovirus morphology. The scale bar represents 200 nm, with tick marks indicating 20 nm intervals.
Table: Genome and Sequencing Characteristics of Bacteriophages LastNadiia and Mireles.
","imageTitle":"Transmission electron micrographs of LastNadiia and Mireles
","methods":"","reagents":"","patternDescription":"Continued efforts to isolate and characterize novel bacteriophages have expanded our understanding of phage diversity, evolution, and genome organization (Heller et al., 2024). Here, we report the isolation, morphological characterization, and genome sequencing and annotation of LastNadiia and Mireles, two novel bacteriophages with predicted lytic lifestyles that infect Arthrobacter globiformis B-2979. LastNadiia and Mireles were isolated from soil samples obtained in eastern Texas. The sample containing phage LastNadiia was collected on the East Texas A&M University campus near Charles S. Garvin Lake (33.24377° N, 95.91124° W), whereas phage Mireles was isolated from a sample collected from a natural storm water basin in Caddo Mills, Texas, USA (33.04428° N, 96.2313° W). The phages were isolated following the established protocol(Zorawik et al., 2024). Briefly, soil samples were suspended in PYCa medium, vortexed, and filtered through a 0.22-µm membrane. The filtrates were inoculated with Arthrobacter globiformis B-2979 and incubated at 30°C for 48 h. Following enrichment, the cultures were filtered and filtrates plated with A. globiformis B-2979 using the soft-agar overlay method. Initial plaques were small and heterogeneous; after three rounds of plaque purification, both LastNadiia and Mireles formed clear, well-defined plaques ranging in size between 1.5 to 3 mm in diameter. Transmission electron microscopy (TEM) of high-titer lysates performed using Hitachi HT7800 is 120 kV TEM equipped with an AMT Nanosprint15 B camera, and a brightfield STEM and an Oxford Xplore EDS detector revealed that both phages exhibit siphovirus morphology, characterized by an icosahedral capsid and a long, flexible, noncontractile tail (Fig. 1 A and B). TEM analyses showed that LastNadiia has a capsid diameter of approximately 60 nm and a tail length of 122 nm (n=1) while Mireles has 53-nm head and a 120-nm tail (n=1). Genomic DNA was extracted from high-titer lysates using the Promega Wizard DNA Clean-Up Kit. Sequencing libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit and sequenced on an Illumina NextSeq 1000 (XLEAP-P1 kit) at the Pittsburgh Bacteriophage Institute. Raw reads were trimmed with cutadapt 4.7 (using the option: –nextseq-trim 30) and filtered with skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly (Jiang et al., 2014; Martin, 2011; Wick et al., 2017). Illumina shotgun sequencing reads for both LastNadiia and Mireles were assembled using Newbler v2.9 (Miller et al., 2010), producing a single contig for each genome. Assembly completeness, accuracy, and genomic termini were verified using Consed v29 (Chung et al., 2017; Gordon et al., 1998; Russell, 2018). The LastNadiia and Mireles genomes are 41,591 bp and 41,147 bp, with GC contents of 58.5% and 58.6%, respectively. Both genomes contain identical 10-base 3′ cohesive ends (5′-TTTACGGCAT-3′). A summary of the sequencing results and genomic characteristics of LastNadiia and Mireles is provided in Table 1. Genome annotation of LastNadiia and Mireles began with automated gene prediction using Glimmer v3.02 (Delcher et al., 2007) and GeneMark v2.5 (Besemer and Borodovsky, 2005), followed by manual refinement in PECAAN v2.0 (http://discover.kbringsgd.org) which integrates multiple annotation tools. Gene start sites were evaluated using Phamerator (Actino_draft database v578) (Cresawn et al., 2011) and Starterator v627 (phages.wustl.edu/starterator/). Putative gene functions were assigned based on BLASTp v2.2.26 searches against the Actinobacteriophage and NCBI databases (Boratyn et al., 2013), and HHPred searches against the PDB_mmCIF70, pfam-A-v37.4, NCBI_Conserved_Domains (CD), and SCOPe70_2.08 and tRNAscan-SE databases (Soding et al., 2005). Membrane proteins were predicted with DeepTMHMM v1.0.42 (Hallgren et al., 2022). No tRNA genes were identified in either genome using Aragorn v1.2.38 (Chan and Lowe, 2019; Laslett and Canback, 2004). All software was run with default settings. The LastNadiia genome contains 66 predicted protein-coding genes were predicted, 35 of which were assigned putative functions. Of the remaining hypothetical genes, one was classified as an orpham. In Mireles, 68 protein-coding genes were predicted, including 33 with putative functional assignments. Among the remaining hypothetical genes, five were identified as orphams. No immunity-related genes were detected in either genome, consistent with the predicted lytic lifestyle of both phages.\n\nLastNadiia and Mireles were assigned to the cluster FR based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, phagesdb (Pope et al., 2017; Russell and Hatfull, 2017). The cluster FR is a recently established cluster, with its first members reported in 2024, and currently comprises 11 fully annotated bacteriophages (Robinson et al., 2025). All FR phages exhibit a conserved genome organization, with most forward-transcribed genes located in the first half of the genome and predominantly reverse-transcribed genes in the second half. A single forward-transcribed gene is embedded within the reverse-transcribed region, followed by a terminal forward-transcribed gene at the end of the genome. These findings expand our understanding of Arthrobacter phages in the recently established cluster FR by defining key genomic and morphological features of LastNadiia and Mireles.","references":[{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 33: W451–4. 1.","pubmedId":"15980510","doi":"10.1093/nar/gki487"},{"reference":"Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N, et al., Zaretskaya I. 2013. BLAST: a more efficient report with usability improvements. Nucleic Acids Res. 41: W29–33. 2.","pubmedId":"23609542","doi":"10.1093/nar/gkt282"},{"reference":"Chan PP, Lowe TM. 2019. tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods Mol Biol. 1962: 1–14. 3.","pubmedId":"31020551","doi":"10.1007/978-1-4939-9173-0_1"},{"reference":"Chung CH, Walter MH, Yang L, Chen SG, Winston V, Thomas MA. 2017. 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Methods Mol Biol. 1681: 109–125. 20.","pubmedId":"29134591","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Russell DA, Hatfull GF. 2017. PhagesDB: the actinobacteriophage database. Bioinformatics. 33: 784–786. 16.","pubmedId":"28365761","doi":"10.1093/bioinformatics/btw711"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33: W244–8. 17.","pubmedId":"15980461","doi":"10.1093/nar/gki408"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 13: e1005595. 18.","pubmedId":"28594827","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zorawik M, Jacobs Sera D, Freise AC, Sea P, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods Mol Biol. 2793: 273–298. 19.","pubmedId":"38526736","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Discovery and Genome Annotation of Arthrobacter Bacteriophages LastNadiia and Mireles Isolated from Soil in Eastern Texas
","reviews":[{"reviewer":{"displayName":"Victoria Frost"},"openAcknowledgement":false,"status":{"submitted":true}}],"curatorReviews":[]},{"id":"ab41c77b-2c92-4495-aa0d-9f5ed2ab5add","decision":"accept","abstract":"LastNadiia and Mireles are novel bacteriophages of Arthrobacter globiformis isolated from eastern Texas soil. Both exhibit siphoviral morphology and belong to the recently established cluster FR. Their genomes display the characteristic cluster FR organization, with predominantly forward-transcribed genes in the first half and reverse-transcribed genes in the second half. Neither genome contains identifiable lysogeny-associated genes, suggesting a lytic lifestyle.
","acknowledgements":"LastNadiia and Mireles were isolated and annotated at East Texas A&M University through the Science Education Alliance–Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program. This work was supported by the Howard Hughes Medical Institute (HHMI) SEA-PHAGES program and the School of Science and Engineering at East Texas A&M University. We thank the SEA-PHAGES Review-to-Improve Quality Control (QC) team for their guidance during genome annotation and review and gratefully acknowledge the MINT team for their assistance during manuscript revision. We are grateful to T. deCarvalho at the Keith R. Porter Imaging Facility, University of Maryland, Baltimore County, for generating the transmission electron micrographs. We also thank Graham F. Hatfull, Deborah Jacobs-Sera, and Daniel A. Russell at the University of Pittsburgh for genome sequencing and assembly.
","authors":[{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"kvoroshylo@leomail.tamuc.edu","firstName":"Kateryna","lastName":"Voroshylo","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration"],"email":"nfigueroa3@leomail.tamuc.edu","firstName":"Neyda","lastName":"Figueroa","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"ksantana@leomail.tamuc.edu","firstName":"Karina","lastName":"Santana","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"tbizzell@leomail.tamuc.edu","firstName":"Traniece","lastName":"Bizzell","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"gcerda1@leomail.tamuc.edu","firstName":"Gerardo","lastName":"Cerda","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"calixto@leomail.tamuc.edu","firstName":"Lesly","lastName":"Calixto","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"mhowell6@leomail.tamuc.edu","firstName":"Makayla","lastName":"Howell","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":""},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","writing_originalDraft"],"email":"pbelt1@leomail.tamuc.edu","firstName":"Payten","lastName":"Belt","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","project"],"email":"sfathima1@leomail.tamuc.edu","firstName":"Shabnam","lastName":"Fathima","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["conceptualization","project","formalAnalysis","resources"],"email":"venu.cheriyath@etamu.edu","firstName":"Venugopalan","lastName":"Cheriyath","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-6424-2813"},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","investigation","project","supervision","writing_originalDraft"],"email":"archana.srinivas@etamu.edu","firstName":"Archana","lastName":"Srinivas","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["formalAnalysis","project","supervision","validation","writing_originalDraft","writing_reviewEditing"],"email":"hyun-joo.nam@etamu.edu","firstName":"Hyun-Joo","lastName":"Nam","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":true,"WBId":null,"orcid":"0000-0002-0235-9311"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":"https://portal.micropublication.org/uploads/963733122b5a2d675cb5904ea307e1d9.csv"},"extendedData":[],"funding":"Funding was provided by the Department of Biological and Environmental Sciences, East Texas A&M University.
","image":{"url":"https://portal.micropublication.org/uploads/08a609a7f2b970c4dce815cefcffbfc1.png"},"imageCaption":"Transmission electron micrographs of LastNadiia (A) and Mireles (B), negatively stained with 1% uranyl acetate, showing siphovirus morphology. Scale bars represent 200 nm, with tick marks indicating 20 nm intervals.
Table: Genome and Sequencing Characteristics of Bacteriophages LastNadiia and Mireles.
","imageTitle":"Transmission electron micrographs of LastNadiia and Mireles
","methods":"","reagents":"","patternDescription":"Continued efforts to isolate and characterize novel bacteriophages have expanded our understanding of phage diversity, evolution, and genome organization (Heller et al., 2024). Here, we report the isolation, morphological characterization, and genome sequencing and annotation of LastNadiia and Mireles, two novel bacteriophages with predicted lytic lifestyles that infect Arthrobacter globiformis B-2979. LastNadiia and Mireles were isolated from soil samples obtained in eastern Texas. The sample containing phage LastNadiia was collected on the East Texas A&M University campus near Charles S. Garvin Lake (33.24377° N, 95.91124° W), whereas phage Mireles was isolated from a sample collected from a natural stormwater basin in Caddo Mills, Texas, USA (33.04428° N, 96.2313° W). The phages were isolated following the established protocol(Zorawik et al., 2024). Briefly, soil samples were suspended in PYCa medium, vortexed, and filtered through a 0.22-µm membrane. The filtrates were inoculated with Arthrobacter globiformis B-2979 and incubated at 30°C for 48 h. Following enrichment, the cultures were filtered, and the filtrates were plated with A. globiformis B-2979 using the soft-agar overlay method. Initial plaques were small and heterogeneous; after three rounds of plaque purification, both LastNadiia and Mireles formed clear, well-defined plaques ranging from 1.5 to 3 mm in diameter (n = 6). Transmission electron microscopy (TEM) of high-titer lysates was performed using a Hitachi HT7800 microscope operated at an accelerating voltage of 120 kV and equipped with an AMT Nanosprint15 B camera, bright-field STEM, and an Oxford Xplore EDS detector. TEM images showed that both phages exhibit siphovirus morphology, characterized by an icosahedral capsid and a long, flexible, noncontractile tail (Fig. 1 A and B). TEM analyses showed that LastNadiia has a capsid diameter of approximately 60 nm and a tail length of 122 nm (n = 1), while Mireles has a 53 nm head diameter and a 120 nm tail length (n = 1). Genomic DNA was extracted from high-titer lysates using the Promega Wizard DNA Clean-Up Kit. Sequencing libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit and sequenced on an Illumina NextSeq 1000 (XLEAP-P1 kit) at the Pittsburgh Bacteriophage Institute. Raw reads were trimmed with cutadapt 4.7 (using the option: –nextseq-trim 30) and filtered with skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly (Jiang et al., 2014; Martin, 2011; Wick et al., 2017). Illumina shotgun sequencing reads for both LastNadiia and Mireles were assembled using Newbler v2.9 (Miller et al., 2010), producing a single contig for each genome. Assembly completeness, accuracy, and genomic termini were verified using Consed v29 (Chung et al., 2017; Gordon et al., 1998; Russell, 2018). The LastNadiia and Mireles genomes are 41,591 bp and 41,147 bp, with GC contents of 58.5% and 58.6%, respectively. Both genomes contain identical 10-base 3′ cohesive ends (5′-TTTACGGCAT-3′). A summary of the sequencing results and genomic characteristics of LastNadiia and Mireles is provided in Table 1. Genome annotation of LastNadiia and Mireles began with automated gene prediction using Glimmer v3.02 (Delcher et al., 2007) and GeneMark v2.5 (Besemer and Borodovsky, 2005), followed by manual refinement in PECAAN v2.0 (http://discover.kbringsgd.org) which integrates multiple annotation tools. Gene start sites were evaluated using Phamerator (Actino_draft database v578) (Cresawn et al., 2011) and Starterator v627 (phages.wustl.edu/starterator/). Putative gene functions were assigned based on BLASTp v2.2.26 searches against the Actinobacteriophage and NCBI databases (Boratyn et al., 2013), and HHPred searches against the PDB_mmCIF70, pfam-A-v37.4, NCBI_Conserved_Domains (CD), and SCOPe70_2.08 and tRNAscan-SE databases (Soding et al., 2005). Membrane proteins were predicted with DeepTMHMM v1.0.42 (Hallgren et al., 2022). No tRNA genes were identified in either genome using Aragorn v1.2.38 (Chan and Lowe, 2019; Laslett and Canback, 2004). All software was run with default settings. The LastNadiia genome contains 66 predicted protein-coding genes, 35 of which were assigned putative functions. Of the remaining hypothetical genes, one was classified as an orpham. In Mireles, 68 protein-coding genes were predicted, including 33 with putative functional assignments. Among the remaining hypothetical genes, five were identified as orphams. No immunity-related genes were detected in either genome, consistent with the predicted lytic lifestyle of both phages. LastNadiia and Mireles were assigned to the cluster FR based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, phagesdb (Pope et al., 2017; Russell and Hatfull, 2017). The cluster FR is a recently established cluster, with its first members reported in 2024, and currently comprises 11 fully annotated bacteriophages (Robinson et al., 2025). All FR phages exhibit a conserved genome organization, with most forward-transcribed genes located in the first half of the genome and predominantly reverse-transcribed genes in the second half. A single forward-transcribed gene is embedded within the reverse-transcribed region, followed by a terminal forward-transcribed gene at the end of the genome. These findings expand our understanding of Arthrobacter phages in the recently established cluster FR by defining key genomic and morphological features of LastNadiia and Mireles.
","references":[{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 33: W451–4. 1.","pubmedId":"15980510","doi":"10.1093/nar/gki487"},{"reference":"Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N, et al., Zaretskaya I. 2013. BLAST: a more efficient report with usability improvements. Nucleic Acids Res. 41: W29–33. 2.","pubmedId":"23609542","doi":"10.1093/nar/gkt282"},{"reference":"Chan PP, Lowe TM. 2019. tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods Mol Biol. 1962: 1–14. 3.","pubmedId":"31020551","doi":"10.1007/978-1-4939-9173-0_1"},{"reference":"Chung CH, Walter MH, Yang L, Chen SG, Winston V, Thomas MA. 2017. Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data. BMC Genomics. 18: 350. 4.","pubmedId":"28472946","doi":"10.1186/s12864-017-3744-0"},{"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: 395. 5.","pubmedId":"21991981","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: 673–9. 6.","pubmedId":"17237039","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8: 195–202. 7.","pubmedId":"9521923","doi":"10.1101/gr.8.3.195"},{"reference":"Hallgren J, Tsirigos K, Pedersen M, Armenteros J, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. 8.","pubmedId":"","doi":""},{"reference":"Heller DM, Sivanathan V, Asai DJ, Hatfull GF. 2024. SEA-PHAGES and SEA-GENES: Advancing Virology and Science Education. Annu Rev Virol. 11: 1–20. 9.","pubmedId":"38684129","doi":"10.1146/annurev-virology-113023-110757"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics. 15: 182. 10.","pubmedId":"24925680","doi":"10.1186/1471-2105-15-182"},{"reference":"Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32: 11–6. 11.","pubmedId":"14704338","doi":"10.1093/nar/gkh152"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. 17 12.","pubmedId":"","doi":"https://doi.org/10.14806/ej.17.1.200"},{"reference":"Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data. Genomics. 95: 315–27. 13.","pubmedId":"20211242","doi":"10.1016/j.ygeno.2010.03.001"},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero Bustamante CA, Jacobs Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships. mBio. 8 14.","pubmedId":"28811342","doi":"10.1128/mBio.01069-17"},{"reference":"Robinson SE, Stanford E, Abraham S, Aguilera R, Anantoji NS, Barillas M, et al., Pollenz RS. 2025. Genome Sequences of Alatato and Audell, two Phages that infect Arthrobacter globiformis and have Different Life Cycles. MicroPubl Biol. 2025 15.","pubmedId":"41426959","doi":"10.17912/micropub.biology.001786"},{"reference":"Russell DA. 2018. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods Mol Biol. 1681: 109–125. 20.","pubmedId":"29134591","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Russell DA, Hatfull GF. 2017. PhagesDB: the actinobacteriophage database. Bioinformatics. 33: 784–786. 16.","pubmedId":"28365761","doi":"10.1093/bioinformatics/btw711"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33: W244–8. 17.","pubmedId":"15980461","doi":"10.1093/nar/gki408"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 13: e1005595. 18.","pubmedId":"28594827","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zorawik M, Jacobs Sera D, Freise AC, Sea P, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods Mol Biol. 2793: 273–298. 19.","pubmedId":"38526736","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Discovery and Genome Annotation of Arthrobacter Bacteriophages LastNadiia and Mireles Isolated from Soil in Eastern Texas
","reviews":[],"curatorReviews":[]},{"id":"f1f3362b-95b4-4a10-9c85-bc69c173f5e4","decision":"revise","abstract":"LastNadiia and Mireles are novel bacteriophages of Arthrobacter globiformis isolated from eastern Texas soil. Both exhibit siphoviral morphology and belong to the recently established cluster FR. Their genomes display the characteristic cluster FR organization, with predominantly forward-transcribed genes in the first half and reverse-transcribed genes in the second half. Neither genome contains identifiable lysogeny-associated genes, suggesting a lytic lifestyle.
","acknowledgements":"LastNadiia and Mireles were isolated and annotated at East Texas A&M University through the Science Education Alliance–Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program. This work was supported by the Howard Hughes Medical Institute (HHMI) SEA-PHAGES program and the School of Science and Engineering at East Texas A&M University. We thank the SEA-PHAGES Review-to-Improve Quality Control (QC) team for their guidance during genome annotation and review and gratefully acknowledge the MINT team for their assistance during manuscript revision. We are grateful to T. deCarvalho at the Keith R. Porter Imaging Facility, University of Maryland, Baltimore County, for generating the transmission electron micrographs. We also thank Graham F. Hatfull, Deborah Jacobs-Sera, and Daniel A. Russell at the University of Pittsburgh for genome sequencing and assembly.
","authors":[{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"kvoroshylo@leomail.tamuc.edu","firstName":"Kateryna","lastName":"Voroshylo","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration"],"email":"nfigueroa3@leomail.tamuc.edu","firstName":"Neyda","lastName":"Figueroa","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"ksantana@leomail.tamuc.edu","firstName":"Karina","lastName":"Santana","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"tbizzell@leomail.tamuc.edu","firstName":"Traniece","lastName":"Bizzell","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"gcerda1@leomail.tamuc.edu","firstName":"Gerardo","lastName":"Cerda","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"calixto@leomail.tamuc.edu","firstName":"Lesly","lastName":"Calixto","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"mhowell6@leomail.tamuc.edu","firstName":"Makayla","lastName":"Howell","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":""},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","writing_originalDraft"],"email":"pbelt1@leomail.tamuc.edu","firstName":"Payten","lastName":"Belt","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","project"],"email":"sfathima1@leomail.tamuc.edu","firstName":"Shabnam","lastName":"Fathima","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["conceptualization","project","formalAnalysis","resources"],"email":"venu.cheriyath@etamu.edu","firstName":"Venugopalan","lastName":"Cheriyath","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-6424-2813"},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","investigation","project","supervision","writing_originalDraft"],"email":"archana.srinivas@etamu.edu","firstName":"Archana","lastName":"Srinivas","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M University"],"departments":["Biological and Environmental Sciences"],"credit":["formalAnalysis","project","supervision","validation","writing_originalDraft","writing_reviewEditing"],"email":"hyun-joo.nam@etamu.edu","firstName":"Hyun-Joo","lastName":"Nam","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":true,"WBId":null,"orcid":"0000-0002-0235-9311"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":"https://portal.micropublication.org/uploads/963733122b5a2d675cb5904ea307e1d9.csv"},"extendedData":[],"funding":"Funding was provided by the Department of Biological and Environmental Sciences, East Texas A&M University.
","image":{"url":"https://portal.micropublication.org/uploads/08a609a7f2b970c4dce815cefcffbfc1.png"},"imageCaption":"Transmission electron micrographs of LastNadiia (A) and Mireles (B), negatively stained with 1% uranyl acetate, showing siphovirus morphology. Scale bars represent 200 nm, with tick marks indicating 20 nm intervals.
Table: Genome and Sequencing Characteristics of Bacteriophages LastNadiia and Mireles.
","imageTitle":"Transmission electron micrographs of LastNadiia and Mireles
","methods":"","reagents":"","patternDescription":"Continued efforts to isolate and characterize novel bacteriophages have expanded our understanding of phage diversity, evolution, and genome organization (Heller et al., 2024). Here, we report the isolation, morphological characterization, and genome sequencing and annotation of LastNadiia and Mireles, two novel bacteriophages with predicted lytic lifestyles that infect Arthrobacter globiformis B-2979. LastNadiia and Mireles were isolated from soil samples obtained in eastern Texas. The sample containing phage LastNadiia was collected on the East Texas A&M University campus near Charles S. Garvin Lake (33.24377° N, 95.91124° W), whereas phage Mireles was isolated from a sample collected from a natural stormwater basin in Caddo Mills, Texas, USA (33.04428° N, 96.2313° W). The phages were isolated following the established protocol (Zorawik et al., 2024). Briefly, soil samples were suspended in PYCa medium, vortexed, and filtered through a 0.22-µm membrane. The filtrates were inoculated with Arthrobacter globiformis B-2979 and incubated at 30°C for 48 h. Following enrichment, the cultures were filtered, and the filtrates were plated with A. globiformis B-2979 using the soft-agar overlay method. Initial plaques were small and heterogeneous; after three rounds of plaque purification, both LastNadiia and Mireles formed clear, well-defined plaques ranging from 1.5 to 3 mm in diameter (n = 6). Transmission electron microscopy (TEM) of high-titer lysates was performed using a Hitachi HT7800 microscope operated at an accelerating voltage of 120 kV and equipped with an AMT Nanosprint15 B camera, bright-field STEM, and an Oxford Xplore EDS detector. TEM images showed that both phages exhibit siphovirus morphology, characterized by an icosahedral capsid and a long, flexible, noncontractile tail (Fig. 1 A and B). TEM analyses showed that LastNadiia has a capsid diameter of approximately 60 nm and a tail length of 122 nm (n = 1), while Mireles has a 53 nm head diameter and a 120 nm tail length (n = 1). Genomic DNA was extracted from high-titer lysates using the Promega Wizard DNA Clean-Up Kit. Sequencing libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit and sequenced on an Illumina NextSeq 1000 (XLEAP-P1 kit) at the Pittsburgh Bacteriophage Institute. Raw reads were trimmed with cutadapt 4.7 (using the option: –nextseq-trim 30) and filtered with skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly (Jiang et al., 2014; Martin, 2011; Wick et al., 2017). Illumina shotgun sequencing reads for both LastNadiia and Mireles were assembled using Newbler v2.9 (Miller et al., 2010), producing a single contig for each genome. Assembly completeness, accuracy, and genomic termini were verified using Consed v29 (Chung et al., 2017; Gordon et al., 1998; Russell, 2018). The LastNadiia and Mireles genomes are 41,591 bp and 41,147 bp, with GC contents of 58.5% and 58.6%, respectively. Both genomes contain identical 10-base 3′ cohesive ends (5′-TTTACGGCAT-3′). A summary of the sequencing results and genomic characteristics of LastNadiia and Mireles is provided in Table 1. Genome annotation of LastNadiia and Mireles began with automated gene prediction using Glimmer v3.02 (Delcher et al., 2007) and GeneMark v2.5 (Besemer and Borodovsky, 2005), followed by manual refinement in PECAAN v2.0 (http://discover.kbringsgd.org) which integrates multiple annotation tools. Gene start sites were evaluated using Phamerator (Actino_draft database v578) (Cresawn et al., 2011) and Starterator v627 (phages.wustl.edu/starterator/). Putative gene functions were assigned based on BLASTp v2.2.26 searches against the Actinobacteriophage and NCBI databases (Boratyn et al., 2013), and HHPred searches against the PDB_mmCIF70, pfam-A-v37.4, NCBI_Conserved_Domains (CD), and SCOPe70_2.08 and tRNAscan-SE databases (Soding et al., 2005). Membrane proteins were predicted with DeepTMHMM v1.0.42 (Hallgren et al., 2022). No tRNA genes were identified in either genome using Aragorn v1.2.38 (Chan and Lowe, 2019; Laslett and Canback, 2004). All software was run with default settings. The LastNadiia genome contains 66 predicted protein-coding genes, 35 of which were assigned putative functions. Of the remaining hypothetical genes, one was classified as an orpham. In Mireles, 68 protein-coding genes were predicted, including 33 with putative functional assignments. Among the remaining hypothetical genes, five were identified as orphams. No immunity-related genes were detected in either genome, consistent with the predicted lytic lifestyle of both phages. LastNadiia and Mireles were assigned to the cluster FR based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, phagesdb (Pope et al., 2017; Russell and Hatfull, 2017). The cluster FR is a recently established cluster, with its first members reported in 2024, and currently comprises 11 fully annotated bacteriophages (Robinson et al., 2025). All FR phages exhibit a conserved genome organization, with most forward-transcribed genes located in the first half of the genome and predominantly reverse-transcribed genes in the second half. A single forward-transcribed gene is embedded within the reverse-transcribed region, followed by a terminal forward-transcribed gene at the end of the genome. These findings expand our understanding of Arthrobacter phages in the recently established cluster FR by defining key genomic and morphological features of LastNadiia and Mireles.
","references":[{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 33: W451–4. 1.","pubmedId":"15980510","doi":"10.1093/nar/gki487"},{"reference":"Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N, et al., Zaretskaya I. 2013. BLAST: a more efficient report with usability improvements. Nucleic Acids Res. 41: W29–33. 2.","pubmedId":"23609542","doi":"10.1093/nar/gkt282"},{"reference":"Chan PP, Lowe TM. 2019. tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods Mol Biol. 1962: 1–14. 3.","pubmedId":"31020551","doi":"10.1007/978-1-4939-9173-0_1"},{"reference":"Chung CH, Walter MH, Yang L, Chen SG, Winston V, Thomas MA. 2017. Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data. BMC Genomics. 18: 350. 4.","pubmedId":"28472946","doi":"10.1186/s12864-017-3744-0"},{"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: 395. 5.","pubmedId":"21991981","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: 673–9. 6.","pubmedId":"17237039","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8: 195–202. 7.","pubmedId":"9521923","doi":"10.1101/gr.8.3.195"},{"reference":"Hallgren J, Tsirigos K, Pedersen M, Armenteros J, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. 8.","pubmedId":"","doi":""},{"reference":"Heller DM, Sivanathan V, Asai DJ, Hatfull GF. 2024. SEA-PHAGES and SEA-GENES: Advancing Virology and Science Education. Annu Rev Virol. 11: 1–20. 9.","pubmedId":"38684129","doi":"10.1146/annurev-virology-113023-110757"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics. 15: 182. 10.","pubmedId":"24925680","doi":"10.1186/1471-2105-15-182"},{"reference":"Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32: 11–6. 11.","pubmedId":"14704338","doi":"10.1093/nar/gkh152"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. 17 12.","pubmedId":"","doi":"https://doi.org/10.14806/ej.17.1.200"},{"reference":"Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data. Genomics. 95: 315–27. 13.","pubmedId":"20211242","doi":"10.1016/j.ygeno.2010.03.001"},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero Bustamante CA, Jacobs Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships. mBio. 8 14.","pubmedId":"28811342","doi":"10.1128/mBio.01069-17"},{"reference":"Robinson SE, Stanford E, Abraham S, Aguilera R, Anantoji NS, Barillas M, et al., Pollenz RS. 2025. Genome Sequences of Alatato and Audell, two Phages that infect Arthrobacter globiformis and have Different Life Cycles. MicroPubl Biol. 2025 15.","pubmedId":"41426959","doi":"10.17912/micropub.biology.001786"},{"reference":"Russell DA. 2018. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods Mol Biol. 1681: 109–125. 20.","pubmedId":"29134591","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Russell DA, Hatfull GF. 2017. PhagesDB: the actinobacteriophage database. Bioinformatics. 33: 784–786. 16.","pubmedId":"28365761","doi":"10.1093/bioinformatics/btw711"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33: W244–8. 17.","pubmedId":"15980461","doi":"10.1093/nar/gki408"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 13: e1005595. 18.","pubmedId":"28594827","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zorawik M, Jacobs Sera D, Freise AC, Sea P, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods Mol Biol. 2793: 273–298. 19.","pubmedId":"38526736","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Discovery and Genome Annotation of Arthrobacter Bacteriophages LastNadiia and Mireles Isolated from Soil in Eastern Texas
","reviews":[],"curatorReviews":[]},{"id":"40b876d7-d1fe-416d-9ed6-7b10ff7f7bcd","decision":"publish","abstract":"LastNadiia and Mireles are novel bacteriophages of Arthrobacter globiformis isolated from eastern Texas soil. Both exhibit siphoviral morphology and belong to the recently established cluster FR. Their genomes display the characteristic cluster FR organization, with predominantly forward-transcribed genes in the first half and reverse-transcribed genes in the second half. Neither genome contains identifiable lysogeny-associated genes, suggesting a lytic lifestyle.
","acknowledgements":"LastNadiia and Mireles were isolated and annotated at East Texas A&M University through the Science Education Alliance–Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program. This work was supported by the Howard Hughes Medical Institute (HHMI) SEA-PHAGES program and the School of Science and Engineering at East Texas A&M University. We thank the SEA-PHAGES Review-to-Improve Quality Control (QC) team for their guidance during genome annotation and review and gratefully acknowledge the MINT team for their assistance during manuscript revision. We are grateful to T. deCarvalho at the Keith R. Porter Imaging Facility, University of Maryland, Baltimore County, for generating the transmission electron micrographs. We also thank Graham F. Hatfull, Deborah Jacobs-Sera, and Daniel A. Russell at the University of Pittsburgh for genome sequencing and assembly.
","authors":[{"affiliations":["East Texas A&M, Commerce, TX, United States"],"departments":["Department of Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"kvoroshylo@leomail.tamuc.edu","firstName":"Kateryna","lastName":"Voroshylo","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M, Commerce, TX, United States"],"departments":["Department of Biological and Environmental Sciences"],"credit":["dataCuration"],"email":"nfigueroa3@leomail.tamuc.edu","firstName":"Neyda","lastName":"Figueroa","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M, Commerce, TX, United States"],"departments":["Department of Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"ksantana@leomail.tamuc.edu","firstName":"Karina","lastName":"Santana","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M, Commerce, TX, United States"],"departments":["Department of Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"tbizzell@leomail.tamuc.edu","firstName":"Traniece","lastName":"Bizzell","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M, Commerce, TX, United States"],"departments":["Department of Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"gcerda1@leomail.tamuc.edu","firstName":"Gerardo","lastName":"Cerda","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M, Commerce, TX, United States"],"departments":["Department of Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"calixto@leomail.tamuc.edu","firstName":"Lesly","lastName":"Calixto","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M, Commerce, TX, United States"],"departments":["Department of Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","writing_originalDraft"],"email":"mhowell6@leomail.tamuc.edu","firstName":"Makayla","lastName":"Howell","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":""},{"affiliations":["East Texas A&M, Commerce, TX, United States"],"departments":["Department of Biological and Environmental Sciences"],"credit":["dataCuration","writing_originalDraft"],"email":"pbelt1@leomail.tamuc.edu","firstName":"Payten","lastName":"Belt","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M, Commerce, TX, United States"],"departments":["Department of Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","project"],"email":"sfathima1@leomail.tamuc.edu","firstName":"Shabnam","lastName":"Fathima","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M, Commerce, TX, United States"],"departments":["Department of Biological and Environmental Sciences"],"credit":["conceptualization","project","formalAnalysis","resources"],"email":"venu.cheriyath@etamu.edu","firstName":"Venugopalan","lastName":"Cheriyath","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":false,"WBId":null,"orcid":"0000-0002-6424-2813"},{"affiliations":["East Texas A&M, Commerce, TX, United States"],"departments":["Department of Biological and Environmental Sciences"],"credit":["dataCuration","formalAnalysis","investigation","project","supervision","writing_originalDraft"],"email":"archana.srinivas@etamu.edu","firstName":"Archana","lastName":"Srinivas","submittingAuthor":false,"correspondingAuthor":false,"equalContribution":true,"WBId":null,"orcid":null},{"affiliations":["East Texas A&M, Commerce, TX, United States"],"departments":["Department of Biological and Environmental Sciences"],"credit":["formalAnalysis","project","supervision","validation","writing_originalDraft","writing_reviewEditing"],"email":"hyun-joo.nam@etamu.edu","firstName":"Hyun-Joo","lastName":"Nam","submittingAuthor":true,"correspondingAuthor":true,"equalContribution":true,"WBId":null,"orcid":"0000-0002-0235-9311"}],"awards":[],"conflictsOfInterest":"The authors declare that there are no conflicts of interest present.
","dataTable":{"url":"https://portal.micropublication.org/uploads/963733122b5a2d675cb5904ea307e1d9.csv"},"extendedData":[],"funding":"Funding was provided by the Department of Biological and Environmental Sciences, East Texas A&M University.
","image":{"url":"https://portal.micropublication.org/uploads/08a609a7f2b970c4dce815cefcffbfc1.png"},"imageCaption":"Transmission electron micrographs of LastNadiia (A) and Mireles (B), negatively stained with 1% uranyl acetate, showing siphovirus morphology. Scale bars represent 200 nm, with tick marks indicating 20 nm intervals.
Table: Genome and Sequencing Characteristics of Bacteriophages LastNadiia and Mireles.
","imageTitle":"Transmission electron micrographs of LastNadiia and Mireles
","methods":"","reagents":"","patternDescription":"Continued efforts to isolate and characterize novel bacteriophages have expanded our understanding of phage diversity, evolution, and genome organization (Heller et al., 2024). Here, we report the isolation, morphological characterization, and genome sequencing and annotation of LastNadiia and Mireles, two novel bacteriophages with predicted lytic lifestyles that infect Arthrobacter globiformis B-2979. LastNadiia and Mireles were isolated from soil samples obtained in eastern Texas. The sample containing phage LastNadiia was collected on the East Texas A&M University campus near Charles S. Garvin Lake (33.24377° N, 95.91124° W), whereas phage Mireles was isolated from a sample collected from a natural stormwater basin in Caddo Mills, Texas, USA (33.04428° N, 96.2313° W). The phages were isolated following the established protocol (Zorawik et al., 2024). Briefly, soil samples were suspended in PYCa medium, vortexed, and filtered through a 0.22-µm membrane. The filtrates were inoculated with Arthrobacter globiformis B-2979 and incubated at 30°C for 48 h. Following enrichment, the cultures were filtered, and the filtrates were plated with A. globiformis B-2979 using the soft-agar overlay method. Initial plaques were small and heterogeneous; after three rounds of plaque purification, both LastNadiia and Mireles formed clear, well-defined plaques ranging from 1.5 to 3 mm in diameter (n = 6). Transmission electron microscopy (TEM) of high-titer lysates was performed using a Hitachi HT7800 microscope operated at an accelerating voltage of 120 kV and equipped with an AMT Nanosprint15 B camera, bright-field STEM, and an Oxford Xplore EDS detector. TEM images showed that both phages exhibit siphovirus morphology, characterized by an icosahedral capsid and a long, flexible, noncontractile tail (Fig. 1 A and B). TEM analyses showed that LastNadiia has a capsid diameter of approximately 60 nm and a tail length of 122 nm (n = 1), while Mireles has a 53 nm head diameter and a 120 nm tail length (n = 1). Genomic DNA was extracted from high-titer lysates using the Promega Wizard DNA Clean-Up Kit. Sequencing libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit and sequenced on an Illumina NextSeq 1000 (XLEAP-P1 kit) at the Pittsburgh Bacteriophage Institute. Raw reads were trimmed with cutadapt 4.7 (using the option: –nextseq-trim 30) and filtered with skewer 0.2.2 (using the options: -q 20 -Q 30 -n -l 50) prior to assembly (Jiang et al., 2014; Martin, 2011; Wick et al., 2017). Illumina shotgun sequencing reads for both LastNadiia and Mireles were assembled using Newbler v2.9 (Miller et al., 2010), producing a single contig for each genome. Assembly completeness, accuracy, and genomic termini were verified using Consed v29 (Chung et al., 2017; Gordon et al., 1998; Russell, 2018). The LastNadiia and Mireles genomes are 41,591 bp and 41,147 bp, with GC contents of 58.5% and 58.6%, respectively. Both genomes contain identical 10-base 3′ cohesive ends (5′-TTTACGGCAT-3′). A summary of the sequencing results and genomic characteristics of LastNadiia and Mireles is provided in Table 1. Genome annotation of LastNadiia and Mireles began with automated gene prediction using Glimmer v3.02 (Delcher et al., 2007) and GeneMark v2.5 (Besemer and Borodovsky, 2005), followed by manual refinement in PECAAN v2.0 (http://discover.kbringsgd.org) which integrates multiple annotation tools. Gene start sites were evaluated using Phamerator (Actino_draft database v578) (Cresawn et al., 2011) and Starterator v627 (phages.wustl.edu/starterator/). Putative gene functions were assigned based on BLASTp v2.2.26 searches against the Actinobacteriophage and NCBI databases (Boratyn et al., 2013), and HHPred searches against the PDB_mmCIF70, pfam-A-v37.4, NCBI_Conserved_Domains (CD), and SCOPe70_2.08 and tRNAscan-SE databases (Soding et al., 2005). Membrane proteins were predicted with DeepTMHMM v1.0.42 (Hallgren et al., 2022). No tRNA genes were identified in either genome using Aragorn v1.2.38 (Chan and Lowe, 2019; Laslett and Canback, 2004). All software was run with default settings. The LastNadiia genome contains 66 predicted protein-coding genes, 35 of which were assigned putative functions. Of the remaining hypothetical genes, one was classified as an orpham. In Mireles, 68 protein-coding genes were predicted, including 33 with putative functional assignments. Among the remaining hypothetical genes, five were identified as orphams. No immunity-related genes were detected in either genome, consistent with the predicted lytic lifestyle of both phages. LastNadiia and Mireles were assigned to the cluster FR based on gene content similarity of at least 35% to phages in the Actinobacteriophage database, phagesdb (Pope et al., 2017; Russell and Hatfull, 2017). The cluster FR is a recently established cluster, with its first members reported in 2024, and currently comprises 11 fully annotated bacteriophages (Robinson et al., 2025). All FR phages exhibit a conserved genome organization, with most forward-transcribed genes located in the first half of the genome and predominantly reverse-transcribed genes in the second half. A single forward-transcribed gene is embedded within the reverse-transcribed region, followed by a terminal forward-transcribed gene at the end of the genome. These findings expand our understanding of Arthrobacter phages in the recently established cluster FR by defining key genomic and morphological features of LastNadiia and Mireles.
","references":[{"reference":"Besemer J, Borodovsky M. 2005. GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res. 33: W451–4. 1.","pubmedId":"15980510","doi":"10.1093/nar/gki487"},{"reference":"Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N, et al., Zaretskaya I. 2013. BLAST: a more efficient report with usability improvements. Nucleic Acids Res. 41: W29–33. 2.","pubmedId":"23609542","doi":"10.1093/nar/gkt282"},{"reference":"Chan PP, Lowe TM. 2019. tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. Methods Mol Biol. 1962: 1–14. 3.","pubmedId":"31020551","doi":"10.1007/978-1-4939-9173-0_1"},{"reference":"Chung CH, Walter MH, Yang L, Chen SG, Winston V, Thomas MA. 2017. Predicting genome terminus sequences of Bacillus cereus-group bacteriophage using next generation sequencing data. BMC Genomics. 18: 350. 4.","pubmedId":"28472946","doi":"10.1186/s12864-017-3744-0"},{"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: 395. 5.","pubmedId":"21991981","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: 673–9. 6.","pubmedId":"17237039","doi":"10.1093/bioinformatics/btm009"},{"reference":"Gordon D, Abajian C, Green P. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8: 195–202. 7.","pubmedId":"9521923","doi":"10.1101/gr.8.3.195"},{"reference":"Hallgren J, Tsirigos K, Pedersen M, Armenteros J, Marcatili P, Nielsen H, Krogh A, Winther O. 2022. DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks. 8.","pubmedId":"","doi":""},{"reference":"Heller DM, Sivanathan V, Asai DJ, Hatfull GF. 2024. SEA-PHAGES and SEA-GENES: Advancing Virology and Science Education. Annu Rev Virol. 11: 1–20. 9.","pubmedId":"38684129","doi":"10.1146/annurev-virology-113023-110757"},{"reference":"Jiang H, Lei R, Ding SW, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics. 15: 182. 10.","pubmedId":"24925680","doi":"10.1186/1471-2105-15-182"},{"reference":"Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 32: 11–6. 11.","pubmedId":"14704338","doi":"10.1093/nar/gkh152"},{"reference":"Martin M. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. 17 12.","pubmedId":"","doi":"https://doi.org/10.14806/ej.17.1.200"},{"reference":"Miller JR, Koren S, Sutton G. 2010. Assembly algorithms for next-generation sequencing data. Genomics. 95: 315–27. 13.","pubmedId":"20211242","doi":"10.1016/j.ygeno.2010.03.001"},{"reference":"Pope WH, Mavrich TN, Garlena RA, Guerrero Bustamante CA, Jacobs Sera D, Montgomery MT, et al., Hatfull GF. 2017. Bacteriophages of Gordonia spp. Display a Spectrum of Diversity and Genetic Relationships. mBio. 8 14.","pubmedId":"28811342","doi":"10.1128/mBio.01069-17"},{"reference":"Robinson SE, Stanford E, Abraham S, Aguilera R, Anantoji NS, Barillas M, et al., Pollenz RS. 2025. Genome Sequences of Alatato and Audell, two Phages that infect Arthrobacter globiformis and have Different Life Cycles. MicroPubl Biol. 2025 15.","pubmedId":"41426959","doi":"10.17912/micropub.biology.001786"},{"reference":"Russell DA. 2018. Sequencing, Assembling, and Finishing Complete Bacteriophage Genomes. Methods Mol Biol. 1681: 109–125. 20.","pubmedId":"29134591","doi":"10.1007/978-1-4939-7343-9_9"},{"reference":"Russell DA, Hatfull GF. 2017. PhagesDB: the actinobacteriophage database. Bioinformatics. 33: 784–786. 16.","pubmedId":"28365761","doi":"10.1093/bioinformatics/btw711"},{"reference":"Soding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33: W244–8. 17.","pubmedId":"15980461","doi":"10.1093/nar/gki408"},{"reference":"Wick RR, Judd LM, Gorrie CL, Holt KE. 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 13: e1005595. 18.","pubmedId":"28594827","doi":"10.1371/journal.pcbi.1005595"},{"reference":"Zorawik M, Jacobs Sera D, Freise AC, Sea P, Reddi K. 2024. Isolation of Bacteriophages on Actinobacteria Hosts. Methods Mol Biol. 2793: 273–298. 19.","pubmedId":"38526736","doi":"10.1007/978-1-0716-3798-2_17"}],"title":"Discovery and Genome Annotation of Arthrobacter Bacteriophages LastNadiia and Mireles Isolated from Soil in Eastern Texas
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