--- id: "edwards-2018-arlo" title: "Complete Genome Sequence of Cluster A1 Mycobacterium smegmatis Bacteriophage Arlo" authors: - "Brittany Stewart" - "Megan Adams" - "Miranda Fuentes" - "Leeila Hanson" - "Esperanza Sandoval" - "Mario Tovar" - "Camille Trautman" - "Bianca Willis" - "Keith Emmert" - "Julie Edwards" - "Jesse Meik" - "James Pierce" - "Dustin Edwards" venue: "Microbiology Resource Announcements" year: 2018 date: "2018-10-25" doi: "10.1128/mra.01242-18" url: "/research/publications/10-1128-mra-01242-18/" pdf: "/research/publications/10-1128-mra-01242-18/dustin-edwards-10-1128-mra-01242-18.pdf" pmc: "https://pmc.ncbi.nlm.nih.gov/articles/PMC6256580/" openAccess: true license: "cc-by" accessions: - "genbank:MH576971" - "sra:SRX4721440" citedBy: 1 citedBySource: "OpenAlex, read 2026-09-12" --- # Complete Genome Sequence of Cluster A1 Mycobacterium smegmatis Bacteriophage Arlo Genome of phage Arlo, isolated from Bluff Dale soil; 52,960 bp, 96 genes, cluster A1. ## Abstract Mycobacteriophage Arlo is a newly isolated Siphoviridae bacteriophage isolated from soil samples collected in Bluff Dale, Texas. Mycobacteriophage Arlo has a 52,960 base-pair double-stranded DNA genome that is predicted to contain 96 protein-coding genes. ## Full text Machine-extracted from the PDF linked above. It carries the artifacts that come with reading a typeset two-column page: running heads, figure captions in the flow of the prose, and words broken across line ends. The abstract above is the registry's deposit and is the authoritative text. Complete Genome Sequence of Cluster A1 Mycobacterium smegmatis Bacteriophage Arlo Brittany Stewart,a Megan Adams,a Miranda Fuentes,a Leeila Hanson,a Esperanza Sandoval,a Mario Tovar,a Camille Trautman,a Bianca Willis,a Keith Emmert,b Julie Edwards,a Jesse Meik,a James Pierce,a Dustin Edwardsa aDepartment of Biological Sciences, Tarleton State University, Stephenville, Texas, USA bDepartment of Mathematics, Tarleton State University, Stephenville, Texas, USA ABSTRACT Mycobacteriophage Arlo is a newly isolated Siphoviridae bacteriophage isolated from soil samples collected in Bluff Dale, Texas. Mycobacteriophage Arlo has a 52,960 base-pair double-stranded DNA genome that is predicted to contain 96 protein-coding genes. Mycobacteriophage Arlo is related to mycobacteriophage DD5 and other cluster A1 bacteriophages. We report the whole-genome sequence of mycobacteriophage Arlo (1, 2), which was directly isolated from a strain of Mycobacterium smegmatis, a rapidly growing environmental species that is generally nonpathogenic but can act as an opportunistic pathogen in immunosuppressed individuals (3). Mycobacteriophage Arlo was isolated from compost-containing community vegetable garden soil samples collected in Bluff Dale, Texas (32°19=08.0004, -098°01=14.9016). Soil samples were washed with 7H9 liquid medium, and bacteriophages were extracted from the mixture through a 0.22- m filter. For virus replication, filtered medium was incubated with Mycobacterium smegmatis mc2155 at 37°C for 48 h. Plaque assays of isolated mycobacteriophage Arlo resulted in medium-sized turbid plaques. Negative-staining transmission electron mi- croscopy showed that mycobacteriophage Arlo has a siphoviral morphology with a 60-nm-diameter nonenveloped icosahedral capsid and a 125 nm flexible noncontractile tail, which is typical of viruses in the Caudovirales order (Fig. 1). DNA was isolated from purified bacteriophage with the Promega Wizard DNA clean-up kit, and sequencing libraries were prepared from genomic DNA with the NEBNext Ultra II kit. Libraries were sequenced with Illumina MiSeq at the Pittsburgh Bacteriophage Institute to approximately 1,987-fold coverage from 742,500 total reads of 150-base read length (4). Sequence reads were assembled with Newbler 2.9 with default settings to produce a single-bacteriophage contig, which was checked for completeness, accuracy, and genome termini using consed v29.0 (5). The virus was determined to contain a linear double-stranded DNA genome that is 52,960 base pairs in length, with 63.8% GC content, and a 3= single-stranded terminal overhang of 5=-CGGATGGTAA-3=. Whole-genome nucleotide alignment with NCBI BLASTn (https:// blast.ncbi.nlm.nih.gov/) (6) showed 96 –97% nucleotide identity to cluster A1 mycobac- teriophages Oogway (GenBank accession number MH230878) and DD5 (GenBank accession number NC_011022) (2). Autoannotation of the genome was performed using GLIMMER v3.02 (7, 8) and GeneMark v2.5p (9, 10), followed by manual inspection, refinement of start sites, and annotation revision using Phamerator (https://phamerator.org/) (11), DNA Mas- ter v5.23.2 (http://phagesdb.org/DNAMaster/), and PECAAN (https://pecaan.kbrinsgd .org/). Mycobacteriophage Arlo is predicted to contain 96 protein-coding genes. No tRNAs genes were identified by ARAGORN v1.2.38 (12) or tRNAscan-SE v2.0 (13). Start codon usage was determined to be 90.12% AUG, 8.72% GUG, and 1.16% UUG. HHpred v3.0beta (14, 15) and NCBI BLASTp (6) software were used to assign putative Received 9 September 2018 Accepted 1 October 2018 Published 25 October 2018 Citation Stewart B, Adams M, Fuentes M, Hanson L, Sandoval E, Tovar M, Trautman C, Willis B, Emmert K, Edwards J, Meik J, Pierce J, Edwards D. 2018. Complete genome sequence of cluster A1 Mycobacterium smegmatis bacteriophage Arlo. Microbiol Resour Announc 7:e01242-18. https://doi.org/10.1128/MRA .01242-18. Editor Julie C. Dunning Hotopp, University of Maryland School of Medicine Copyright © 2018 Stewart et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Dustin Edwards, dcedwards@tarleton.edu. GENOME SEQUENCES crossm Volume 7 Issue 16 e01242-18 mra.asm.org 1 Downloaded from https://journals.asm.org/journal/mra on 26 July 2026 by 156.146.253.207. functions to 34 (35.4%) of 96 predicted protein-coding genes. The mycobacteriophage Arlo genome is arranged with rightwards-transcribed genes (genes 1 to 36, 58.4% of genome) encoding virion structural and assembly proteins and a lysis cassette consist- ing of lysin A and lysin B genes. Leftwards-transcribed genes encode DNA polymerase I, metallophosphoesterase, DNA primase, DNA methylase, endonuclease VII, NrdH-like glutaredoxin, DnaB-like dsDNA helicase, RecB-like exonuclease/helicase, and immunity repressor proteins. Data availability. The mycobacteriophage Arlo genome is available at GenBank as accession number MH576971. Raw reads are available in the SRA under accession number SRX4721440. ACKNOWLEDGMENTS Support for this research was provided by Tarleton State University College of Science and Technology and by the Howard Hughes Medical Institute Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) research and education program. We thank Graham Hatfull, Welkin Pope, Deborah Jacobs-Sera, Daniel Russell, Rebecca Garlena, Sally Molloy, Tamarah Adair, Phoebe Doss, and Keely Wilson for their technical support during the imaging of the virion and the isolation, sequencing, and annotation of this genome. REFERENCES 1. Pope WH, Bowman CA, Russell DA, Jacobs-Sera D, Asai DJ, Cresawn SG, Jacobs WR, Jr, Hendrix RW, Lawrence JG, Hatfull GF; Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science, Phage Hunters Integrating Research and Education, Mycobacterial Genetics Course. 2015. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. 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