--- id: "edwards-2021-indylu" title: "Complete Genome Sequence of Bacteriophage IndyLu, Isolated from a Microbacterium foliorum Culture" authors: - "Ashley Suris" - "Selina Alvarado" - "Tommy Butler" - "Carlos Canales" - "Matthew Castro" - "Julia Gaston" - "Marlee Goppert" - "Raylon Huckaby" - "Jesse Laposky" - "Jessica Lee" - "Elizabeth Mullins" - "Damla Ustundag" - "Josue Zuniga" - "Faith Cox" - "Dustin Edwards" venue: "Microbiology Resource Announcements" year: 2021 date: "2021-12-16" doi: "10.1128/MRA.01079-21" url: "/research/publications/10-1128-mra-01079-21/" pdf: "/research/publications/10-1128-mra-01079-21/dustin-edwards-10-1128-mra-01079-21.pdf" pmc: "https://pmc.ncbi.nlm.nih.gov/articles/PMC8675261/" openAccess: true license: "cc-by" accessions: - "genbank:OK318958" - "sra:SRX12683423" citedBy: 1 citedBySource: "OpenAlex, read 2026-09-12" --- # Complete Genome Sequence of Bacteriophage IndyLu, Isolated from a Microbacterium foliorum Culture Genome of phage IndyLu, isolated from Stephenville soil; 41,958 bp, 71 genes, one tRNA. ## Abstract Microbacteriophage IndyLu was isolated from Microbacterium foliorum NRRL B-24224. The 41,958-bp double-stranded DNA genome has 71 predicted protein coding genes and 1 tRNA. The lytic actinobacteriophage was extracted from soil samples collected in Stephenville, TX, and is related to cluster EB bacteriophages Didgeridoo and Lahqtemish. ## 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 Bacteriophage IndyLu, Isolated from a Microbacterium foliorum Culture Ashley Suris,a Selina Alvarado,a Tommy Butler,a Carlos Canales,a Matthew Castro,a Julia Gaston,a Marlee Goppert,a Raylon Huckaby,a Jesse Laposky,a Jessica Lee,a Elizabeth Mullins,a Damla Ustundag,a Josue Zuniga,a Faith Cox,a Dustin Edwardsa aDepartment of Biological Sciences, Tarleton State University, Stephenville, Texas, USA ABSTRACT Microbacteriophage IndyLu was isolated from Microbacterium foliorum NRRL B-24224. The 41,958-bp double-stranded DNA genome has 71 predicted protein coding genes and 1 tRNA. The lytic actinobacteriophage was extracted from soil samples collected in Stephenville, TX, and is related to cluster EB bacteriophages Didgeridoo and Lahqtemish. M icrobacterium foliorum NRRL B-24224 is a rod-shaped Gram-positive aerobic bacte- rium from the order Actinomycetales that contains no intact prophages or apparent antibacteriophage restriction-modification or CRISPR systems (1). Here, we report the whole- genome sequence of actinobacteriophage IndyLu (2), collected from a dry soil sample near a horse barn in Stephenville, TX, USA (global positioning system [GPS] coordinates, 32.248 N, 98.209 W). Soil samples were suspended in peptone-yeast extract-calcium (PYCa) medium and incubated for 2 h in a shaking incubator at 29°C and 200 rpm. The supernatant was centrifuged and filtered through a 0.22- mm filter. Filtrates were plated with the isolation host Microbacterium foliorum NRRL B-24224 using a soft agar overlay. Bacteriophages were isolated by two rounds of picking a single, well-separated plaque, followed by diluting the bacteriophage sample in a 10-fold dilution series and plating with M. foliorum. IndyLu formed small, lytic plaques. Negative-staining transmission electron microscopy (Fig. 1) showed a siphoviral morphology. ImageJ v1.53m (3) measured a tail length of 155 nm and a capsid diameter of 65 nm. High-titer lysates were prepared from flooded plates as described in the Phage Discovery Guide and used to extract bacteriophage DNA using a modified zinc chloride precipitation method (4, 5). The Pittsburgh Bacteriophage Institute prepared the sequencing library from genomic DNA with the NEBNext Ultra II kit (New England Biolabs, Ipswich, MA) using an Illumina MiSeq instrument (6), with 1,156-fold coverage and 445,388 total single-end 150-bp reads. A single bacteriophage contig was assembled using the default settings in Newbler v2.9. Quality control checks for assembly, precision, and genome termini were performed using Consed v29.0 (6, 7). The linear viral genome comprises 41,958 bp (G1C content, 66.2%) with a 39 single-stranded terminal overhang 10 bp long of 59-ACTCCCGACA-39. Whole-genome alignment with NCBI BLASTn (https://blast.ncbi.nlm.nih.gov/) (8) showed greater than 93% nucleotide sequence identity to cluster EB bacteriophages Didgeridoo (GenBank accession number MH045566) and Lahqtemish (GenBank accession number MT889392). Auto-annotation using GLIMMER v3.02 (9) and GeneMark v2.5p (10, 11) was manually refined using Phamerator (12), DNA Master v5.23.2 (http://phagesdb.org/DNAMaster/), and PECAAN. Microbacteriophage IndyLu is predicted to contain 70 protein-coding genes and 1 tRNA coding for glutamine, identified using ARAGORN v1.2.38 (13) and tRNAscan-SE v2.0 (14). Putative functions were assigned to 32 of the 71 protein-coding genes using HHpred (15, 16) and NCBI BLASTp (8). All tools were run with default parameters. Sixty-seven genes are encoded rightwards, including virion structural and assembly proteins, DNA primase/polymerase, endolysin, Cas4 family exonuclease, and two HNH endonucleases. IndyLu is among the 6.8% of cluster EB bacteriophages coding for a tRNA. Editor John J. Dennehy, Queens College CUNY Copyright © 2021 Suris 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. The authors declare no conflict of interest. Received 4 November 2021 Accepted 16 November 2021 Published 16 December 2021 Volume 10 Issue 50 e01079-21 mra.asm.org 1 GENOME SEQUENCES Downloaded from https://journals.asm.org/journal/mra on 26 July 2026 by 156.146.253.207. Data availability. The actinobacteriophage IndyLu genome sequence is available in GenBank under accession number OK318958. The raw reads are available in the SRA under accession number SRX12683423. 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, JoAnn Whitefleet-Smith, and Phoebe Doss for technical support during the imaging of the virion and the isolation, sequencing, and annotation of this genome. REFERENCES 1. Russell DA, Garlena RA, Hatfull GF. 2019. Complete genome sequence of Micro- bacterium foliorum NRRL B-24224, a host for bacteriophage discovery. Micro- biol Resour Announc 8:e01467-18. https://doi.org/10.1128/MRA.01467-18. 2. Russell DA, Hatfull GF. 2017. PhagesDB: the actinobacteriophage database. Bio- informatics 33:784–786. https://doi.org/10.1093/bioinformatics/btw711. 3. Schneider CA, Rasband WS, Eliceiri KW. 2012. 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Imaging using an FEI Tecnai G2 Spirit BioTWIN transmission electron microscope (NL1.160G) revealed a capsid diameter of 65 nm, tail length of 155 nm, and a morphology consistent with other Siphoviridae family members. Suris et al. Volume 10 Issue 50 e01079-21 mra.asm.org 2 Downloaded from https://journals.asm.org/journal/mra on 26 July 2026 by 156.146.253.207.