--- id: "edwards-2019-finny" title: "Complete Genome Sequence of Bacteriophage Finny, Isolated from a Microbacterium foliorum Culture" authors: - "Tiffany Lee" - "Michaela Aguirre" - "Shey Andrews" - "Kayla Bahr" - "Abigail Ballard" - "Matthew Bristerpostma" - "Faith Cox" - "Leah Dowell" - "David Kiker" - "Tiffany Lujan" - "Stacy Luka" - "Abbigal Ramirez" - "Rheaven Sandoval" - "Kenneth Underhill" - "Haze Murphy" - "Cecilia Cabrera" - "Dustin Edwards" venue: "Microbiology Resource Announcements" year: 2019 date: "2019-10-03" doi: "10.1128/mra.01039-19" url: "/research/publications/10-1128-mra-01039-19/" pdf: "/research/publications/10-1128-mra-01039-19/dustin-edwards-10-1128-mra-01039-19.pdf" pmc: "https://pmc.ncbi.nlm.nih.gov/articles/PMC6776782/" openAccess: true license: "cc-by" accessions: - "genbank:MK894432" - "sra:SRX6700907" citedBy: 2 citedBySource: "OpenAlex, read 2026-09-12" --- # Complete Genome Sequence of Bacteriophage Finny, Isolated from a Microbacterium foliorum Culture Genome of phage Finny, isolated from New Braunfels soil; 40,313 bp, 63 genes. ## Abstract Actinobacteriophage Finny contains a circularly permuted 40,313-bp double-stranded DNA genome with 63 predicted protein-coding genes. Finny was directly isolated from a soil sample collected in New Braunfels, Texas, that was incubated with Microbacterium foliorum SEA B-24224. Finny is closely related to bacteriophages MCubed, Andromedas, ColaCorta, Eleri, and Sansa. ## 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 Finny, Isolated from a Microbacterium foliorum Culture Tiffany Lee,a Michaela Aguirre,a Shey Andrews,a Kayla Bahr,a Abigail Ballard,a Matthew Bristerpostma,a Faith Cox,a Leah Dowell,a David Kiker,a Tiffany Lujan,a Stacy Luka,a Abbigal Ramirez,a Rheaven Sandoval,a Kenneth Underhill,a Haze Murphy,a Cecilia Cabrera,a Dustin Edwardsa aDepartment of Biological Sciences, Tarleton State University, Stephenville, Texas, USA ABSTRACT Actinobacteriophage Finny contains a circularly permuted 40,313-bp double-stranded DNA genome with 63 predicted protein-coding genes. Finny was directly isolated from a soil sample collected in New Braunfels, Texas, that was incu- bated with Microbacterium foliorum SEA B-24224. Finny is closely related to bacterio- phages MCubed, Andromedas, ColaCorta, Eleri, and Sansa. Characterization of actinobacteriophage genomes provides valuable information on virus evolution and genetic diversity, including conservation of shared genes within a population (1). We report the genome sequence of actinobacteriophage Finny (2), directly isolated from soil inside a chicken coop in New Braunfels, TX (global positioning system [GPS] coordinates 29.782774N, 98.128783W). Soil samples were washed with peptone-yeast extract-calcium (PYCa) liquid medium and filtered through 0.22- m filters to extract the bacteriophage. The filtered medium was plated using a softagar overlay method on PYCa agar with Microbacterium foliorum strain SEA B-24224 at 29°C for 24 h. Bacteriophage replication formed small and medium lytic plaques with turbid halo rings. Finny was purified by picking a single plaque and placing it in 100 l phage buffer (10 mM Tris [pH 7.5], 10 mM MgSO4, 68 mM NaCl, 1 mM CaCl2, 10% glycerol), followed by two consecutive serial dilutions. Negative-staining transmission electron microscopy showed that the isolated bacteriophage had siphoviral morphology, with an approximate tail length of 150 nm and capsid diameter of 65 nm. The bacteriophage DNA was extracted by a modified zinc chloride precipitation method (3) that included proteinase K (20 mg/ml) treatment to deactivate the nu- cleases prior to potassium acetate precipitation. Genomic sequencing libraries were prepared using the NEBNext Ultra II kit (New England BioLabs, Ipswich, MA); the libraries were pooled and sequenced with an Illumina MiSeq instrument at the Pitts- burgh Bacteriophage Institute (Pittsburgh, PA). Sequencing was performed to approx- imately 7,918-fold coverage from 2,253,035 total single-end 150-base read length (4). A single bacteriophage contig was assembled from sequence reads using Newbler 2.9, with default settings, and Consed v29.0 (5) was used to perform quality control on assembly for inclusiveness and precision. We determined that the virus contains a double-stranded DNA genome 40,313 base pairs long, with 62.1% GC content. There were no accumulations of read starts or substantial coverage variations, so the genome was determined to be circularly permuted. The beginning of the genome was chosen by comparison to similar bacteriophage genomes. Whole-genome nucleotide alignment with BLASTn (https://blast.ncbi.nlm.nih .gov/) (6) showed similar nucleotide identity to the bacteriophages summarized in Table 1 (2, 7). Along with manual inspection, genome annotation was performed using GLIMMER v3.02 (8) and GeneMark v2.5p (9, 10) for correction and refinement of start sites and Citation Lee T, Aguirre M, Andrews S, Bahr K, Ballard A, Bristerpostma M, Cox F, Dowell L, Kiker D, Lujan T, Luka S, Ramirez A, Sandoval R, Underhill K, Murphy H, Cabrera C, Edwards D. 2019. Complete genome sequence of bacteriophage Finny, isolated from a Microbacterium foliorum culture. Microbiol Resour Announc 8:e01039-19. https://doi.org/ 10.1128/MRA.01039-19. Editor John J. Dennehy, Queens College Copyright © 2019 Lee 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. Received 23 August 2019 Accepted 30 August 2019 Published 3 October 2019 GENOME SEQUENCES crossm Volume 8 Issue 40 e01039-19 mra.asm.org 1 Downloaded from https://journals.asm.org/journal/mra on 26 July 2026 by 156.146.253.207. revisions utilizing Phamerator (https://phamerator.org/) (11), DNA Master v5.23.2 (http://phagesdb.org/DNAMaster/), and PECAAN (https://discover.kbrinsgd.org). We predicted that Finny contained 63 protein-coding genes. One tRNA gene was identified by tRNAscan-SE v2.0 (12) and positioned at nucleotides 28924 through 28857. Start codon usage was determined to be 80.95% AUG and 19.05% GUG. Putative functions for 25 of the 63 predicted protein-coding genes were assigned using HHpred v3.0beta (13, 14) and NCBI BLASTp (6). The Finny genome is organized with genes 1 through 26 transcribed rightwards and encoding terminase, lysin A, and virion assembly and structural proteins. Genes transcribed leftwards encode RecA-like DNA recombinase, AAA-ATPase, Cas4 family exonuclease, DNA polymerase I, DNA helicase, MazG-like nucleotide pyrophosphohydrolase, thymidylate kinase, glycosyltransferase, and ThyX thymidylate synthase. Data availability. The genome sequence of actinobacteriophage Finny is avail- able at GenBank under accession number MK894432. The raw reads are available in the SRA under accession number SRX6700907. ACKNOWLEDGMENTS Support for this research was provided by Tarleton State University College of Science and Technology and by the Howard Hughes Medical Institute Science Educa- tion 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, Re- becca Garlena, and Phoebe Doss 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 Ge- netics Course. 2015. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. 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BMC Bioinformatics 12:395. https://doi.org/10.1186/1471-2105-12-395. 12. Lowe TM, Chan PP. 2016. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes. Nucleic Acids Res 44: W54 –W57. https://doi.org/10.1093/nar/gkw413. 13. Söding J, Biegert A, Lupas AN. 2005. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33:W244 –W248. https://doi.org/10.1093/nar/gki408. 14. Zimmermann L, Stephens A, Nam S-Z, Rau D, Kübler J, Lozajic M, Gabler F, Söding J, Lupas AN, Alva V. 2018. A completely reimplemented MPI Bioinformatics Toolkit with a new HHpred server at its core. J Mol Biol 430:2237–2243. https://doi.org/10.1016/j.jmb.2017.12.007. TABLE 1 Characteristics of similar bacteriophages with M. foliorum as a hosta Name GenBank accession no. Genome size (bp) GC content (%) No. of ORFsb No. of tRNAs % identity to Finny Finny MK894432 40,313 62.1 63 1 MCubed MN096378 40,381 62.0 63 0 97.44 Andromedas MH590606 40,494 62.0 63 1 96.86 Eleri MG839027 40,366 62.0 63 0 96.82 ColaCorta MH590604 40,494 62.0 64 1 96.80 Sansa MH513982 40,306 61.8 62 1 96.41 a Similarity defined as an identity of 95%. b ORFs, open reading frames. Lee et al. Volume 8 Issue 40 e01039-19 mra.asm.org 2 Downloaded from https://journals.asm.org/journal/mra on 26 July 2026 by 156.146.253.207.