Waterfoul is a new isolated temperate siphovirus of Mycobacterium smegmatis mc2155. It was identified as a member of the K5 cluster of Mycobacterium phages and has a 61,248-bp genome with 95 predicted genes

D\u27Angelo, William A.

Douglas, Jessica R.

Embry, Ella K.

Jackson, Paige N.

Johnson, Christa O.

Mavrodi, Dmitri V.

Sellers, J. Michael

English

Aquila Digital Community (University of Southern Mississippi, USM)

The University of Southern MississippiThe Aquila Digital CommunityFaculty Publications11-17-2016Genome Sequence of Mycobacterium PhageWaterfoulPaige N. JacksonUniversity of Southern MississippiElla K. EmbryUniversity of Southern MississippiChrista O. JohnsonUniversity of Southern MississippiJessica R. DouglasUniversity of Southern MississippiJ. Michael SellersUniversity of Southern Mississippi, johnny.sellers@usm.eduSee next page for additional authorsFollow this and additional works at: https://aquila.usm.edu/fac_pubsPart of the Biology CommonsThis Article is brought to you for free and open access by The Aquila Digital Community. It has been accepted for inclusion in Faculty Publications byan authorized administrator of The Aquila Digital Community. For more information, please contact Joshua.Cromwell@usm.edu.Recommended CitationJackson, P. N., Embry, E. K., Johnson, C. O., Douglas, J. R., Sellers, J., D'Angelo, W. A., Mavrodi, D. V. (2016). Genome Sequence ofMycobacterium Phage Waterfoul. Genome Announcements, 4(6).Available at: https://aquila.usm.edu/fac_pubs/15179AuthorsPaige N. Jackson, Ella K. Embry, Christa O. Johnson, Jessica R. Douglas, J. Michael Sellers, William A.D'Angelo, and Dmitri V. MavrodiThis article is available at The Aquila Digital Community: https://aquila.usm.edu/fac_pubs/15179Genome Sequence of Mycobacterium Phage WaterfoulPaige N. Jackson,a Ella K. Embry,a Christa O. Johnson,a Tiara L. Watson,a Sayre K. Weast,a Caroline J. DeGraw,a Jessica R. Douglas,bJ. Michael Sellers,a William A. D’Angelo,a Dmitri V. MavrodiaDepartment of Biological Sciences, University of Southern Mississippi, Hattiesburg, Mississippi, USAa; School of Polymers and High Performance Materials, University ofSouthern Mississippi, Hattiesburg, Mississippi, USAbWaterfoul is a newly isolated temperate siphovirus ofMycobacterium smegmatismc2155. It was identified as a member of the K5cluster ofMycobacterium phages and has a 61,248-bp genome with 95 predicted genes.Received 18 September 2016 Accepted 3 October 2016 Published 17 November 2016Citation Jackson PN, Embry EK, Johnson CO, Watson TL, Weast SK, DeGraw CJ, Douglas JR, Sellers JM, D’Angelo WA, Mavrodi DV. 2016. Genome sequence ofMycobacteriumphage Waterfoul. Genome Announc 4(6):e01281-16. doi:10.1128/genomeA.01281-16.Copyright © 2016 Jackson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.Address correspondence to Dmitri V. Mavrodi, dmitri.mavrodi@usm.edu.Mycobacteriophage Waterfoul was isolated from soil col-lected in Hattiesburg, Mississippi, USA, using Mycobac-terium smegmatis mc2155 as a host. The soil sample was harvestedon the shoreline of a pond at the Hattiesburg Zoo (GPS coordi-nates 31.323056 N, 89.316389 W). The isolation and genome anal-ysis of Waterfoul were conducted as part of the undergraduatelaboratory course called “Phage Hunters,” which was organized atthe University of Southern Mississippi with the help of the ScienceEducation Alliance and the Howard Hughes Medical Institute (1).The phage was isolated using a standard enrichment techniquewith incubation at 22°C. Electron microscopy revealed that Wa-terfoul has an isometric head of 60 nm and a flexible 200-nm-longnoncontractile tail. The phage was purified and amplified, and itsDNA was isolated and sequenced at the Pittsburgh BacteriophageInstitute using an Illumina MiSeq instrument. Single-end runreads were assembled to give a single contig with 3,046-fold cov-erage. The 61,248-bp genome is flanked by cos ends with 11-bp 3=extensions of the sequence 5=-CTCAGTGGCAT. The GC con-tent of Waterfoul is 64.9% and is close to that of M. smegmatis.Putative genes in the Waterfoul genome were identified usingGlimmer (2), GeneMark (3), Aragorn (4), and tRNAscan-SE (5),followed by manual inspection and annotation revision usingDNA Master (http://cobamide2.bio.pitt.edu). Gene functionswere assigned using BLAST (6) and HHPred (7). A total of 94protein-coding genes were predicted, accounting for a 93.1% cod-ing capacity of the genome. BLASTn analysis revealed that Water-foul is a member of the K5 subcluster and closely related to my-cobacteriophages Gengar, Leston, and OkiRoe (8).The Waterfoul genome has features common to other sipho-viruses, including structural genes that encode a major capsid sub-unit (gp11), a maturation protease (gp8), a scaffolding protein(gp10), a terminase (gp5 and gp6), a portal protein (gp7), head-to-tail connector proteins (gp12 to gp15), a tape-measure protein(gp19), and a major (gp16) and several minor (gp20 to gp25) tailproteins. Genes involved in DNA replication and nucleic acid me-tabolism encoded a DNA primase/polymerase (gp65), a DNA he-licase (gp66), a DnaQ-like exonuclease (gp54), an RNA ligase(gp78), a RusA resolvase (gp67), a glutaredoxin (gp62), and pro-teins with predicted HNH endonuclease motifs (gp63, gp64, andgp95). Regulatory proteins included an immunity repressor with thehelix-turn-helix DNA binding motif (gp42) and a putative WhiB-liketranscriptional regulator (gp53). Like some other temperate myco-bacteriophages, Waterfoul had a tyrosine recombinase type integrase(gp39), a tRNA-Trp (CCA) (gp4), as well as the lysis system repre-sented by the holin (gp31), lysin A (gp29), and lysin B (gp30).Accession number(s). The genome of bacteriophage Water-foul was deposited in GenBank under the accession numberKX585251.ACKNOWLEDGMENTSThe Phage Hunters course is supported by the Department of BiologicalSciences and the Honors College of the University of Southern Missis-sippi. We thank Véronique Delesalle (Gettysburg College) for proofread-ing the draft annotation of the Waterfoul genome.FUNDING INFORMATIONThis research received no specific grant from any funding agency in thepublic, commercial, or not-for-profit sectors.REFERENCES1. Jordan TC, Burnett SH, Carson S, Caruso SM, Clase K, DeJong RJ,Dennehy JJ, Denver DR, Dunbar D, Elgin SC, Findley AM, Gissendan-ner CR, Golebiewska UP, Guild N, Hartzog GA, Grillo WH, HollowellGP, Hughes LE, Johnson A, King RA, Lewis LO, Li W, Rosenzweig F,Rubin MR, Saha MS, Sandoz J, Shaffer CD, Taylor B, Temple L, VazquezE, Ware VC, Barker LP, Bradley KW, Jacobs-Sera D, Pope WH, RussellDA, Cresawn SG, Lopatto D, Bailey CP, Hatfull GF. 2014. A broadlyimplementable research course in phage discovery and genomics for first-year undergraduate students. mBio 5:e01051– e01013. http://dx.doi.org/10.1128/mBio.01051-13.2. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bac-terial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673– 679. http://dx.doi.org/10.1093/bioinformatics/btm009.3. Besemer J, BorodovskyM. 2005. GeneMark: web software for gene findingin prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33:W451–W454.http://dx.doi.org/10.1093/nar/gki487.4. Laslett D, Canback B. 2004. ARAGORN, a program to detect tRNA genesand tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16.http://dx.doi.org/10.1093/nar/gkh152.5. Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detec-tion of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. http://dx.doi.org/10.1093/nar/25.5.0955.crossmarkGenome AnnouncementsNovember/December 2016 Volume 4 Issue 6 e01281-16 genomea.asm.org 1 on May 24, 2018 by guesthttp://genomea.asm.org/Downloaded from 6. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic localalignment search tool. J Mol Biol 215:403– 410. http://dx.doi.org/10.1016/S0022-2836(05)80360-2.7. Söding J, Biegert A, Lupas AN. 2005. The HHpred interactive server forprotein homology detection and structure prediction. Nucleic Acids Res33:W244 –W248. http://dx.doi.org/10.1093/nar/gki408.8. Pope WH, Bowman CA, Russell DA, Jacobs-Sera D, Asai DJ, Cresawn SG,Jacobs WR, Hendrix RW, Lawrence JG, Hatfull GF, Science EducationAlliance Phage Hunters Advancing Genomics and Evolutionary Science,Phage Hunters Integrating Research and Education, Mycobacterial GeneticsCourse. 2015. Whole genome comparison of a large collection of mycobacte-riophages reveals a continuum of phage genetic diversity. Elife 4:e06416.Jackson et al.Genome Announcements2 genomea.asm.org November/December 2016 Volume 4 Issue 6 e01281-16 on May 24, 2018 by guesthttp://genomea.asm.org/Downloaded from 

Genome Sequence of Mycobacterium Phage Waterfoul

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Genome Sequence of Mycobacterium Phage Waterfoul

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