title: Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.
abstract: Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.
authors.affiliation: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America.
authors.forename: Welkin H
authors.initials: WH
authors.lastname: Pope
authors.forename: Deborah
authors.initials: D
authors.lastname: Jacobs-Sera
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Russell
authors.forename: Craig L
authors.initials: CL
authors.lastname: Peebles
authors.forename: Zein
authors.initials: Z
authors.lastname: Al-Atrache
authors.forename: Turi A
authors.initials: TA
authors.lastname: Alcoser
authors.forename: Lisa M
authors.initials: LM
authors.lastname: Alexander
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Alfano
authors.forename: Samantha T
authors.initials: ST
authors.lastname: Alford
authors.forename: Nichols E
authors.initials: NE
authors.lastname: Amy
authors.forename: Marie D
authors.initials: MD
authors.lastname: Anderson
authors.forename: Alexander G
authors.initials: AG
authors.lastname: Anderson
authors.forename: Andrew A S
authors.initials: AA
authors.lastname: Ang
authors.forename: Manuel
authors.initials: M
authors.lastname: Ares
authors.forename: Amanda J
authors.initials: AJ
authors.lastname: Barber
authors.forename: Lucia P
authors.initials: LP
authors.lastname: Barker
authors.forename: Jonathan M
authors.initials: JM
authors.lastname: Barrett
authors.forename: William D
authors.initials: WD
authors.lastname: Barshop
authors.forename: Cynthia M
authors.initials: CM
authors.lastname: Bauerle
authors.forename: Ian M
authors.initials: IM
authors.lastname: Bayles
authors.forename: Katherine L
authors.initials: KL
authors.lastname: Belfield
authors.forename: Aaron A
authors.initials: AA
authors.lastname: Best
authors.forename: Agustin
authors.initials: A
authors.lastname: Borjon
authors.forename: Charles A
authors.initials: CA
authors.lastname: Bowman
authors.forename: Christine A
authors.initials: CA
authors.lastname: Boyer
authors.forename: Kevin W
authors.initials: KW
authors.lastname: Bradley
authors.forename: Victoria A
authors.initials: VA
authors.lastname: Bradley
authors.forename: Lauren N
authors.initials: LN
authors.lastname: Broadway
authors.forename: Keshav
authors.initials: K
authors.lastname: Budwal
authors.forename: Kayla N
authors.initials: KN
authors.lastname: Busby
authors.forename: Ian W
authors.initials: IW
authors.lastname: Campbell
authors.forename: Anne M
authors.initials: AM
authors.lastname: Campbell
authors.forename: Alyssa
authors.initials: A
authors.lastname: Carey
authors.forename: Steven M
authors.initials: SM
authors.lastname: Caruso
authors.forename: Rebekah D
authors.initials: RD
authors.lastname: Chew
authors.forename: Chelsea L
authors.initials: CL
authors.lastname: Cockburn
authors.forename: Lianne B
authors.initials: LB
authors.lastname: Cohen
authors.forename: Jeffrey M
authors.initials: JM
authors.lastname: Corajod
authors.forename: Steven G
authors.initials: SG
authors.lastname: Cresawn
authors.forename: Kimberly R
authors.initials: KR
authors.lastname: Davis
authors.forename: Lisa
authors.initials: L
authors.lastname: Deng
authors.forename: Dee R
authors.initials: DR
authors.lastname: Denver
authors.forename: Breyon R
authors.initials: BR
authors.lastname: Dixon
authors.forename: Sahrish
authors.initials: S
authors.lastname: Ekram
authors.forename: Sarah C R
authors.initials: SC
authors.lastname: Elgin
authors.forename: Angela E
authors.initials: AE
authors.lastname: Engelsen
authors.forename: Belle E V
authors.initials: BE
authors.lastname: English
authors.forename: Marcella L
authors.initials: ML
authors.lastname: Erb
authors.forename: Crystal
authors.initials: C
authors.lastname: Estrada
authors.forename: Laura Z
authors.initials: LZ
authors.lastname: Filliger
authors.forename: Ann M
authors.initials: AM
authors.lastname: Findley
authors.forename: Lauren
authors.initials: L
authors.lastname: Forbes
authors.forename: Mark H
authors.initials: MH
authors.lastname: Forsyth
authors.forename: Tyler M
authors.initials: TM
authors.lastname: Fox
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Fritz
authors.forename: Roberto
authors.initials: R
authors.lastname: Garcia
authors.forename: Zindzi D
authors.initials: ZD
authors.lastname: George
authors.forename: Anne E
authors.initials: AE
authors.lastname: Georges
authors.forename: Christopher R
authors.initials: CR
authors.lastname: Gissendanner
authors.forename: Shannon
authors.initials: S
authors.lastname: Goff
authors.forename: Rebecca
authors.initials: R
authors.lastname: Goldstein
authors.forename: Kobie C
authors.initials: KC
authors.lastname: Gordon
authors.forename: Russell D
authors.initials: RD
authors.lastname: Green
authors.forename: Stephanie L
authors.initials: SL
authors.lastname: Guerra
authors.forename: Krysta R
authors.initials: KR
authors.lastname: Guiney-Olsen
authors.forename: Bridget G
authors.initials: BG
authors.lastname: Guiza
authors.forename: Leila
authors.initials: L
authors.lastname: Haghighat
authors.forename: Garrett V
authors.initials: GV
authors.lastname: Hagopian
authors.forename: Catherine J
authors.initials: CJ
authors.lastname: Harmon
authors.forename: Jeremy S
authors.initials: JS
authors.lastname: Harmson
authors.forename: Grant A
authors.initials: GA
authors.lastname: Hartzog
authors.forename: Samuel E
authors.initials: SE
authors.lastname: Harvey
authors.forename: Siping
authors.initials: S
authors.lastname: He
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: He
authors.forename: Kaitlin E
authors.initials: KE
authors.lastname: Healy
authors.forename: Ellen R
authors.initials: ER
authors.lastname: Higinbotham
authors.forename: Erin N
authors.initials: EN
authors.lastname: Hildebrandt
authors.forename: Jason H
authors.initials: JH
authors.lastname: Ho
authors.forename: Gina M
authors.initials: GM
authors.lastname: Hogan
authors.forename: Victoria G
authors.initials: VG
authors.lastname: Hohenstein
authors.forename: Nathan A
authors.initials: NA
authors.lastname: Holz
authors.forename: Vincent J
authors.initials: VJ
authors.lastname: Huang
authors.forename: Ericka L
authors.initials: EL
authors.lastname: Hufford
authors.forename: Peter M
authors.initials: PM
authors.lastname: Hynes
authors.forename: Arrykka S
authors.initials: AS
authors.lastname: Jackson
authors.forename: Erica C
authors.initials: EC
authors.lastname: Jansen
authors.forename: Jonathan
authors.initials: J
authors.lastname: Jarvik
authors.forename: Paul G
authors.initials: PG
authors.lastname: Jasinto
authors.forename: Tuajuanda C
authors.initials: TC
authors.lastname: Jordan
authors.forename: Tomas
authors.initials: T
authors.lastname: Kasza
authors.forename: Murray A
authors.initials: MA
authors.lastname: Katelyn
authors.forename: Jessica S
authors.initials: JS
authors.lastname: Kelsey
authors.forename: Larisa A
authors.initials: LA
authors.lastname: Kerrigan
authors.forename: Daryl
authors.initials: D
authors.lastname: Khaw
authors.forename: Junghee
authors.initials: J
authors.lastname: Kim
authors.forename: Justin Z
authors.initials: JZ
authors.lastname: Knutter
authors.forename: Ching-Chung
authors.initials: CC
authors.lastname: Ko
authors.forename: Gail V
authors.initials: GV
authors.lastname: Larkin
authors.forename: Jennifer R
authors.initials: JR
authors.lastname: Laroche
authors.forename: Asma
authors.initials: A
authors.lastname: Latif
authors.forename: Kohana D
authors.initials: KD
authors.lastname: Leuba
authors.forename: Sequoia I
authors.initials: SI
authors.lastname: Leuba
authors.forename: Lynn O
authors.initials: LO
authors.lastname: Lewis
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Loesser-Casey
authors.forename: Courtney A
authors.initials: CA
authors.lastname: Long
authors.forename: A Javier
authors.initials: AJ
authors.lastname: Lopez
authors.forename: Nicholas
authors.initials: N
authors.lastname: Lowery
authors.forename: Tina Q
authors.initials: TQ
authors.lastname: Lu
authors.forename: Victor
authors.initials: V
authors.lastname: Mac
authors.forename: Isaac R
authors.initials: IR
authors.lastname: Masters
authors.forename: Jazmyn J
authors.initials: JJ
authors.lastname: McCloud
authors.forename: Molly J
authors.initials: MJ
authors.lastname: McDonough
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Medenbach
authors.forename: Anjali
authors.initials: A
authors.lastname: Menon
authors.forename: Rachel
authors.initials: R
authors.lastname: Miller
authors.forename: Brandon K
authors.initials: BK
authors.lastname: Morgan
authors.forename: Patrick C
authors.initials: PC
authors.lastname: Ng
authors.forename: Elvis
authors.initials: E
authors.lastname: Nguyen
authors.forename: Katrina T
authors.initials: KT
authors.lastname: Nguyen
authors.forename: Emilie T
authors.initials: ET
authors.lastname: Nguyen
authors.forename: Kaylee M
authors.initials: KM
authors.lastname: Nicholson
authors.forename: Lindsay A
authors.initials: LA
authors.lastname: Parnell
authors.forename: Caitlin E
authors.initials: CE
authors.lastname: Peirce
authors.forename: Allison M
authors.initials: AM
authors.lastname: Perz
authors.forename: Luke J
authors.initials: LJ
authors.lastname: Peterson
authors.forename: Rachel E
authors.initials: RE
authors.lastname: Pferdehirt
authors.forename: Seegren V
authors.initials: SV
authors.lastname: Philip
authors.forename: Kit
authors.initials: K
authors.lastname: Pogliano
authors.forename: Joe
authors.initials: J
authors.lastname: Pogliano
authors.forename: Tamsen
authors.initials: T
authors.lastname: Polley
authors.forename: Erica J
authors.initials: EJ
authors.lastname: Puopolo
authors.forename: Hannah S
authors.initials: HS
authors.lastname: Rabinowitz
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Resiss
authors.forename: Corwin N
authors.initials: CN
authors.lastname: Rhyan
authors.forename: Yetta M
authors.initials: YM
authors.lastname: Robinson
authors.forename: Lauren L
authors.initials: LL
authors.lastname: Rodriguez
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Rose
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Rubin
authors.forename: Jessica A
authors.initials: JA
authors.lastname: Ruby
authors.forename: Margaret S
authors.initials: MS
authors.lastname: Saha
authors.forename: James W
authors.initials: JW
authors.lastname: Sandoz
authors.forename: Judith
authors.initials: J
authors.lastname: Savitskaya
authors.forename: Dale J
authors.initials: DJ
authors.lastname: Schipper
authors.forename: Christine E
authors.initials: CE
authors.lastname: Schnitzler
authors.forename: Amanda R
authors.initials: AR
authors.lastname: Schott
authors.forename: J Bradley
authors.initials: JB
authors.lastname: Segal
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Shaffer
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Sheldon
authors.forename: Erica M
authors.initials: EM
authors.lastname: Shepard
authors.forename: Jonathan W
authors.initials: JW
authors.lastname: Shepardson
authors.forename: Madav K
authors.initials: MK
authors.lastname: Shroff
authors.forename: Jessica M
authors.initials: JM
authors.lastname: Simmons
authors.forename: Erika F
authors.initials: EF
authors.lastname: Simms
authors.forename: Brandy M
authors.initials: BM
authors.lastname: Simpson
authors.forename: Kathryn M
authors.initials: KM
authors.lastname: Sinclair
authors.forename: Robert L
authors.initials: RL
authors.lastname: Sjoholm
authors.forename: Ingrid J
authors.initials: IJ
authors.lastname: Slette
authors.forename: Blaire C
authors.initials: BC
authors.lastname: Spaulding
authors.forename: Clark L
authors.initials: CL
authors.lastname: Straub
authors.forename: Joseph
authors.initials: J
authors.lastname: Stukey
authors.forename: Trevor
authors.initials: T
authors.lastname: Sughrue
authors.forename: Tin-Yun
authors.initials: TY
authors.lastname: Tang
authors.forename: Lyons M
authors.initials: LM
authors.lastname: Tatyana
authors.forename: Stephen B
authors.initials: SB
authors.lastname: Taylor
authors.forename: Barbara J
authors.initials: BJ
authors.lastname: Taylor
authors.forename: Louise M
authors.initials: LM
authors.lastname: Temple
authors.forename: Jasper V
authors.initials: JV
authors.lastname: Thompson
authors.forename: Michael P
authors.initials: MP
authors.lastname: Tokarz
authors.forename: Stephanie E
authors.initials: SE
authors.lastname: Trapani
authors.forename: Alexander P
authors.initials: AP
authors.lastname: Troum
authors.forename: Jonathan
authors.initials: J
authors.lastname: Tsay
authors.forename: Anthony T
authors.initials: AT
authors.lastname: Tubbs
authors.forename: Jillian M
authors.initials: JM
authors.lastname: Walton
authors.forename: Danielle H
authors.initials: DH
authors.lastname: Wang
authors.forename: Hannah
authors.initials: H
authors.lastname: Wang
authors.forename: John R
authors.initials: JR
authors.lastname: Warner
authors.forename: Emilie G
authors.initials: EG
authors.lastname: Weisser
authors.forename: Samantha C
authors.initials: SC
authors.lastname: Wendler
authors.forename: Kathleen A
authors.initials: KA
authors.lastname: Weston-Hafer
authors.forename: Hilary M
authors.initials: HM
authors.lastname: Whelan
authors.forename: Kurt E
authors.initials: KE
authors.lastname: Williamson
authors.forename: Angelica N
authors.initials: AN
authors.lastname: Willis
authors.forename: Hannah S
authors.initials: HS
authors.lastname: Wirtshafter
authors.forename: Theresa W
authors.initials: TW
authors.lastname: Wong
authors.forename: Phillip
authors.initials: P
authors.lastname: Wu
authors.forename: Yun jeong
authors.initials: Yj
authors.lastname: Yang
authors.forename: Brandon C
authors.initials: BC
authors.lastname: Yee
authors.forename: David A
authors.initials: DA
authors.lastname: Zaidins
authors.forename: Bo
authors.initials: B
authors.lastname: Zhang
authors.forename: Melina Y
authors.initials: MY
authors.lastname: Zúniga
authors.forename: Roger W
authors.initials: RW
authors.lastname: Hendrix
authors.forename: Graham F
authors.initials: GF
authors.lastname: Hatfull
mesh_terms: D001483:Base Sequence; D005075:Biological Evolution; D004279:DNA, Viral / Q000235:genetics; D014644:Genetic Variation; D016679:Genome, Viral / Q000235:genetics*; D005843:Geography; D009160:Mycobacteriophages / Q000235:genetics* / Q000276:immunology / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D014481:United States
chemical_list: D004279:DNA, Viral