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1. Expanding the diversity of mycobacteriophages: Insights into genome architecture and evolution

Author

Pope, WH, Jacobs-Sera, D, Russel, DA, Peebles, CL, Al-Atrache, Z, Alcoser, TA, Alexander, LM, Alfano, MB, Alford, ST, Amy, NE, Anderson, MD, Anderson, AG, Ang, AAS, Manuel, A, Barber, AJ, Barker, LP, Barrett, JM, Barshop, WD, Bauerle, CM, Bayles, IM, Belfield, KL, Best, AA, Agustin, B, Bowman, CA, Boyer, CA, Bradley, KW, Bradley, VA, Broadway, LN, Budwal, K, Busby, KN, Campbell, IW, Campbell, AM, Carey, A, Caruso, SM, Chew, RD, Cockburn, CL, Cohen, LB, Corajod, JM, Cresawn, SG, Davis, KR, Deng, L, Denver, DR, Dixon, BR, Ekram, S, Elgin, SCR, Engelsen, AE, English, BEV, Erb, ML, Estrada, C, Filliger, LZ, Findley, AM, Forbes, L, Forsyth, MH, Fox, TM, Fritz, MJ, Garcia, R, George, ZD, Georges, AE, Gissendanner, CR, Goff, S, Goldstein, R, Gordon, KC, Green, RD, Guerra, SL, Guiney-Olsen, KR, Guiza, BG, Haghighat, L, Hagopian, GV, Harmon, CJ, Harmson, JS, Hartzog, GA, Harvey, SE, He, S, He, KJ, Healy, KE, Higinbotham, ER, Hildebrandt, EN, Ho, JH, Hogan, GM, Hohenstein, VG, Holz, NA, Huang, VJ, Hufford, EL, Hynes, PM, Jackson, AS, Jansen, EC, Jarvik, J, Jasinto, PG, Jordan, TC, Kasza, T, Katelyn, MA, Kelsey, JS, Kerrigan, LA, Khaw, D, Kim, J, Knutter, JZ, Ko, CC, Larkin, GV, and Laroche, JR

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. © 2011 Hatfull et al.

Published
2011
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2. Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Author

Pope WH, Jacobs-Sera D, Russell DA, Peebles CL, Al-Atrache Z, Alcoser TA, Alexander LM, Alfano MB, Alford ST, Amy NE, Anderson MD, Anderson AG, Ang AA, Ares M Jr, Barber AJ, Barker LP, Barrett JM, Barshop WD, Bauerle CM, Bayles IM, Belfield KL, Best AA, Borjon A Jr, Bowman CA, Boyer CA, Bradley KW, Bradley VA, Broadway LN, Budwal K, Busby KN, Campbell IW, Campbell AM, Carey A, Caruso SM, Chew RD, Cockburn CL, Cohen LB, Corajod JM, Cresawn SG, Davis KR, Deng L, Denver DR, Dixon BR, Ekram S, Elgin SC, Engelsen AE, English BE, Erb ML, Estrada C, Filliger LZ, Findley AM, Forbes L, Forsyth MH, Fox TM, Fritz MJ, Garcia R, George ZD, Georges AE, Gissendanner CR, Goff S, Goldstein R, Gordon KC, Green RD, Guerra SL, Guiney-Olsen KR, Guiza BG, Haghighat L, Hagopian GV, Harmon CJ, Harmson JS, Hartzog GA, Harvey SE, He S, He KJ, Healy KE, Higinbotham ER, Hildebrandt EN, Ho JH, Hogan GM, Hohenstein VG, Holz NA, Huang VJ, Hufford EL, Hynes PM, Jackson AS, Jansen EC, Jarvik J, Jasinto PG, Jordan TC, Kasza T, Katelyn MA, Kelsey JS, Kerrigan LA, Khaw D, Kim J, Knutter JZ, Ko CC, Larkin GV, Laroche JR, Latif A, Leuba KD, Leuba SI, Lewis LO, Loesser-Casey KE, Long CA, Lopez AJ, Lowery N, Lu TQ, Mac V, Masters IR, McCloud JJ, McDonough MJ, Medenbach AJ, Menon A, Miller R, Morgan BK, Ng PC, Nguyen E, Nguyen KT, Nguyen ET, Nicholson KM, Parnell LA, Peirce CE, Perz AM, Peterson LJ, Pferdehirt RE, Philip SV, Pogliano K, Pogliano J, Polley T, Puopolo EJ, Rabinowitz HS, Resiss MJ, Rhyan CN, Robinson YM, Rodriguez LL, Rose AC, Rubin JD, Ruby JA, Saha MS, Sandoz JW, Savitskaya J, Schipper DJ, Schnitzler CE, Schott AR, Segal JB, Shaffer CD, Sheldon KE, Shepard EM, Shepardson JW, Shroff MK, Simmons JM, Simms EF, Simpson BM, Sinclair KM, Sjoholm RL, Slette IJ, Spaulding BC, Straub CL, Stukey J, Sughrue T, Tang TY, Tatyana LM, Taylor SB, Taylor BJ, Temple LM, Thompson JV, Tokarz MP, Trapani SE, Troum AP, Tsay J, Tubbs AT, Walton JM, Wang DH, Wang H, Warner JR, Weisser EG, Wendler SC, Weston-Hafer KA, Whelan HM, Williamson KE, Willis AN, Wirtshafter HS, Wong TW, Wu P, Yang Yj, Yee BC, Zaidins DA, Zhang B, Zúniga MY, Hendrix RW, and Hatfull GF

Subjects
Base Sequence, DNA, Viral genetics, Geography, Mycobacteriophages immunology, Mycobacteriophages isolation & purification, Sequence Analysis, DNA, United States, Biological Evolution, Genetic Variation, Genome, Viral genetics, Mycobacteriophages genetics
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.

Published
2011
Full Text
View/download PDF

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