Frost, L. S., Leplae, R., Summers, A. O., & Toussaint, A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol, 2005, 3(9), 722-732. doi:10.1038/nrmicro1235
Rankin DJ, Rocha EP, Brown SP: What traits are carried on mobile genetic elements, and why? Heredity (Edinb) 2011, 106(1):1-10.
Malachowa N, DeLeo FR. Mobile genetic elements of Staphylococcus aureus. Cell Mol Life Sci. 2010;67(18):3057–3071. doi:10.1007/s00018-010-0389-4.
Dimitriu T, Misevic D, Lindner AB, Taddei F. Mobile genetic elements are involved in bacterial sociality. Mob Genet Elements. 2015;5(1):7–11.
Toussaint A, Chandler M: Prokaryote genome fluidity: toward a system approach of the mobilome. Methods Mol Biol 2012, 804:57-80.
Menconi G, Battaglia G, Grossi R, Pisanti N, Marangoni R. Mobilomics in Saccharomyces cerevisiae strains. BMC Bioinformatics. 2013, 14:102. Published 2013 Mar 20. doi:10.1186/1471-2105-14-102
Jørgensen TS, Kiil AS, Hansen MA, Sørensen SJ, Hansen LH. Current strategies for mobilome research. Front Microbiol. 20155:750. Published 2015 Jan 22. doi:10.3389/fmicb.2014.00750
Brito, I. L., Yilmaz, S., Huang, K., Xu, L., Jupiter, S. D., Jenkins, A. P., Naisilisili,
W., Tamminen, M., Smillie, C. S., Wortman, J. R., Birren, B. W., Xavier, R. J., Blainey,
P. C., Singh, A. K., Gevers, D., & Alm, E. J. Mobile genes in the human microbiome are structured from global to individual scales. Nature,2016, 535(7612), 435-439. doi:10.1038/nature18927.
Parkhill J, Sebaihia M, Preston A, Murphy LD, Thomson N, et al. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussisand Bordetella bronchiseptica. Nat Genet, 2003, 35: 32–40.
Parkhill, J., Wren, B. W., Thomson, N. R., Titball, R. W., Holden, M. T. G., Prentice,
M. B., Sebaihia, M., James, K. D., Churcher, C., Mungall, K. L., Baker, S., Basham,
D., Bentley, S. D., Brooks, K., Cerdeño-Tárraga, A. M., Chillingworth, T., Cronin,
A., Davies, R. M., Davis, P., Dougan, G., Feltwell, T., Hamlin, N., Holroyd, S., Jagels,
K., Karlyshev, A. V., Leather, S., Moule, S., Oyston, P. C. F., Quail, M., Rutherford,
K., Simmonds, M., Skelton, J., Stevens, K., Whitehead, S., & Barrell, B. G. Genome sequence of Yersinia pestis, the causative agent of plague. Nature, 2001, 413, 523. doi:10.1038/35097083
Chain, P. S. G., Carniel, E., Larimer, F. W., Lamerdin, J., Stoutland, P. O., Regala,
W. M., Georgescu, A. M., Vergez, L. M., Land, M. L., Motin, V. L., Brubaker, R. R.,
Fowler, J., Hinnebusch, J., Marceau, M., Medigue, C., Simonet, M., Chenal-Francisque,
V., Souza, B., Dacheux, D., Elliott, J. M., Derbise, A., Hauser, L. J., & Garcia,
E. Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis. Proceedings of the National Academy of Sciences of the United States of America, 2004,
101(38), 13826-13831. doi:10.1073/pnas.0404012101
Marrs, B. Genetic recombination in Rhodopseudomonas capsulata. Proceedings of the National Academy of Sciences of the United States of America, 1974,
71(3), 971-973.
Lang AS, Westbye AB, Beatty JT: The Distribution, Evolution, and Roles of Gene Transfer Agents in Prokaryotic Genetic
Exchange. Annu Rev Virol 2017, 4(1):87-104.
Westbye AB, Beatty JT, Lang AS: Guaranteeing a captive audience: coordinated regulation of gene transfer agent (GTA)
production and recipient capability by cellular regulators. Curr Opin Microbiol 2017, 38:122-129.
Tomasch J, Wang H, Hall ATK, Patzelt D, Preusse M, Petersen J, Brinkmann H, Bunk B,
Bhuju S, Jarek M et al: Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not
Random. Genome Biol Evol 2018, 10(1):359-369.
Rodriguez-R, L. M., Grajales, A., Arrieta-Ortiz, M. L., Salazar, C., Restrepo, S.,
& Bernal, A. Genomes-based phylogeny of the genus Xanthomonas. BMC Microbiol, 2012, 12, 43. doi:10.1186/1471-2180-12-43
Ryan, R. P., Vorhölter, F. J., Potnis, N., Jones, J. B., Van Sluys, M. A., Bogdanove,
A. J., & Dow, J. M.. Pathogenomics of Xanthomonas: understanding bacterium-plant interactions. Nat Rev Microbiol, 2011, 9(5), 344-355. doi:10.1038/nrmicro2558
Jones, J. B., Lacy, G. H., Bouzar, H., Stall, R. E., & Schaad, N. W. Reclassification of the xanthomonads associated with bacterial spot disease of tomato
and pepper. Syst Appl Microbiol, 2004, 27(6), 755-762. doi:10.1078/0723202042369884
Jibrin MO, Potnis N, Timilsina S, Minsavage GV, Vallad GE, Roberts PD, Jones JB, Goss
EM: Genomic Inference of Recombination-Mediated Evolution in Xanthomonas euvesicatoria
and X. perforans. Appl Environ Microbiol 2018, 84(13).
Schwartz AR, Potnis N, Timilsina S, Wilson M, Patané J, Martins J, Minsavage GV, Dahlbeck
D, Akhunova A, Almeida Net al: Phylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity
in effector repertoires and identifies determinants of host specificity. Front Microbiol 2015, 6:535.
Timilsina, S., Jibrin, M. O., Potnis, N., Minsavage, G. V., Kebede, M., Schwartz,
A., Bart, R., Staskawicz, B., Boyer, C., Vallad, G. E., Pruvost, O., Jones, J. B.,
& Goss, E. M. Multilocus sequence analysis of xanthomonads causing bacterial spot of tomato and
pepper plants reveals strains generated by recombination among species and recent
global spread of Xanthomonas gardneri. Appl Environ Microbiol, 2015, 81(4), 1520-1529. doi:10.1128/AEM.03000-14
Lang AS, Beatty JT: The gene transfer agent of Rhodobacter capsulatus and "constitutive transduction"
in prokaryotes. Arch Microbiol 2001, 175(4):241-249.
Lang AS, Zhaxybayeva O, Beatty JT: Gene transfer agents: phage-like elements of genetic exchange. Nat Rev Microbiol 2012, 10(7):472-482.
Feiss, M, Catalano, C.E. Bacteriophage lambda terminase and the mechanisms of viral DNA packaging. C.E. Catalano (Ed.), Viral Genome Packaging Machines: Genetics, Structure, and Mechanism, Landes
Bioscience, Georgetown, TX (2005), pp. 5-39
Ponchon L, Boulanger P, Labesse G, Letellier L: The endonuclease domain of bacteriophage terminases belongs to the resolvase/integrase/ribonuclease
H superfamily: A bioinformatics analysis validated by a functional study on bacteriophage
T5. J Biol Chem 2006, 281: 5829-5836. 10.1074/jbc.M511817200
Murphy KC, Ritchie JM, Waldor MK, Løbner-Olesen A, Marinus MG: Dam methyltransferase is required for stable lysogeny of the Shiga toxin (Stx2)-encoding
bacteriophage 933W of enterohemorrhagic Escherichia coli O157:H7. J Bacteriol 2008, 190(1):438-441.
Hynes AP, Shakya M, Mercer RG, Grüll MP, Bown L, et al. Functional and evolutionary characterization of a gene transfer agent's multilocus
“genome.” Mol. Biol. Evol. 2016, 33:2530–43
Fogg PCM: Identification and characterization of a direct activator of a gene transfer agent. Nat Commun 2019, 10(1):595.
Shakya M, Soucy SM, Zhaxybayeva O: Insights into origin and evolution of α-proteobacterial gene transfer agents. Virus Evol 2017, 3(2):vex036.
Guy L, Nystedt B, Toft C, Zaremba-Niedzwiedzka K, Berglund EC, Granberg F, Näslund
K, Eriksson AS, Andersson SG: A gene transfer agent and a dynamic repertoire of secretion systems hold the keys
to the explosive radiation of the emerging pathogen Bartonella. PLoS Genet 2013, 9(3):e1003393.
Tamarit D, Neuvonen MM, Engel P, Guy L, Andersson SGE: Origin and Evolution of the Bartonella Gene Transfer Agent. Mol Biol Evol 2018, 35(2):451-464.
Sternberg N, Coulby J. Cleavage of the bacteriophage P1 packaging site (pac) is regulated by adenine methylation. Proc Natl Acad Sci U S A. 1990;87(20):8070–8074. doi:10.1073/pnas.87.20.8070
Bochow S, Elliman J, Owens L: Bacteriophage adenine methyltransferase: a life cycle regulator? Modelled using Vibrio
harveyi myovirus like. J Appl Microbiol 2012, 113(5):1001-1013.
Timilsina S, Pereira-Martin JA, Minsavage GV, et al. Multiple Recombination Events Drive the Current Genetic Structure of Xanthomonas perforans in Florida. Front Microbiol. 2019;10:448. Published 2019 Mar 13. doi:10.3389/fmicb.2019.00448
Duda RL, Oh B, Hendrix RW: Functional domains of the HK97 capsid maturation protease and the mechanisms of protein
encapsidation. J Mol Biol 2013, 425(15):2765-2781.
Ahmad AA, Askora A, Kawasaki T, Fujie M, Yamada T: The filamentous phage XacF1 causes loss of virulence in Xanthomonas axonopodis pv.
citri, the causative agent of citrus canker disease. Front Microbiol 2014, 5:321.
Ahmad AA, Ogawa M, Kawasaki T, Fujie M, Yamada T: Characterization of bacteriophages Cp1 and Cp2, the strain-typing agents for Xanthomonas
axonopodis pv. citri. Appl Environ Microbiol 2014, 80(1):77-85.
Chae JC, Hung NB, Yu SM, Lee HK, Lee YH: Diversity of bacteriophages infecting Xanthomonas oryzae pv. oryzae in paddy fields
and its potential to control bacterial leaf blight of rice. J Microbiol Biotechnol 2014, 24(6):740-747.
Buttimer C, McAuliffe O, Ross RP, Hill C, O'Mahony J, Coffey A: Bacteriophages and Bacterial Plant Diseases. Front Microbiol 2017, 8:34.
Redfield RJ, Soucy SM: Evolution of Bacterial Gene Transfer Agents. Front Microbiol 2018, 9:2527.
Westbye AB, Leung MM, Florizone SM, Taylor TA, Johnson JA, et al. Phosphate concentration and the putative sensor kinase protein CckA modulate cell
lysis and release of the Rhodobacter capsulatus gene transfer agent. J. Bacteriol. 2013. 195:5025–40
McDaniel LD, Young EC, Ritchie KB, Paul JH. Environmental factors influencing gene transfer agent (GTA) mediated transduction
in the subtropical ocean. PLoS One. ;7(8):e43506. doi:10.1371/journal.pone.0043506
Westbye AB, O'Neill Z, Schellenberg-Beaver T, Beatty JT: The Rhodobacter capsulatus gene transfer agent is induced by nutrient depletion and
the RNAP omega subunit. Microbiology 2017, 163(9):1355-1363.
Triplett LR, Hamilton JP, Buell CR, Tisserat NA, Verdier V, Zink F, Leach JE: Genomic analysis of Xanthomonas oryzae isolates from rice grown in the United States
reveals substantial divergence from known X. oryzae pathovars. Appl Environ Microbiol 2011, 77(12):3930-3937.
Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MT, Fookes M, Falush D, Keane
JA, Parkhill J: Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015, 31(22):3691-3693.
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood
phylogenies. Mol Biol Evol, 2015., 32:268–274. doi:10.1093/molbev/msu300
Didelot X, Wilson DJ: ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput Biol 2015, 11(2):e1004041.