期刊论文详细信息
BMC Genomics
Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt
Alan R Hauser1  Jonathan P Allen1  Egon A Ozer2 
[1] Department of Microbiology-Immunology, Northwestern University, 303 East Chicago Avenue, Ward 8-296, Chicago, IL 60611, USA;Department of Medicine, Division of Infectious Diseases, Northwestern University, 645 North Michigan Avenue, Suite 900, Chicago, IL 60611, USA
关键词: Whole-genome sequencing;    AGEnt;    Spine;    Comparative genomics;    Accessory genome;    Core genome;    Pseudomonas aeruginosa;   
Others  :  1141129
DOI  :  10.1186/1471-2164-15-737
 received in 2014-01-27, accepted in 2014-08-22,  发布年份 2014
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【 摘 要 】

Background

Pseudomonas aeruginosa is an important opportunistic pathogen responsible for many infections in hospitalized and immunocompromised patients. Previous reports estimated that approximately 10% of its 6.6 Mbp genome varies from strain to strain and is therefore referred to as “accessory genome”. Elements within the accessory genome of P. aeruginosa have been associated with differences in virulence and antibiotic resistance. As whole genome sequencing of bacterial strains becomes more widespread and cost-effective, methods to quickly and reliably identify accessory genomic elements in newly sequenced P. aeruginosa genomes will be needed.

Results

We developed a bioinformatic method for identifying the accessory genome of P. aeruginosa. First, the core genome was determined based on sequence conserved among the completed genomes of twelve reference strains using Spine, a software program developed for this purpose. The core genome was 5.84 Mbp in size and contained 5,316 coding sequences. We then developed an in silico genome subtraction program named AGEnt to filter out core genomic sequences from P. aeruginosa whole genomes to identify accessory genomic sequences of these reference strains. This analysis determined that the accessory genome of P. aeruginosa ranged from 6.9-18.0% of the total genome, was enriched for genes associated with mobile elements, and was comprised of a majority of genes with unknown or unclear function. Using these genomes, we showed that AGEnt performed well compared to other publically available programs designed to detect accessory genomic elements. We then demonstrated the utility of the AGEnt program by applying it to the draft genomes of two previously unsequenced P. aeruginosa strains, PA99 and PA103.

Conclusions

The P. aeruginosa genome is rich in accessory genetic material. The AGEnt program accurately identified the accessory genomes of newly sequenced P. aeruginosa strains, even when draft genomes were used. As P. aeruginosa genomes become available at an increasingly rapid pace, this program will be useful in cataloging the expanding accessory genome of this bacterium and in discerning correlations between phenotype and accessory genome makeup. The combination of Spine and AGEnt should be useful in defining the accessory genomes of other bacterial species as well.

【 授权许可】

   
2014 Ozer et al.; licensee BioMed Central Ltd.

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【 参考文献 】
  • [1]Silby MW, Winstanley C, Godfrey SA, Levy SB, Jackson RW: Pseudomonas genomes: diverse and adaptable. FEMS Microbiol Rev 2011, 35(4):652-680.
  • [2]Jarvis WR: Epidemiology and Control of Pseudomonas aeruginosa Infections in the Intensive Care Unit. In Severe Infections Caused by Pseudomonas aeruginosa. Edited by Hauser AR, Rello J. Boston: Kluwer Academic Publishers; 2003:153-168.
  • [3]Obritsch MD, Fish DN, MacLaren R, Jung R: National surveillance of antimicrobial resistance in Pseudomonas aeruginosa isolates obtained from intensive care unit patients from 1993 to 2002. Antimicrob Agents Chemother 2004, 48(12):4606-4610.
  • [4]Fagon JY, Chastre J, Domart Y, Trouillet JL, Pierre J, Carne C, Gibert C: Nosocomial pneumonia in patients receiving continuous mechanical ventilation. Am Rev Respir Dis 1989, 139:877-884.
  • [5]Rakhimova E, Wiehlmann L, Brauer AL, Sethi S, Murphy TF, Tummler B: Pseudomonas aeruginosa population biology in chronic obstructive pulmonary disease. J Infect Dis 2009, 200(12):1928-1935.
  • [6]Pier GB, Ramphal R: Pseudomonas aeruginosa. In Principles and Practice of Infectious Diseases. 7th edition. Edited by Mandell GL, Bennett JE, Dolin R. Philadelphia, PA: Elsevier, Churchill, Livingstone; 2010:2835-2860.
  • [7]Bodey GP, Bolivar R, Fainstein V, Jadeja L: Infections Caused by Pseudomonas aeruginosa. Rev Infect Dis 1983, 5:279-313.
  • [8]Dantas G, Sommer MO, Oluwasegun RD, Church GM: Bacteria subsisting on antibiotics. Science 2008, 320(5872):100-103.
  • [9]Serres MH, Kerr AR, McCormack TJ, Riley M: Evolution by leaps: gene duplication in bacteria. Biol Direct 2009, 4:46.
  • [10]Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FSL, Hufnagle WO, Kowalk DJ, Lagrou M, Garber RL, Goltry L, Tolentino E, Westbrock-Wadman S, Yuan Y, Brody LL, Coulter SN, Folger KR, Kas A, Larbig K, Lim R, Smith K, Spencer D, Wong GK-S, Wu Z, Paulsen IT, Reizer J, Saler MH, Hancock REW, Lory S, et al.: Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 2000, 406:959-964.
  • [11]Wolfgang MC, Kulasekara BR, Liang X, Boyd D, Wu K, Yang Q, Miyada CG, Lory S: Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2003, 100(14):8484-8489.
  • [12]Mathee K, Narasimhan G, Valdes C, Qiu X, Matewish JM, Koehrsen M, Rokas A, Yandava CN, Engels R, Zeng E, Olavarietta R, Doud M, Smith RS, Montgomery P, White JR, Godfrey PA, Kodira C, Birren B, Galagan JE, Lory S: Dynamics of Pseudomonas aeruginosa genome evolution. Proc Natl Acad Sci U S A 2008, 105(8):3100-3105.
  • [13]Dobrindt U, Hochhut B, Hentschel U, Hacker J: Genomic islands in pathogenic and environmental microorganisms. Nat Rev Microbiol 2004, 2(5):414-424.
  • [14]Hentschel U, Hacker J: Pathogenicity islands: the tip of the iceberg. Microbes Infect 2001, 3(7):545-548.
  • [15]Juhas M, Van der Meer JR, Gaillard M, Harding RM, Hood DW, Crook DW: Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol Rev 2009, 33(2):376-393.
  • [16]Kung VL, Ozer EA, Hauser AR: The accessory genome of Pseudomonas aeruginosa. Microbiol Mol Biol Rev 2010, 74(4):621-641.
  • [17]Aguilar-Barajas E, Ramírez-Díaz MI, Riveros-Rosas H, Cervantes C: Heay Metal Resistance in Pseudomonads. In Pseudomonas. Edited by Ramos JL, Filloux A. New York: Springer; 2010:255-282. [Molecular Microbiology, Infection and Biodiversity, Volume 6]
  • [18]Campos-García J: Metabolism of Acyclic Terpenes by Pseudomonas. In Pseudomonas . Edited by Ramos JL, Filloux A. New York: Springer; 2010:235-254. [Molecular Microbiology, Infection and Biodiversity, Volume 6]
  • [19]Ho Sui SJ, Fedynak A, Hsiao WW, Langille MG, Brinkman FS: The association of virulence factors with genomic islands. PLoS One 2009, 4(12):e8094.
  • [20]Shen K, Sayeed S, Antalis P, Gladitz J, Ahmed A, Dice B, Janto B, Dopico R, Keefe R, Hayes J, Johnson S, Yu S, Ehrlich N, Jocz J, Kropp L, Wong R, Wadowsky RM, Slifkin M, Preston RA, Erdos G, Post JC, Ehrlich GD, Hu FZ: Extensive genomic plasticity in Pseudomonas aeruginosa revealed by identification and distribution studies of novel genes among clinical isolates. Infect Immun 2006, 74(9):5272-5283.
  • [21]He J, Baldini RL, Deziel E, Saucier M, Zhang Q, Liberati NT, Lee D, Urbach J, Goodman HM, Rahme LG: The broad host range pathogen Pseudomonas aeruginosa strain PA14 carries two pathogenicity islands harboring plant and animal virulence genes. Proc Natl Acad Sci U S A 2004, 101(8):2530-2535.
  • [22]Finck-Barbançon V, Goranson J, Zhu L, Sawa T, Wiener-Kronish JP, Fleiszig SMJ, Wu C, Mende-Mueller L, Frank D: ExoU expression by Pseudomonas aeruginosa correlates with acute cytotoxicity and epithelial injury. Mol Microbiol 1997, 25:547-557.
  • [23]Hauser AR, Cobb E, Bodí M, Mariscal D, Vallés J, Engel JN, Rello J: Type III protein secretion is associated with poor clinical outcomes in patients with ventilator-associated pneumonia caused by Pseudomonas aeruginosa. Crit Care Med 2002, 30:521-528.
  • [24]Roy-Burman A, Savel RH, Racine S, Swanson BL, Revadigar NS, Fujimoto J, Sawa T, Frank DW, Wiener-Kronish JP: Type III protein secretion is associated with death in lower respiratory and systemic Pseudomonas aeruginosa infections. J Infect Dis 2001, 183:1767-1774.
  • [25]Schulert GS, Feltman H, Rabin SDP, Martin CG, Battle SE, Rello J, Hauser AR: Secretion of the toxin ExoU is a marker for highly virulent Pseudomonas aeruginosa isolates obtained from patients with hospital-acquired pneumonia. J Infect Dis 2003, 188(11):12p.
  • [26]El-Solh AA, Hattemer A, Hauser AR, Alhajhusain A, Vora H: Clinical outcomes of type III Pseudomonas aeruginosa bacteremia. Crit Care Med 2012, 40(4):1157-1163.
  • [27]Mesaros N, Nordmann P, Plesiat P, Roussel-Delvallez M, Van Eldere J, Glupczynski Y, Van Laethem Y, Jacobs F, Lebecque P, Malfroot A, Tulkens PM, Van Bambeke F: Pseudomonas aeruginosa: resistance and therapeutic options at the turn of the new millennium. Clin Microbiol Infect 2007, 13(6):19p.
  • [28]Riccio ML, Pallecchi L, Docquier JD, Cresti S, Catania MR, Pagani L, Lagatolla C, Cornaglia G, Fontana R, Rossolini GM: Clonal relatedness and conserved integron structures in epidemiologically unrelated Pseudomonas aeruginosa strains producing the VIM-1 metallo-{beta}-lactamase from different Italian hospitals. Antimicrob Agents Chemother 2005, 49(1):104-110.
  • [29]Siarkou VI, Vitti D, Protonotariou E, Ikonomidis A, Sofianou D: Molecular epidemiology of outbreak-related pseudomonas aeruginosa strains carrying the novel variant blaVIM-17 metallo-beta-lactamase gene. Antimicrob Agents Chemother 2009, 53(4):1325-1330.
  • [30]Tsakris A, Poulou A, Kristo I, Pittaras T, Spanakis N, Pournaras S, Markou F: Large dissemination of VIM-2-metallo-{beta}-lactamase-producing pseudomonas aeruginosa strains causing health care-associated community-onset infections. J Clin Microbiol 2009, 47(11):3524-3529.
  • [31]Tseng SP, Tsai JC, Teng LJ, Hsueh PR: Dissemination of transposon Tn6001 in carbapenem-non-susceptible and extensively drug-resistant Pseudomonas aeruginosa in Taiwan. J Antimicrob Chemother 2009, 64(6):1170-1174.
  • [32]Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D, Ward NL, Angiuoli SV, Crabtree J, Jones AL, Durkin AS, Deboy RT, Davidsen TM, Mora M, Scarselli M, Margarit y Ros I, Peterson JD, Hauser CR, Sundaram JP, Nelson WC, Madupu R, Brinkac LM, Dodson RJ, Rosovitz MJ, Sullivan SA, Daugherty SC, Haft DH, Selengut J, Gwinn ML, Zhou L, Zafar N, et al.: Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci U S A 2005, 102(39):13950-13955.
  • [33]Chun J, Grim CJ, Hasan NA, Lee JH, Choi SY, Haley BJ, Taviani E, Jeon YS, Kim DW, Lee JH, Brettin TS, Bruce DC, Challacombe JF, Detter JC, Han CS, Munk AC, Chertkov O, Meincke L, Saunders E, Walters RA, Huq A, Nair GB, Colwell RR: Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae. Proc Natl Acad Sci U S A 2009, 106(36):15442-15447.
  • [34]Kittichotirat W, Bumgarner RE, Asikainen S, Chen C: Identification of the pangenome and its components in 14 distinct Aggregatibacter actinomycetemcomitans strains by comparative genomic analysis. PLoS One 2011, 6(7):e22420.
  • [35]Langille MG, Hsiao WW, Brinkman FS: Evaluation of genomic island predictors using a comparative genomics approach. BMC Bioinformatics 2008, 9:329.
  • [36]Laing C, Buchanan C, Taboada EN, Zhang Y, Kropinski A, Villegas A, Thomas JE, Gannon VP: Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. BMC Bioinformatics 2010, 11:461.
  • [37]Laing C, Villegas A, Taboada EN, Kropinski A, Thomas JE, Gannon VP: Identification of Salmonella enterica species- and subgroup-specific genomic regions using Panseq 2.0. Infect Genet Evol 2011, 11(8):2151-2161.
  • [38]Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R: Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 2006, 7:142.
  • [39]Hsiao W, Wan I, Jones SJ, Brinkman FS: IslandPath: aiding detection of genomic islands in prokaryotes. Bioinformatics 2003, 19(3):418-420.
  • [40]Vernikos GS, Parkhill J: Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 2006, 22(18):2196-2203.
  • [41]Lawrence JG, Ochman H: Amelioration of bacterial genomes: rates of change and exchange. J Mol Evol 1997, 44:383-397.
  • [42]Langille MG, Brinkman FS: IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 2009, 25(5):664-665.
  • [43]Wu DQ, Ye J, Ou HY, Wei X, Huang X, He YW, Xu Y: Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18. BMC Genomics 2011, 12:438.
  • [44]Roy PH, Tetu SG, Larouche A, Elbourne L, Tremblay S, Ren Q, Dodson R, Harkins D, Shay R, Watkins K, Mahamoud Y, Paulsen IT: Complete genome sequence of the multiresistant taxonomic outlier Pseudomonas aeruginosa PA7. PLoS One 2010, 5(1):e8842.
  • [45]Kiil K, Binnewies TT, Willenbrock H, Hansen SK, Yang L, Jelsbak L, Ussery DW, Friis C: Comparative Genomics of Pseudomonas. In Pseudomonas: Model Organism, Pathogen, Cell Factory, Volume 1. Edited by Rehm BHA. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA; 2008:1-24.
  • [46]Tatusov RL, Koonin EV, Lipman DJ: A genomic perspective on protein families. Science 1997, 278(5338):631-637.
  • [47]Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV: The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res 2001, 29(1):22-28.
  • [48]Spine/AGEnt [http://vfsmspineagent.fsm.northwestern.edu webcite]
  • [49]Winstanley C, Langille MG, Fothergill JL, Kukavica-Ibrulj I, Paradis-Bleau C, Sanschagrin F, Thomson NR, Winsor GL, Quail MA, Lennard N, Bignell A, Clarke L, Seeger K, Saunders D, Harris D, Parkhill J, Hancock RE, Brinkman FS, Levesque RC: Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the liverpool epidemic strain of pseudomonas aeruginosa. Genome Res 2009, 19(1):12-23.
  • [50]Battle SE, Rello J, Hauser AR: Genomic islands of Pseudomonas aeruginosa. FEMS Microbiol Lett 2009, 290(1):70-78.
  • [51]Klockgether J, Cramer N, Wiehlmann L, Davenport CF, Tummler B: Pseudomonas aeruginosa genomic structure and diversity. Front Microbiol 2011, 2:150.
  • [52]Feltman H, Schulert G, Khan S, Jain M, Peterson L, Hauser AR: Prevalence of type III secretion genes in clinical and environmental isolates of Pseudomonas aeruginosa. Microbiology 2001, 147:2659-2669.
  • [53]Shaver CM, Hauser AR: Relative contributions of Pseudomonas aeruginosa ExoU, ExoS, and ExoT to virulence in the lung. Infect Immun 2004, 72:6969-6977.
  • [54]Shaver CM, Hauser AR: Interactions between effector proteins of the Pseudomonas aeruginosa type III secretion system do not significantly affect several measures of disease severity in mammals. Microbiology 2006, 152:143-152.
  • [55]Matz C, Moreno AM, Alhede M, Manefield M, Hauser AR, Givskov M, Kjelleberg S: Pseudomonas aeruginosa uses type III secretion system to kill biofilm-associated amoebae. ISME J 2008, 2(8):843-852.
  • [56]Howell HA, Logan LK, Hauser AR: Type III secretion of ExoU is critical during early Pseudomonas aeruginosa pneumonia. mBio 2013, 4(2):e00032-e00013.
  • [57]Liu PV: The roles of various fractions of Pseudomonas aeruginosa in its pathogenesis: II: effects of lecithinase and protease. J Infect Dis 1966, 116:112-116.
  • [58]Nicas T, Iglewski BH: The contribution of exoproducts to virulence of Pseudomonas aeruginosa. Can J Microbiol 1985, 31:387-392.
  • [59]Pukatzki S, Kessin RH, Mekalanos JJ: The human pathogen Pseudomonas aeruginosa utilizes conserved virulence pathways to infect the social amoeba Dictyostelium discoideum. Proc Natl Acad Sci U S A 2002, 99:3159-3164.
  • [60]Sato H, Hunt ML, Weiner JJ, Hansen AT, Frank DW: Modified needle-tip PcrV proteins reveal distinct phenotypes relevant to the control of type III secretion and intoxication by Pseudomonas aeruginosa. PLoS One 2011, 6(3):e18356.
  • [61]Boisvert S, Laviolette F, Corbeil J: Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. J Comput Biol 2010, 17(11):1519-1533.
  • [62]Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O: The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008, 9:75.
  • [63]Tummler B: Clonal Variations in Pseudomonas aeruginosa. In Pseudomonas. Edited by Ramos J-L, Levesque RC. New York City, USA: Springer; 2006:35-68. [Molecular Biology of Emerging Issues, Volume 4]
  • [64]Spencer DH, Kas A, Smith EE, Raymond CK, Sims EH, Hastings M, Burns JL, Kaul R, Olson MV: Whole-genome sequence variation among multiple isolates of Pseudomonas aeruginosa. J Bacteriol 2003, 185(4):1316-1325.
  • [65]Lukjancenko O, Wassenaar TM, Ussery DW: Comparison of 61 sequenced Escherichia coli genomes. Microb Ecol 2010, 60(4):708-720.
  • [66]Di Nocera PP, Rocco F, Giannouli M, Triassi M, Zarrilli R: Genome organization of epidemic Acinetobacter baumannii strains. BMC Microbiol 2011, 11:224.
  • [67]den Bakker HC, Desjardins CA, Griggs AD, Peters JE, Zeng Q, Young SK, Kodira CD, Yandava C, Hepburn TA, Haas BJ, Birren BW, Wiedmann M: Evolutionary dynamics of the accessory genome of Listeria monocytogenes. PLoS One 2013, 8(6):e67511.
  • [68]Lindsay JA, Holden MT: Understanding the rise of the superbug: investigation of the evolution and genomic variation of Staphylococcus aureus. Funct Integr Genomics 2006, 6(3):186-201.
  • [69]Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R: The microbial pan-genome. Curr Opin Genet Dev 2005, 15(6):589-594.
  • [70]Broekhuijsen M, Larsson P, Johansson A, Bystrom M, Eriksson U, Larsson E, Prior RG, Sjostedt A, Titball RW, Forsman M: Genome-wide DNA microarray analysis of Francisella tularensis strains demonstrates extensive genetic conservation within the species but identifies regions that are unique to the highly virulent F. tularensis subsp. tularensis. J Clin Microbiol 2003, 41(7):2924-2931.
  • [71]Bentley S: Sequencing the species pan-genome. Nat Rev Microbiol 2009, 7(4):258-259.
  • [72]Ferrara S, Brugnoli M, De Bonis A, Righetti F, Delvillani F, Deho G, Horner D, Briani F, Bertoni G: Comparative profiling of Pseudomonas aeruginosa strains reveals differential expression of novel unique and conserved small RNAs. PLoS One 2012, 7(5):e36553.
  • [73]Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T, et al.: Genomics: genome project standards in a new era of sequencing. Science 2009, 326(5950):236-237.
  • [74]Kingsford C, Schatz MC, Pop M: Assembly complexity of prokaryotic genomes using short reads. BMC Bioinformatics 2010, 11:21.
  • [75]Lee DG, Urbach JM, Wu G, Liberati NT, Feinbaum RL, Miyata S, Diggins LT, He J, Saucier M, Deziel E, Friedman L, Li L, Grills G, Montgomery K, Kucherlapati R, Rahme LG, Ausubel FM: Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial. Genome Biol 2006, 7(10):R90.
  • [76]Morales-Espinosa R, Soberon-Chavez G, Delgado-Sapien G, Sandner-Miranda L, Mendez JL, Gonzalez-Valencia G, Cravioto A: Genetic and phenotypic characterization of a Pseudomonas aeruginosa population with high frequency of genomic islands. PLoS One 2012, 7(5):e37459.
  • [77]Ou HY, He X, Harrison EM, Kulasekara BR, Thani AB, Kadioglu A, Lory S, Hinton JC, Barer MR, Deng Z, Rajakumar K: MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands. Nucleic Acids Res 2007, 35(Web Server issue):W97-W104.
  • [78]Chiapello H, Bourgait I, Sourivong F, Heuclin G, Gendrault-Jacquemard A, Petit MA, El Karoui M: Systematic determination of the mosaic structure of bacterial genomes: species backbone versus strain-specific loops. BMC Bioinformatics 2005, 6:171.
  • [79]Chiapello H, Gendrault A, Caron C, Blum J, Petit MA, El Karoui M: MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level. BMC Bioinformatics 2008, 9:498.
  • [80]Shao Y, He X, Harrison EM, Tai C, Ou HY, Rajakumar K, Deng Z: mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes. Nucleic Acids Res 2010, 38(Web Server issue):W194-W200.
  • [81]Soares SC, Abreu VA, Ramos RT, Cerdeira L, Silva A, Baumbach J, Trost E, Tauch A, Hirata R Jr, Mattos-Guaraldi AL, Miyoshi A, Azevedo V: PIPS: pathogenicity island prediction software. PLoS One 2012, 7(2):e30848.
  • [82]Staley JT: The bacterial species dilemma and the genomic-phylogenetic species concept. Philos Trans R Soc Lond B Biol Sci 2006, 361(1475):1899-1909.
  • [83]Imperi F, Antunes LC, Blom J, Villa L, Iacono M, Visca P, Carattoli A: The genomics of Acinetobacter baumannii: insights into genome plasticity, antimicrobial resistance and pathogenicity. IUBMB Life 2011, 63(12):1068-1074.
  • [84]Goebel BM, Stackebrandt E: Cultural and phylogenetic analysis of mixed microbial populations found in natural and commercial bioleaching environments. Appl Environ Microbiol 1994, 60(5):1614-1621.
  • [85]Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM: DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007, 57(Pt 1):81-91.
  • [86]Richter M, Rossello-Mora R: Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009, 106(45):19126-19131.
  • [87]Riley MA, Lizotte-Waniewski M: Population genomics and the bacterial species concept. Methods Mol Biol 2009, 532:367-377.
  • [88]Chan JZ, Halachev MR, Loman NJ, Constantinidou C, Pallen MJ: Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol 2012, 12:302.
  • [89]Ozen AI, Ussery DW: Defining the Pseudomonas genus: where do we draw the line with Azotobacter? Microb Ecol 2012, 63(2):239-248.
  • [90]Dettman JR, Rodrigue N, Aaron SD, Kassen R: Evolutionary genomics of epidemic and nonepidemic strains of Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2013, 110(52):21065-21070.
  • [91]Bezuidt OK, Klockgether J, Elsen S, Attree I, Davenport CF, Tummler B: Intraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TB. BMC Genomics 2013, 14:416.
  • [92]Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402.
  • [93]Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL: BLAST+: architecture and applications. BMC Bioinformatics 2009, 10:421.
  • [94]Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS: PHAST: a fast phage search tool. Nucleic Acids Res 2011, 39(Web Server issue):W347-W352.
  • [95]Bi D, Xu Z, Harrison EM, Tai C, Wei Y, He X, Jia S, Deng Z, Rajakumar K, Ou HY: ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. Nucleic Acids Res 2012, 40(Database issue):D621-D626.
  • [96]Winsor GL, Lam DK, Fleming L, Lo R, Whiteside MD, Yu NY, Hancock RE, Brinkman FS: Pseudomonas genome database: improved comparative analysis and population genomics capability for Pseudomonas genomes. Nucleic Acids Res 2011, 39(Database issue):D596-D600.
  • [97]Delcher AL, Phillippy A, Carlton J, Salzberg SL: Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 2002, 30(11):2478-2483.
  • [98]Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL: Versatile and open software for comparing large genomes. Genome Biol 2004, 5(2):R12.
  • [99]Stothard P, Wishart DS: Circular genome visualization and exploration using CGView. Bioinformatics 2005, 21(4):537-539.
  • [100]Edgar RC: Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010, 26(19):2460-2461.
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