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Volumn 8, Issue 11, 2013, Pages

Testing the reproducibility of multiple displacement amplification on genomes of clonal endosymbiont populations

Author keywords

[No Author keywords available]

Indexed keywords

BARTONELLA; DNA, BACTERIAL; GENOME, BACTERIAL; REPRODUCIBILITY OF RESULTS; SYMBIOSIS;

EID: 84894263761     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0082319     Document Type: Article
Times cited : (17)

References (58)
  • 1
    • 84866332775 scopus 로고    scopus 로고
    • Growing unculturable bacteria
    • doi:10.1128/JB.00345-12. PubMed: 22661685
    • Stewart EJ (2012) Growing unculturable bacteria. J Bacteriol 194: 4151-4160. doi:10.1128/JB.00345-12. PubMed: 22661685.
    • (2012) J Bacteriol , vol.194 , pp. 4151-4160
    • Stewart, E.J.1
  • 2
    • 40249095175 scopus 로고    scopus 로고
    • Something from (almost) nothing: The impact of multiple displacement amplification on microbial ecology
    • doi:10.1038/ismej.2008.10. PubMed: 18256705
    • Binga EK, Lasken RS, Neufeld JD (2008) Something from (almost) nothing: the impact of multiple displacement amplification on microbial ecology. ISME J 2: 233-241. doi:10.1038/ismej.2008.10. PubMed: 18256705.
    • (2008) ISME J , vol.2 , pp. 233-241
    • Binga, E.K.1    Lasken, R.S.2    Neufeld, J.D.3
  • 3
    • 84876122754 scopus 로고    scopus 로고
    • The future is now: Single-cell genomics of bacteria and archaea
    • doi:10.1111/1574-6976.12015. PubMed: 23298390
    • Blainey PC (2013) The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol Rev 37: 407-427. doi:10.1111/1574-6976.12015. PubMed: 23298390.
    • (2013) FEMS Microbiol Rev , vol.37 , pp. 407-427
    • Blainey, P.C.1
  • 4
    • 84864394611 scopus 로고    scopus 로고
    • Genomic sequencing of uncultured microorganisms from single cells
    • doi:10.1038/nrmicro2857. PubMed: 22890147
    • Lasken RS (2012) Genomic sequencing of uncultured microorganisms from single cells. Nat Rev Microbiol 10: 631-640. doi:10.1038/nrmicro2857. PubMed: 22890147.
    • (2012) Nat Rev Microbiol , vol.10 , pp. 631-640
    • Lasken, R.S.1
  • 5
    • 20444472433 scopus 로고    scopus 로고
    • Multiple displacement amplification as a pre-polymerase chain reaction (pre-PCR) to process difficult to amplify samples and low copy number sequences from natural environments
    • doi:10.1111/j.1462-2920.2005.00779.x. PubMed: 15946299
    • Gonzalez JM, Portillo MC, Saiz-Jimenez C (2005) Multiple displacement amplification as a pre-polymerase chain reaction (pre-PCR) to process difficult to amplify samples and low copy number sequences from natural environments. Environ Microbiol 7: 1024-1028. doi:10.1111/j.1462-2920.2005.00779.x. PubMed: 15946299.
    • (2005) Environ Microbiol , vol.7 , pp. 1024-1028
    • Gonzalez, J.M.1    Portillo, M.C.2    Saiz-Jimenez, C.3
  • 6
    • 3242665288 scopus 로고    scopus 로고
    • Multiple displacement amplification in combination with high-fidelity PCR improves detection of bacteria from single females or eggs of Metaseiulus occidentalis (Nesbitt) (Acari: Phytoseiidae)
    • doi:10.1016/j.jip.2004.05.005. PubMed: 15261775
    • Jeyaprakash A, Hoy MA (2004) Multiple displacement amplification in combination with high-fidelity PCR improves detection of bacteria from single females or eggs of Metaseiulus occidentalis (Nesbitt) (Acari: Phytoseiidae). J Invertebr Pathol 86: 111-116. doi:10.1016/j.jip.2004.05.005. PubMed: 15261775.
    • (2004) J Invertebr Pathol , vol.86 , pp. 111-116
    • Jeyaprakash, A.1    Hoy, M.A.2
  • 7
    • 33745118646 scopus 로고    scopus 로고
    • Whole-metagenome amplification of a microbial community associated with scleractinian coral by multiple displacement amplification using phi29 polymerase
    • doi:10.1111/j.1462-2920.2006.01005.x. PubMed: 16817924
    • Yokouchi H, Fukuoka Y, Mukoyama D, Calugay R, Takeyama H et al. (2006) Whole-metagenome amplification of a microbial community associated with scleractinian coral by multiple displacement amplification using phi29 polymerase. Environ Microbiol 8: 1155-1163. doi:10.1111/j.1462-2920.2006.01005. x. PubMed: 16817924.
    • (2006) Environ Microbiol , vol.8 , pp. 1155-1163
    • Yokouchi, H.1    Fukuoka, Y.2    Mukoyama, D.3    Calugay, R.4    Takeyama, H.5
  • 8
    • 33646559836 scopus 로고    scopus 로고
    • Environmental whole-genome amplification to access microbial populations in contaminated sediments
    • doi:10.1128/AEM.72.5.3291-3301.2006. PubMed: 16672469
    • Abulencia CB, Wyborski DL, Garcia JA, Podar M, Chen W et al. (2006) Environmental whole-genome amplification to access microbial populations in contaminated sediments. Appl Environ Microbiol 72: 3291-3301. doi:10.1128/AEM.72.5.3291-3301.2006. PubMed: 16672469.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 3291-3301
    • Abulencia, C.B.1    Wyborski, D.L.2    Garcia, J.A.3    Podar, M.4    Chen, W.5
  • 9
    • 33745595097 scopus 로고    scopus 로고
    • Using pyrosequencing to shed light on deep mine microbial ecology
    • doi:10.1186/1471-2164-7-57. PubMed: 16549033
    • Edwards RA, Rodriguez-Brito B, Wegley L, Haynes M, Breitbart M et al. (2006) Using pyrosequencing to shed light on deep mine microbial ecology. BMC Genomics 7: 57. doi:10.1186/1471-2164-7-57. PubMed: 16549033.
    • (2006) BMC Genomics , vol.7 , pp. 57
    • Edwards, R.A.1    Rodriguez-Brito, B.2    Wegley, L.3    Haynes, M.4    Breitbart, M.5
  • 10
    • 33645900569 scopus 로고    scopus 로고
    • Isothermal amplification and molecular typing of the obligate intracellular pathogen Mycobacterium leprae isolated from tissues of unknown origins
    • doi:10.1128/JCM.44.4.1502-1508.2006. PubMed: 16597883
    • Groathouse NA, Brown SE, Knudson DL, Brennan PJ, Slayden RA (2006) Isothermal amplification and molecular typing of the obligate intracellular pathogen Mycobacterium leprae isolated from tissues of unknown origins. J Clin Microbiol 44: 1502-1508. doi:10.1128/JCM.44.4.1502-1508.2006. PubMed: 16597883.
    • (2006) J Clin Microbiol , vol.44 , pp. 1502-1508
    • Groathouse, N.A.1    Brown, S.E.2    Knudson, D.L.3    Brennan, P.J.4    Slayden, R.A.5
  • 11
    • 0038781878 scopus 로고    scopus 로고
    • Unbiased whole-genome amplification directly from clinical samples
    • doi:10.1101/gr.816903. PubMed: 12695328
    • Hosono S, Faruqi AF, Dean FB, Du Y, Sun Z et al. (2003) Unbiased whole-genome amplification directly from clinical samples. Genome Res 13: 954-964. doi:10.1101/gr.816903. PubMed: 12695328.
    • (2003) Genome Res , vol.13 , pp. 954-964
    • Hosono, S.1    Faruqi, A.F.2    Dean, F.B.3    Du, Y.4    Sun, Z.5
  • 12
    • 84877118112 scopus 로고    scopus 로고
    • Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture
    • doi:10.1101/gr.150037.112. PubMed: 23525359
    • Seth-Smith HM, Harris SR, Skilton RJ, Radebe FM, Golparian D et al. (2013) Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture. Genome Res 23: 855-866. doi:10.1101/gr.150037.112. PubMed: 23525359.
    • (2013) Genome Res , vol.23 , pp. 855-866
    • Seth-Smith, H.M.1    Harris, S.R.2    Skilton, R.J.3    Radebe, F.M.4    Golparian, D.5
  • 13
    • 34548688408 scopus 로고    scopus 로고
    • Insights into the genome of large sulfur bacteria revealed by analysis of single filaments
    • doi:10.1371/journal.pbio.0050230. PubMed: 17760503
    • Mussmann M, Hu FZ, Richter M, de Beer D, Preisler A et al. (2007) Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PLoS Biol 5: e230. doi:10.1371/journal.pbio.0050230. PubMed: 17760503.
    • (2007) PLoS Biol , vol.5
    • Mussmann, M.1    Hu, F.Z.2    Richter, M.3    De Beer, D.4    Preisler, A.5
  • 14
    • 79952005150 scopus 로고    scopus 로고
    • A novel method for the isolation of DNA from intracellular bacteria, suitable for genomic studies
    • doi:10.1007/s13213-010-0063-y
    • Epis S, Luciano AM, Franciosi F, Bazzocchi C, Crotti E et al. (2010) A novel method for the isolation of DNA from intracellular bacteria, suitable for genomic studies. Annals of Microbiology 60: 455-460. doi:10.1007/s13213-010- 0063-y.
    • (2010) Annals of Microbiology , vol.60 , pp. 455-460
    • Epis, S.1    Luciano, A.M.2    Franciosi, F.3    Bazzocchi, C.4    Crotti, E.5
  • 15
    • 44449129878 scopus 로고    scopus 로고
    • Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell
    • doi:10.1073/pnas.0801389105. PubMed: 18391199
    • Hongoh Y, Sharma VK, Prakash T, Noda S, Taylor TD et al. (2008) Complete genome of the uncultured Termite Group 1 bacteria in a single host protist cell. Proc Natl Acad Sci U S A 105: 5555-5560. doi:10.1073/pnas.0801389105. PubMed: 18391199.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 5555-5560
    • Hongoh, Y.1    Sharma, V.K.2    Prakash, T.3    Noda, S.4    Taylor, T.D.5
  • 16
    • 77953807223 scopus 로고    scopus 로고
    • One bacterial cell, one complete genome
    • doi:10.1371/journal.pone.0010314. PubMed: 20428247
    • Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A et al. (2010) One bacterial cell, one complete genome. PLOS ONE 5: e10314. doi:10.1371/journal. pone.0010314. PubMed: 20428247.
    • (2010) PLOS ONE , vol.5
    • Woyke, T.1    Tighe, D.2    Mavromatis, K.3    Clum, A.4    Copeland, A.5
  • 18
    • 84868089864 scopus 로고    scopus 로고
    • Comparative genomics suggests an independent origin of cytoplasmic incompatibility in Cardinium hertigii
    • PubMed: 23133394
    • Penz T, Schmitz-Esser S, Kelly SE, Cass BN, Müller A et al. (2012) Comparative genomics suggests an independent origin of cytoplasmic incompatibility in Cardinium hertigii. PLoS Genet 8: e1003012. PubMed: 23133394.
    • (2012) PLoS Genet , vol.8
    • Penz, T.1    Schmitz-Esser, S.2    Kelly, S.E.3    Cass, B.N.4    Müller, A.5
  • 19
    • 84879348435 scopus 로고    scopus 로고
    • Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis
    • doi:10.1016/j.cell.2013.05.040. PubMed: 23791183
    • Husnik F, Nikoh N, Koga R, Ross L, Duncan RP et al. (2013) Horizontal gene transfer from diverse bacteria to an insect genome enables a tripartite nested mealybug symbiosis. Cell 153: 1567-1578. doi:10.1016/j.cell.2013.05.040. PubMed: 23791183.
    • (2013) Cell , vol.153 , pp. 1567-1578
    • Husnik, F.1    Nikoh, N.2    Koga, R.3    Ross, L.4    Duncan, R.P.5
  • 20
    • 77958507828 scopus 로고    scopus 로고
    • Functional convergence in reduced genomes of bacterial symbionts spanning 200 My of evolution
    • PubMed: 20829280
    • McCutcheon JP, Moran NA (2010) Functional convergence in reduced genomes of bacterial symbionts spanning 200 My of evolution. Genome Biol Evol 2: 708-718. PubMed: 20829280.
    • (2010) Genome Biol Evol , vol.2 , pp. 708-718
    • McCutcheon, J.P.1    Moran, N.A.2
  • 21
    • 79952050667 scopus 로고    scopus 로고
    • Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis
    • doi:10.1371/journal.pone.0016626. PubMed: 21364937
    • Blainey PC, Mosier AC, Potanina A, Francis CA, Quake SR (2011) Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PLOS ONE 6: e16626. doi:10.1371/journal.pone.0016626. PubMed: 21364937.
    • (2011) PLOS ONE , vol.6
    • Blainey, P.C.1    Mosier, A.C.2    Potanina, A.3    Francis, C.A.4    Quake, S.R.5
  • 22
    • 84878724342 scopus 로고    scopus 로고
    • Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage
    • doi:10.1038/ncomms2884. PubMed: 23673639
    • Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, Ross CA et al. (2013) Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat Commun 4: 1854. doi:10.1038/ncomms2884. PubMed: 23673639.
    • (2013) Nat Commun , vol.4 , pp. 1854
    • Dodsworth, J.A.1    Blainey, P.C.2    Murugapiran, S.K.3    Swingley, W.D.4    Ross, C.A.5
  • 23
    • 34547492897 scopus 로고    scopus 로고
    • Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time
    • doi:10.1073/pnas.0700496104. PubMed: 17502618
    • Stepanauskas R, Sieracki ME (2007) Matching phylogeny and metabolism in the uncultured marine bacteria, one cell at a time. Proc Natl Acad Sci U S A 104: 9052-9057. doi:10.1073/pnas.0700496104. PubMed: 17502618.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 9052-9057
    • Stepanauskas, R.1    Sieracki, M.E.2
  • 24
    • 65449134335 scopus 로고    scopus 로고
    • Assembling the marine metagenome, one cell at a time
    • doi:10.1371/journal.pone.0005299. PubMed: 19390573
    • Woyke T, Xie G, Copeland A, González JM, Han C et al. (2009) Assembling the marine metagenome, one cell at a time. PLOS ONE 4: e5299. doi:10.1371/journal.pone.0005299. PubMed: 19390573.
    • (2009) PLOS ONE , vol.4
    • Woyke, T.1    Xie, G.2    Copeland, A.3    González, J.M.4    Han, C.5
  • 25
    • 84861895026 scopus 로고    scopus 로고
    • Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB)
    • doi:10.1101/gr.131482.111. PubMed: 22434425
    • Pamp SJ, Harrington ED, Quake SR, Relman DA, Blainey PC (2012) Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB). Genome Res 22: 1107-1119. doi:10.1101/gr.131482.111. PubMed: 22434425.
    • (2012) Genome Res , vol.22 , pp. 1107-1119
    • Pamp, S.J.1    Harrington, E.D.2    Quake, S.R.3    Relman, D.A.4    Blainey, P.C.5
  • 26
    • 20444418081 scopus 로고    scopus 로고
    • Genomic DNA amplification from a single bacterium
    • doi:10.1128/AEM.71.6.3342-3347.2005. PubMed: 15933038
    • Raghunathan A, Ferguson HR Jr., Bornarth CJ, Song W, Driscoll M et al. (2005) Genomic DNA amplification from a single bacterium. Appl Environ Microbiol 71: 3342-3347. doi:10.1128/AEM.71.6.3342-3347.2005. PubMed: 15933038.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 3342-3347
    • Raghunathan, A.1    Ferguson Jr., H.R.2    Bornarth, C.J.3    Song, W.4    Driscoll, M.5
  • 27
    • 70149108769 scopus 로고    scopus 로고
    • Whole genome amplification and de novo assembly of single bacterial cells
    • doi:10.1371/journal.pone.0006864. PubMed: 19724646
    • Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR et al. (2009) Whole genome amplification and de novo assembly of single bacterial cells. PLOS ONE 4: e6864. doi:10.1371/journal.pone.0006864. PubMed: 19724646.
    • (2009) PLOS ONE , vol.4
    • Rodrigue, S.1    Malmstrom, R.R.2    Berlin, A.M.3    Birren, B.W.4    Henn, M.R.5
  • 28
    • 33745085561 scopus 로고    scopus 로고
    • Sequencing genomes from single cells by polymerase cloning
    • doi:10.1038/nbt1214. PubMed: 16732271
    • Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J et al. (2006) Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol 24: 680-686. doi:10.1038/nbt1214. PubMed: 16732271.
    • (2006) Nat Biotechnol , vol.24 , pp. 680-686
    • Zhang, K.1    Martiny, A.C.2    Reppas, N.B.3    Barry, K.W.4    Malek, J.5
  • 29
    • 45849153461 scopus 로고    scopus 로고
    • Genomic sequencing of single microbial cells from environmental samples
    • doi:10.1016/j.mib.2008.05.006. PubMed: 18550420
    • Ishoey T, Woyke T, Stepanauskas R, Novotny M, Lasken RS (2008) Genomic sequencing of single microbial cells from environmental samples. Curr Opin Microbiol 11: 198-204. doi:10.1016/j.mib.2008.05.006. PubMed: 18550420.
    • (2008) Curr Opin Microbiol , vol.11 , pp. 198-204
    • Ishoey, T.1    Woyke, T.2    Stepanauskas, R.3    Novotny, M.4    Lasken, R.S.5
  • 30
    • 84875987691 scopus 로고    scopus 로고
    • A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella
    • Guy L, Nystedt B, Toft C, Zaremba-Niedzwiedzka K, Berglund EC et al. (2013) 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 9: e1003393.
    • (2013) PLOS Genet , vol.9
    • Guy, L.1    Nystedt, B.2    Toft, C.3    Zaremba-Niedzwiedzka, K.4    Berglund, E.C.5
  • 31
    • 79952351866 scopus 로고    scopus 로고
    • Digital MDA for enumeration of total nucleic acid contamination
    • doi:10.1093/nar/gkq768. PubMed: 21071419
    • Blainey PC, Quake SR (2011) Digital MDA for enumeration of total nucleic acid contamination. Nucleic Acids Res 39: e19. doi:10.1093/nar/gkq768. PubMed: 21071419.
    • (2011) Nucleic Acids Res , vol.39
    • Blainey, P.C.1    Quake, S.R.2
  • 33
    • 34247489656 scopus 로고    scopus 로고
    • Mechanism of chimera formation during the Multiple Displacement Amplification reaction
    • doi:10.1186/1472-6750-7-19. PubMed: 17430586
    • Lasken RS, Stockwell TB (2007) Mechanism of chimera formation during the Multiple Displacement Amplification reaction. BMC Biotechnol 7: 19. doi:10.1186/1472-6750-7-19. PubMed: 17430586.
    • (2007) BMC Biotechnol , vol.7 , pp. 19
    • Lasken, R.S.1    Stockwell, T.B.2
  • 34
    • 84860771820 scopus 로고    scopus 로고
    • SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing
    • doi:10.1089/cmb.2012.0021. PubMed: 22506599
    • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19: 455-477. doi:10.1089/cmb.2012.0021. PubMed: 22506599.
    • (2012) J Comput Biol , vol.19 , pp. 455-477
    • Bankevich, A.1    Nurk, S.2    Antipov, D.3    Gurevich, A.A.4    Dvorkin, M.5
  • 35
    • 81855199722 scopus 로고    scopus 로고
    • Phylogenomic evidence for the presence of a flagellum and cbb(3) oxidase in the free-living mitochondrial ancestor
    • doi:10.1093/molbev/msr159. PubMed: 21690562
    • Sassera D, Lo N, Epis S, D'Auria G, Montagna M et al. (2011) Phylogenomic evidence for the presence of a flagellum and cbb(3) oxidase in the free-living mitochondrial ancestor. Mol Biol Evol 28: 3285-3296. doi:10.1093/molbev/msr159. PubMed: 21690562.
    • (2011) Mol Biol Evol , vol.28 , pp. 3285-3296
    • Sassera, D.1    Lo, N.2    Epis, S.3    D'Auria, G.4    Montagna, M.5
  • 36
    • 33746095025 scopus 로고    scopus 로고
    • Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification
    • doi:10.1128/AEM.02738-05. PubMed: 16820490
    • Wu L, Liu X, Schadt CW, Zhou J (2006) Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification. Appl Environ Microbiol 72: 4931-4941. doi:10.1128/AEM. 02738-05. PubMed: 16820490.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 4931-4941
    • Wu, L.1    Liu, X.2    Schadt, C.W.3    Zhou, J.4
  • 37
    • 79960082882 scopus 로고    scopus 로고
    • Microarray-based evaluation of whole-community genome DNA amplification methods
    • doi:10.1128/AEM.01834-10. PubMed: 21498751
    • Wang J, Van Nostrand JD, Wu L, He Z, Li G et al. (2011) Microarray-based evaluation of whole-community genome DNA amplification methods. Appl Environ Microbiol 77: 4241-4245. doi:10.1128/AEM.01834-10. PubMed: 21498751.
    • (2011) Appl Environ Microbiol , vol.77 , pp. 4241-4245
    • Wang, J.1    Van Nostrand, J.D.2    Wu, L.3    He, Z.4    Li, G.5
  • 38
    • 78649707158 scopus 로고    scopus 로고
    • Multiple displacement amplification compromises quantitative analysis of metagenomes
    • doi:10.1038/nmeth1210-943. PubMed: 21116242
    • Yilmaz S, Allgaier M, Hugenholtz P (2010) Multiple displacement amplification compromises quantitative analysis of metagenomes. Nat Methods 7: 943-944. doi:10.1038/nmeth1210-943. PubMed: 21116242.
    • (2010) Nat Methods , vol.7 , pp. 943-944
    • Yilmaz, S.1    Allgaier, M.2    Hugenholtz, P.3
  • 39
    • 79951694175 scopus 로고    scopus 로고
    • Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
    • doi:10.1186/gb-2011-12-s1-p18. PubMed: 21338519
    • Aird D, Ross MG, Chen WS, Danielsson M, Fennell T et al. (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 12: R18. doi:10.1186/gb-2011-12-s1-p18. PubMed: 21338519.
    • (2011) Genome Biol , vol.12
    • Aird, D.1    Ross, M.G.2    Chen, W.S.3    Danielsson, M.4    Fennell, T.5
  • 40
    • 80054732674 scopus 로고    scopus 로고
    • Efficient de novo assembly of single-cell bacterial genomes from short-read data sets
    • doi:10.1038/nbt.1966. PubMed: 21926975
    • Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL et al. (2011) Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat Biotechnol 29: 915-921. doi:10.1038/nbt.1966. PubMed: 21926975.
    • (2011) Nat Biotechnol , vol.29 , pp. 915-921
    • Chitsaz, H.1    Yee-Greenbaum, J.L.2    Tesler, G.3    Lombardo, M.J.4    Dupont, C.L.5
  • 41
    • 78449299173 scopus 로고    scopus 로고
    • SmashCell: A software framework for the analysis of single-cell amplified genome sequences
    • doi:10.1093/bioinformatics/btq564. PubMed: 20966005
    • Harrington ED, Arumugam M, Raes J, Bork P, Relman DA (2010) SmashCell: a software framework for the analysis of single-cell amplified genome sequences. Bioinformatics 26: 2979-2980. doi:10.1093/bioinformatics/btq564. PubMed: 20966005.
    • (2010) Bioinformatics , vol.26 , pp. 2979-2980
    • Harrington, E.D.1    Arumugam, M.2    Raes, J.3    Bork, P.4    Relman, D.A.5
  • 42
    • 80051839847 scopus 로고    scopus 로고
    • Meraculous: De novo genome assembly with short paired-end reads
    • doi:10.1371/journal.pone.0023501. PubMed: 21876754
    • Chapman JA, Ho I, Sunkara S, Luo S, Schroth GP et al. (2011) Meraculous: de novo genome assembly with short paired-end reads. PLOS ONE 6: e23501. doi:10.1371/journal.pone.0023501. PubMed: 21876754.
    • (2011) PLOS ONE , vol.6
    • Chapman, J.A.1    Ho, I.2    Sunkara, S.3    Luo, S.4    Schroth, G.P.5
  • 43
    • 84866419785 scopus 로고    scopus 로고
    • Exploring symbioses by single-cell genomics
    • PubMed: 22983031
    • Kamke J, Bayer K, Woyke T, Hentschel U (2012) Exploring symbioses by single-cell genomics. Biol Bull 223: 30-43. PubMed: 22983031.
    • (2012) Biol Bull , vol.223 , pp. 30-43
    • Kamke, J.1    Bayer, K.2    Woyke, T.3    Hentschel, U.4
  • 44
    • 80054791084 scopus 로고    scopus 로고
    • Decontamination of MDA reagents for single cell whole genome amplification
    • doi:10.1371/journal.pone.0026161. PubMed: 22028825
    • Woyke T, Sczyrba A, Lee J, Rinke C, Tighe D et al. (2011) Decontamination of MDA reagents for single cell whole genome amplification. PLOS ONE 6: e26161. doi:10.1371/journal.pone.0026161. PubMed: 22028825.
    • (2011) PLOS ONE , vol.6
    • Woyke, T.1    Sczyrba, A.2    Lee, J.3    Rinke, C.4    Tighe, D.5
  • 45
    • 84861328656 scopus 로고    scopus 로고
    • Artificial polyploidy improves bacterial single cell genome recovery
    • doi:10.1371/journal.pone.0037387. PubMed: 22666352
    • Dichosa AE, Fitzsimons MS, Lo CC, Weston LL, Preteska LG et al. (2012) Artificial polyploidy improves bacterial single cell genome recovery. PLOS ONE 7: e37387. doi:10.1371/journal.pone.0037387. PubMed: 22666352.
    • (2012) PLOS ONE , vol.7
    • Dichosa, A.E.1    Fitzsimons, M.S.2    Lo, C.C.3    Weston, L.L.4    Preteska, L.G.5
  • 46
    • 0033040987 scopus 로고    scopus 로고
    • Intracellular bacterial symbionts of aphids possess many genomic copies per bacterium
    • doi:10.1007/PL00006516. PubMed: 10229576
    • Komaki K, Ishikawa H (1999) Intracellular bacterial symbionts of aphids possess many genomic copies per bacterium. J Mol Evol 48: 717-722. doi:10.1007/PL00006516. PubMed: 10229576.
    • (1999) J Mol Evol , vol.48 , pp. 717-722
    • Komaki, K.1    Ishikawa, H.2
  • 47
    • 0034059212 scopus 로고    scopus 로고
    • Genomic copy number of intracellular bacterial symbionts of aphids varies in response to developmental stage and morph of their host
    • doi:10.1016/S0965-1748(99)00125-3. PubMed: 10732993
    • Komaki K, Ishikawa H (2000) Genomic copy number of intracellular bacterial symbionts of aphids varies in response to developmental stage and morph of their host. Insect Biochem Mol Biol 30: 253-258. doi:10.1016/S0965- 1748(99)00125-3. PubMed: 10732993.
    • (2000) Insect Biochem Mol Biol , vol.30 , pp. 253-258
    • Komaki, K.1    Ishikawa, H.2
  • 48
    • 3242767830 scopus 로고    scopus 로고
    • Replication of the endosymbiotic bacterium Blochmannia floridanus is correlated with the developmental and reproductive stages of its ant host
    • doi:10.1128/AEM.70.7.4096-4102.2004. PubMed: 15240288
    • Wolschin F, Hölldobler B, Gross R, Zientz E (2004) Replication of the endosymbiotic bacterium Blochmannia floridanus is correlated with the developmental and reproductive stages of its ant host. Appl Environ Microbiol 70: 4096-4102. doi:10.1128/AEM.70.7.4096-4102.2004. PubMed: 15240288.
    • (2004) Appl Environ Microbiol , vol.70 , pp. 4096-4102
    • Wolschin, F.1    Hölldobler, B.2    Gross, R.3    Zientz, E.4
  • 49
    • 55849098139 scopus 로고    scopus 로고
    • Blattabacteria, the endosymbionts of cockroaches, have small genome sizes and high genome copy numbers
    • doi:10.1111/j.1462-2920.2008.01776.x. PubMed: 19025557
    • López-Sánchez MJ, Neef A, Patiño-Navarrete R, Navarro L, Jiménez R et al. (2008) Blattabacteria, the endosymbionts of cockroaches, have small genome sizes and high genome copy numbers. Environ Microbiol 10: 3417-3422. doi:10.1111/j.1462-2920.2008.01776.x. PubMed: 19025557.
    • (2008) Environ Microbiol , vol.10 , pp. 3417-3422
    • López-Sánchez, M.J.1    Neef, A.2    Patiño-Navarrete, R.3    Navarro, L.4    Jiménez, R.5
  • 50
    • 83055180102 scopus 로고    scopus 로고
    • Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA
    • doi:10.1128/AEM.05610-11. PubMed: 21948828
    • Marine R, Polson SW, Ravel J, Hatfull G, Russell D et al. (2011) Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA. Appl Environ Microbiol 77: 8071-8079. doi:10.1128/AEM.05610-11. PubMed: 21948828.
    • (2011) Appl Environ Microbiol , vol.77 , pp. 8071-8079
    • Marine, R.1    Polson, S.W.2    Ravel, J.3    Hatfull, G.4    Russell, D.5
  • 51
    • 49749134637 scopus 로고    scopus 로고
    • Genome evolution of Wolbachia strain wPip from the Culex pipiens group
    • doi:10.1093/molbev/msn133. PubMed: 18550617
    • Klasson L, Walker T, Sebaihia M, Sanders MJ, Quail MA et al. (2008) Genome evolution of Wolbachia strain wPip from the Culex pipiens group. Mol Biol Evol 25: 1877-1887. doi:10.1093/molbev/msn133. PubMed: 18550617.
    • (2008) Mol Biol Evol , vol.25 , pp. 1877-1887
    • Klasson, L.1    Walker, T.2    Sebaihia, M.3    Sanders, M.J.4    Quail, M.A.5
  • 52
    • 0242593808 scopus 로고    scopus 로고
    • Characterization of the natural population of Bartonella henselae by multilocus sequence typing
    • doi:10.1128/JCM.41.11.5071-5079.2003. PubMed: 14605141
    • Iredell J, Blanckenberg D, Arvand M, Grauling S, Feil EJ et al. (2003) Characterization of the natural population of Bartonella henselae by multilocus sequence typing. J Clin Microbiol 41: 5071-5079. doi:10.1128/JCM.41.11.5071- 5079.2003. PubMed: 14605141.
    • (2003) J Clin Microbiol , vol.41 , pp. 5071-5079
    • Iredell, J.1    Blanckenberg, D.2    Arvand, M.3    Grauling, S.4    Feil, E.J.5
  • 53
    • 84864483625 scopus 로고    scopus 로고
    • RobiNA: A user-friendly, integrated software solution for RNA-Seq-based transcriptomics
    • doi:10.1093/nar/gks540. PubMed: 22684630
    • Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE et al. (2012) RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res 40: W622-W627. doi:10.1093/nar/gks540. PubMed: 22684630.
    • (2012) Nucleic Acids Res , vol.40
    • Lohse, M.1    Bolger, A.M.2    Nagel, A.3    Fernie, A.R.4    Lunn, J.E.5
  • 54
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • doi:10.1093/bioinformatics/btp324. PubMed: 19451168
    • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760. doi:10.1093/ bioinformatics/btp324. PubMed: 19451168.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 55
    • 68549104404 scopus 로고    scopus 로고
    • The Sequence Alignment/Map format and SAMtools
    • doi:10.1093/bioinformatics/btp352. PubMed: 19505943
    • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079. doi:10.1093/bioinformatics/btp352. PubMed: 19505943.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3    Fennell, T.4    Ruan, J.5
  • 56
    • 2942538300 scopus 로고    scopus 로고
    • Versatile and open software for comparing large genomes
    • doi:10.1186/gb-2004-5-6-p12. PubMed: 14759262
    • Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. (2004) Versatile and open software for comparing large genomes. Genome Biol 5: R12. doi:10.1186/gb-2004-5-6-p12. PubMed: 14759262.
    • (2004) Genome Biol , vol.5
    • Kurtz, S.1    Phillippy, A.2    Delcher, A.L.3    Smoot, M.4    Shumway, M.5
  • 57
    • 0033635022 scopus 로고    scopus 로고
    • Artemis: Sequence visualization and annotation
    • doi:10.1093/bioinformatics/16.10.944. PubMed: 11120685
    • Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P et al. (2000) Artemis: sequence visualization and annotation. Bioinformatics 16: 944-945. doi:10.1093/bioinformatics/16.10.944. PubMed: 11120685.
    • (2000) Bioinformatics , vol.16 , pp. 944-945
    • Rutherford, K.1    Parkhill, J.2    Crook, J.3    Horsnell, T.4    Rice, P.5
  • 58
    • 0025183708 scopus 로고
    • Basic Local Alignment Search Tool
    • doi:10.1016/S0022-2836(05)80360-2. PubMed: 2231712
    • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic Local Alignment Search Tool. J Mol Biol 215: 403-410. doi:10.1016/S0022-2836(05)80360- 2. PubMed: 2231712.
    • (1990) J Mol Biol , vol.215 , pp. 403-410
    • Altschul, S.F.1    Gish, W.2    Miller, W.3    Myers, E.W.4    Lipman, D.J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.