메뉴 건너뛰기




Volumn 2016, Issue 6, 2016, Pages

Assessing Illumina technology for the high-throughput sequencing of bacteriophage genomes

Author keywords

Assembly; Bacteriophage; Genome; Illumina; Sequencing

Indexed keywords

BACTERIOPHAGE; ERROR; EXPERIMENTAL MODEL; GENOME; HIGH THROUGHPUT SEQUENCING;

EID: 84977091162     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.2055     Document Type: Article
Times cited : (31)

References (77)
  • 2
    • 84879605153 scopus 로고    scopus 로고
    • Viral metagenomics: a tool for virus discovery and diversity in aquaculture
    • Alavandi SV, Poornima M. 2012. Viral metagenomics: a tool for virus discovery and diversity in aquaculture. Indian Journal of Virology 23(2):88-98 DOI 10.1007/s13337-012-0075-2.
    • (2012) Indian Journal of Virology , vol.23 , Issue.2 , pp. 88-98
    • Alavandi, S.V.1    Poornima, M.2
  • 4
    • 67650735586 scopus 로고    scopus 로고
    • ABACAS: algorithm-based automatic contiguation of assembled sequences
    • Assefa S, Keane TM, Otto TD, Newbold C, Berriman M. 2009. ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics 25(15):1968-1969 DOI 10.1093/bioinformatics/btp347.
    • (2009) Bioinformatics , vol.25 , Issue.15 , pp. 1968-1969
    • Assefa, S.1    Keane, T.M.2    Otto, T.D.3    Newbold, C.4    Berriman, M.5
  • 9
    • 84939126973 scopus 로고    scopus 로고
    • Inexpensive multiplexed library preparation for megabase-sized genomes
    • Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM, Kishony R. 2015. Inexpensive multiplexed library preparation for megabase-sized genomes. PLoS ONE 10(5):e128036 DOI 10.1371/journal.pone.0128036.
    • (2015) PLoS ONE , vol.10 , Issue.5
    • Baym, M.1    Kryazhimskiy, S.2    Lieberman, T.D.3    Chung, H.4    Desai, M.M.5    Kishony, R.6
  • 10
    • 83455228523 scopus 로고    scopus 로고
    • Viral metagenomics as an emerging and powerful tool in veterinary medicine
    • Blomstrom AL. 2011. Viral metagenomics as an emerging and powerful tool in veterinary medicine. Veterinary Quarterly 31(3):107-114 DOI 10.1080/01652176.2011.604971.
    • (2011) Veterinary Quarterly , vol.31 , Issue.3 , pp. 107-114
    • Blomstrom, A.L.1
  • 11
    • 78349238864 scopus 로고    scopus 로고
    • Ray: simultaneous assembly of reads from a mix of highthroughput sequencing technologies
    • Boisvert S, Laviolette F, Corbeil J. 2010. Ray: simultaneous assembly of reads from a mix of highthroughput sequencing technologies. Journal of Computational Biology 17(11):1519-1533 DOI 10.1089/cmb.2009.0238.
    • (2010) Journal of Computational Biology , vol.17 , Issue.11 , pp. 1519-1533
    • Boisvert, S.1    Laviolette, F.2    Corbeil, J.3
  • 13
    • 20344382957 scopus 로고    scopus 로고
    • Here a virus, there a virus, everywhere the same virus?
    • Breitbart M, Rohwer F. 2005. Here a virus, there a virus, everywhere the same virus? Trends in Microbiology 13(6):278-284 DOI 10.1016/j.tim.2005.04.003.
    • (2005) Trends in Microbiology , vol.13 , Issue.6 , pp. 278-284
    • Breitbart, M.1    Rohwer, F.2
  • 16
    • 84949117159 scopus 로고    scopus 로고
    • Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes
    • Chan JZ-M, Millard AD, Mann NH, Schäfer H. 2014. Comparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes. Frontiers in Microbiology 5:506 DOI 10.3389/fmicb.2014.00506.
    • (2014) Frontiers in Microbiology , vol.5 , pp. 506
    • Chan, J.Z.-M.1    Millard, A.D.2    Mann, N.H.3    Schäfer, H.4
  • 18
    • 0344255699 scopus 로고    scopus 로고
    • Encapsidation of host DNA by bacteriophages infecting marine Synechococcus strains
    • Clokie MRJ, Millard AD, Wilson WH, Mann NH. 2003. Encapsidation of host DNA by bacteriophages infecting marine Synechococcus strains. FEMS Microbiology Ecology 46(3):349-352 DOI 10.1016/S0168-6496(03)00247-2.
    • (2003) FEMS Microbiology Ecology , vol.46 , Issue.3 , pp. 349-352
    • Clokie, M.R.J.1    Millard, A.D.2    Wilson, W.H.3    Mann, N.H.4
  • 20
    • 84903616167 scopus 로고    scopus 로고
    • Exploiting gut bacteriophages for human health
    • Dalmasso M, Hill C, Ross RP. 2014. Exploiting gut bacteriophages for human health. Trends in Microbiology 22(7):399-405 DOI 10.1016/j.tim.2014.02.010.
    • (2014) Trends in Microbiology , vol.22 , Issue.7 , pp. 399-405
    • Dalmasso, M.1    Hill, C.2    Ross, R.P.3
  • 21
    • 33947607974 scopus 로고    scopus 로고
    • Viral metagenomics
    • Delwart EL. 2007. Viral metagenomics. Reviews in Medical Virology 17(2):115-131 DOI 10.1002/rmv.532.
    • (2007) Reviews in Medical Virology , vol.17 , Issue.2 , pp. 115-131
    • Delwart, E.L.1
  • 22
    • 0020964297 scopus 로고
    • Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements
    • Dunn JJ, Studier FW, Gottesman M. 1983. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. Journal of Molecular Biology 166(4):477-535 DOI 10.1016/S0022-2836(83)80282-4.
    • (1983) Journal of Molecular Biology , vol.166 , Issue.4 , pp. 477-535
    • Dunn, J.J.1    Studier, F.W.2    Gottesman, M.3
  • 25
    • 0021738985 scopus 로고
    • Nucleotide sequence and properties of the cohesive DNA termini from bacteriophage HP1c1 of Haemophilus influenzae Rd
    • Fitzmaurice WP, Waldman AS, Benjamin RC, Huang PC, Scocca JJ. 1984. Nucleotide sequence and properties of the cohesive DNA termini from bacteriophage HP1c1 of Haemophilus influenzae Rd. Gene 31(1-3):197-203 DOI 10.1016/0378-1119(84)90210-5.
    • (1984) Gene , vol.31 , Issue.1-3 , pp. 197-203
    • Fitzmaurice, W.P.1    Waldman, A.S.2    Benjamin, R.C.3    Huang, P.C.4    Scocca, J.J.5
  • 28
    • 84886410346 scopus 로고    scopus 로고
    • Viral metagenomics analysis of planktonic viruses in East Lake, Wuhan, China
    • Ge X, Wu Y, Wang M, Wang J, Wu L, Yang X, Zhang Y, Shi Z. 2013. Viral metagenomics analysis of planktonic viruses in East Lake, Wuhan, China. Virologica Sinica 28(5):280-290 DOI 10.1007/s12250-013-3365-y.
    • (2013) Virologica Sinica , vol.28 , Issue.5 , pp. 280-290
    • Ge, X.1    Wu, Y.2    Wang, M.3    Wang, J.4    Wu, L.5    Yang, X.6    Zhang, Y.7    Shi, Z.8
  • 30
    • 84876266928 scopus 로고    scopus 로고
    • QUAST: quality assessment tool for genome assemblies
    • Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29(8):1072-1075 DOI 10.1093/bioinformatics/btt086.
    • (2013) Bioinformatics , vol.29 , Issue.8 , pp. 1072-1075
    • Gurevich, A.1    Saveliev, V.2    Vyahhi, N.3    Tesler, G.4
  • 33
    • 84857145150 scopus 로고    scopus 로고
    • ART: a next-generation sequencing read simulator
    • Huang W, Li L, Myers JR, Marth GT. 2012. ART: a next-generation sequencing read simulator. Bioinformatics 28(4):593-594 DOI 10.1093/bioinformatics/btr708.
    • (2012) Bioinformatics , vol.28 , Issue.4 , pp. 593-594
    • Huang, W.1    Li, L.2    Myers, J.R.3    Marth, G.T.4
  • 34
    • 84874530236 scopus 로고    scopus 로고
    • The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology
    • Hurwitz BL, Sullivan MB. 2013. The Pacific Ocean Virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS ONE 8(2):e57355 DOI 10.1371/journal.pone.0057355.
    • (2013) PLoS ONE , vol.8 , Issue.2
    • Hurwitz, B.L.1    Sullivan, M.B.2
  • 36
    • 84880693152 scopus 로고    scopus 로고
    • Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans
    • Kang I, Oh H-M, Kang D, Cho J-C. 2013. Genome of a SAR116 bacteriophage shows the prevalence of this phage type in the oceans. Proceedings of the National Academy of Sciences 110(30):12343-12348 DOI 10.1073/pnas.1219930110.
    • (2013) Proceedings of the National Academy of Sciences , vol.110 , Issue.30 , pp. 12343-12348
    • Kang, I.1    Oh, H.-M.2    Kang, D.3    Cho, J.-C.4
  • 37
    • 84903600405 scopus 로고    scopus 로고
    • Comparative viral metagenomics of environmental samples from Korea
    • Kim M-S, Whon TW, Bae J-W. 2013. Comparative viral metagenomics of environmental samples from Korea. Genomics and Informatics 11(3):121-128 DOI 10.5808/GI.2013.11.3.121.
    • (2013) Genomics and Informatics , vol.11 , Issue.3 , pp. 121-128
    • Kim, M.-S.1    Whon, T.W.2    Bae, J.-W.3
  • 39
    • 84878581087 scopus 로고    scopus 로고
    • Next generation sequencing technologies and the changing landscape of phage genomics
    • Klumpp J, Fouts DE, Sozhamannan S. 2012. Next generation sequencing technologies and the changing landscape of phage genomics. Bacteriophage 2(3):190-199 DOI 10.4161/bact.22111.
    • (2012) Bacteriophage , vol.2 , Issue.3 , pp. 190-199
    • Klumpp, J.1    Fouts, D.E.2    Sozhamannan, S.3
  • 41
    • 84896930168 scopus 로고    scopus 로고
    • DPS-a rapid method for genome sequencing of DNA-containing bacteriophages directly from a single plaque
    • Kot W, Vogensen FK, Sørensen SJ, Hansen LH. 2014. DPS-a rapid method for genome sequencing of DNA-containing bacteriophages directly from a single plaque. Journal of Virological Methods 196:152-156 DOI 10.1016/j.jviromet.2013.10.040.
    • (2014) Journal of Virological Methods , vol.196 , pp. 152-156
    • Kot, W.1    Vogensen, F.K.2    Sørensen, S.J.3    Hansen, L.H.4
  • 42
    • 0015886707 scopus 로고
    • Bacteriophage P2 head morphogenesis: cleavage of the major capsid protein
    • Lengyel JA, Goldstein RN, Marsh M, Sunshine MG, Calendar R. 1973. Bacteriophage P2 head morphogenesis: cleavage of the major capsid protein. Virology 53(1):1-23 DOI 10.1016/0042-6822(73)90461-3.
    • (1973) Virology , vol.53 , Issue.1 , pp. 1-23
    • Lengyel, J.A.1    Goldstein, R.N.2    Marsh, M.3    Sunshine, M.G.4    Calendar, R.5
  • 45
    • 27744480467 scopus 로고    scopus 로고
    • Photosynthesis genes in marine viruses yield proteins during host infection
    • Lindell D, Jaffe JD, Johnson ZI, Church GM, Chisholm SW. 2005. Photosynthesis genes in marine viruses yield proteins during host infection. Nature 438(7064):86-89 DOI 10.1038/nature04111.
    • (2005) Nature , vol.438 , Issue.7064 , pp. 86-89
    • Lindell, D.1    Jaffe, J.D.2    Johnson, Z.I.3    Church, G.M.4    Chisholm, S.W.5
  • 48
    • 84943582539 scopus 로고    scopus 로고
    • Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla
    • Malki K, Kula A, Bruder K, Sible E, Hatzopoulos T, Steidel S, Watkins SC, Putonti C. 2015. Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla. Virology Journal 12(1):164 DOI 10.1186/s12985-015-0395-0.
    • (2015) Virology Journal , vol.12 , Issue.1 , pp. 164
    • Malki, K.1    Kula, A.2    Bruder, K.3    Sible, E.4    Hatzopoulos, T.5    Steidel, S.6    Watkins, S.C.7    Putonti, C.8
  • 49
    • 0041736065 scopus 로고    scopus 로고
    • Marine ecosystems: bacterial photosynthesis genes in a virus
    • Mann NH, Cook A, Millard A, Bailey S, Clokie M. 2003. Marine ecosystems: bacterial photosynthesis genes in a virus. Nature 424(6950):741 DOI 10.1038/424741a.
    • (2003) Nature , vol.424 , Issue.6950 , pp. 741
    • Mann, N.H.1    Cook, A.2    Millard, A.3    Bailey, S.4    Clokie, M.5
  • 51
    • 84929353577 scopus 로고    scopus 로고
    • The cost of phage resistance in a plant pathogenic bacterium is context-dependent
    • Meaden S, Paszkiewicz K, Koskella B. 2015. The cost of phage resistance in a plant pathogenic bacterium is context-dependent. Evolution 69(5):1321-1328 DOI 10.1111/evo.12652.
    • (2015) Evolution , vol.69 , Issue.5 , pp. 1321-1328
    • Meaden, S.1    Paszkiewicz, K.2    Koskella, B.3
  • 53
    • 69949104491 scopus 로고    scopus 로고
    • Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence of Synechococcus host genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution
    • Millard AD, Zwirglmaier K, Downey MJ, Mann NH, Scanlan DJ. 2009. Comparative genomics of marine cyanomyoviruses reveals the widespread occurrence of Synechococcus host genes localized to a hyperplastic region: implications for mechanisms of cyanophage evolution. Environmental Microbiology 11(9):2370-2387 DOI 10.1111/j.1462-2920.2009.01966.x.
    • (2009) Environmental Microbiology , vol.11 , Issue.9 , pp. 2370-2387
    • Millard, A.D.1    Zwirglmaier, K.2    Downey, M.J.3    Mann, N.H.4    Scanlan, D.J.5
  • 55
    • 84880509968 scopus 로고    scopus 로고
    • Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome
    • Modi SR, Lee HH, Spina CS, Collins JJ. 2013. Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. Nature 499(7457):219-222 DOI 10.1038/nature12212.
    • (2013) Nature , vol.499 , Issue.7457 , pp. 219-222
    • Modi, S.R.1    Lee, H.H.2    Spina, C.S.3    Collins, J.J.4
  • 56
    • 84925860108 scopus 로고    scopus 로고
    • Revisiting phage therapy: new applications for old resources
    • Nobrega FL, Costa AR, Kluskens LD, Azeredo J. 2015. Revisiting phage therapy: new applications for old resources. Trends in Microbiology 23(4):185-191 DOI 10.1016/j.tim.2015.01.006.
    • (2015) Trends in Microbiology , vol.23 , Issue.4 , pp. 185-191
    • Nobrega, F.L.1    Costa, A.R.2    Kluskens, L.D.3    Azeredo, J.4
  • 57
    • 84941362509 scopus 로고    scopus 로고
    • Spontaneous deletion of an "ORFanage" region facilitates host adaptation in a "Photosynthetic" cyanophage
    • Puxty RJ, Perez-Sepulveda B, Rihtman B, Evans DJ, Millard AD, Scanlan DJ. 2015. Spontaneous deletion of an "ORFanage" region facilitates host adaptation in a "Photosynthetic" cyanophage. PLoS ONE 10(7):e132642 DOI 10.1371/journal.pone.0132642.
    • (2015) PLoS ONE , vol.10 , Issue.7
    • Puxty, R.J.1    Perez-Sepulveda, B.2    Rihtman, B.3    Evans, D.J.4    Millard, A.D.5    Scanlan, D.J.6
  • 58
    • 84865363124 scopus 로고    scopus 로고
    • The limitations of draft assemblies for understanding prokaryotic adaptation and evolution
    • Ricker N, Qian H, Fulthorpe RR. 2012. The limitations of draft assemblies for understanding prokaryotic adaptation and evolution. Genomics 100(3):167-175 DOI 10.1016/j.ygeno.2012.06.009.
    • (2012) Genomics , vol.100 , Issue.3 , pp. 167-175
    • Ricker, N.1    Qian, H.2    Fulthorpe, R.R.3
  • 59
    • 0034947811 scopus 로고    scopus 로고
    • Production of shotgun libraries using random amplification
    • 114-106, 118
    • Rohwer F, Seguritan V, Choi DH, Segall AM, Azam F. 2001. Production of shotgun libraries using random amplification. BioTechniques 31(1):108-112 114-106, 118.
    • (2001) BioTechniques , vol.31 , Issue.1 , pp. 108-112
    • Rohwer, F.1    Seguritan, V.2    Choi, D.H.3    Segall, A.M.4    Azam, F.5
  • 64
    • 85009455606 scopus 로고    scopus 로고
    • Draft genome sequences of 14 Escherichia coli phages isolated from cattle slurry
    • Smith R, O'Hara M, Hobman JL, Millard AD. 2015. Draft genome sequences of 14 Escherichia coli phages isolated from cattle slurry. Genome Announcements 3(6):e1364-15 DOI 10.1128/genomeA.01364-15.
    • (2015) Genome Announcements , vol.3 , Issue.6
    • Smith, R.1    O'Hara, M.2    Hobman, J.L.3    Millard, A.D.4
  • 65
    • 25144506135 scopus 로고    scopus 로고
    • Viruses in the sea
    • Suttle CA. 2005. Viruses in the sea. Nature 437(7057):356-361 DOI 10.1038/nature04160.
    • (2005) Nature , vol.437 , Issue.7057 , pp. 356-361
    • Suttle, C.A.1
  • 66
    • 34548792911 scopus 로고    scopus 로고
    • Marine viruses-major players in the global ecosystem
    • Suttle CA. 2007. Marine viruses-major players in the global ecosystem. Nature Reviews Microbiology 5(10):801-812 DOI 10.1038/nrmicro1750.
    • (2007) Nature Reviews Microbiology , vol.5 , Issue.10 , pp. 801-812
    • Suttle, C.A.1
  • 69
    • 83855165105 scopus 로고    scopus 로고
    • Repetitive DNA and next-generation sequencing: computational challenges and solutions
    • Treangen TJ, Salzberg SL. 2012. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nature Reviews Genetics 13(1):36-46 DOI 10.1038/nrg3117.
    • (2012) Nature Reviews Genetics , vol.13 , Issue.1 , pp. 36-46
    • Treangen, T.J.1    Salzberg, S.L.2
  • 71
    • 84866354618 scopus 로고    scopus 로고
    • Ocean viruses and their effects on microbial communities and biogeochemical cycles
    • Weitz JS, Wilhelm SW. 2012. Ocean viruses and their effects on microbial communities and biogeochemical cycles. F1000 Biology Reports 4:17 DOI 10.3410/B4-17.
    • (2012) F1000 Biology Reports , vol.4 , pp. 17
    • Weitz, J.S.1    Wilhelm, S.W.2
  • 74
    • 67649911268 scopus 로고    scopus 로고
    • Metagenomic signatures of 86 microbial and viral metagenomes
    • Willner D, Thurber RV, Rohwer F. 2009. Metagenomic signatures of 86 microbial and viral metagenomes. Environmental Microbiology 11(7):1752-1766 DOI 10.1111/j.1462-2920.2009.01901.x.
    • (2009) Environmental Microbiology , vol.11 , Issue.7 , pp. 1752-1766
    • Willner, D.1    Thurber, R.V.2    Rohwer, F.3
  • 75
    • 84899090573 scopus 로고    scopus 로고
    • Kraken: ultrafast metagenomic sequence classification using exact alignments
    • Wood DE, Salzberg SL. 2014. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology 15(3):R46 DOI 10.1186/gb-2014-15-3-r46.
    • (2014) Genome Biology , vol.15 , Issue.3 , pp. R46
    • Wood, D.E.1    Salzberg, S.L.2
  • 76
    • 43149115851 scopus 로고    scopus 로고
    • Velvet: algorithms for de novo short read assembly using de Bruijn graphs
    • Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18(5):821-829 DOI 10.1101/gr.074492.107.
    • (2008) Genome Research , vol.18 , Issue.5 , pp. 821-829
    • Zerbino, D.R.1    Birney, E.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.