메뉴 건너뛰기




Volumn 16, Issue 9, 2014, Pages 2764-2776

Identification accuracy and diversity reproducibility associated with internal transcribed spacer-based fungal taxonomic library preparation

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNARIA ALTERNATA; ASPERGILLUS FUMIGATUS; CLADOSPORIUM CLADOSPORIOIDES; EPICOCCUM NIGRUM; FUNGI; PENICILLIUM CHRYSOGENUM;

EID: 84906944163     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.12338     Document Type: Article
Times cited : (16)

References (48)
  • 1
    • 77954748234 scopus 로고    scopus 로고
    • The UNITE database for molecular identification of fungi - recent updates and future perspectives
    • Abarenkov, K., Henrik Nilsson, R., Larsson, K.H., Alexander, I.J., Eberhardt, U., Erland, S., etal. (2010) The UNITE database for molecular identification of fungi - recent updates and future perspectives. New Phytol 186: 281-285.
    • (2010) New Phytol , vol.186 , pp. 281-285
    • Abarenkov, K.1    Henrik Nilsson, R.2    Larsson, K.H.3    Alexander, I.J.4    Eberhardt, U.5    Erland, S.6
  • 2
    • 84880917198 scopus 로고    scopus 로고
    • Dispersal in microbes: Fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances
    • Adams, R.I., Miletto, M., Taylor, J.W., and Bruns, T.D. (2013) Dispersal in microbes: Fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances. ISME J 7: 1262-1263.
    • (2013) ISME J , vol.7 , pp. 1262-1263
    • Adams, R.I.1    Miletto, M.2    Taylor, J.W.3    Bruns, T.D.4
  • 4
    • 78650161976 scopus 로고    scopus 로고
    • Quantifying microbial communities with 454 pyrosequencing: does read abundance count?
    • Amend, A.S., Seifert, K.A., and Bruns, T.D. (2010a) Quantifying microbial communities with 454 pyrosequencing: does read abundance count? Mol Ecol 19: 5555-5565.
    • (2010) Mol Ecol , vol.19 , pp. 5555-5565
    • Amend, A.S.1    Seifert, K.A.2    Bruns, T.D.3
  • 5
    • 77956373482 scopus 로고    scopus 로고
    • Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics
    • Amend, A.S., Seifert, K.A., Samson, R., and Bruns, T.D. (2010b) Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics. Proc Natl Acad Sci USA 107: 13748-13753.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 13748-13753
    • Amend, A.S.1    Seifert, K.A.2    Samson, R.3    Bruns, T.D.4
  • 7
    • 77954336858 scopus 로고    scopus 로고
    • ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases
    • Bellemain, E., Carlsen, T., Brochmann, C., Coissac, E., Taberlet, P., and Kauserud, H. (2010) ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol 10: 189.
    • (2010) BMC Microbiol , vol.10 , pp. 189
    • Bellemain, E.1    Carlsen, T.2    Brochmann, C.3    Coissac, E.4    Taberlet, P.5    Kauserud, H.6
  • 8
    • 84859574463 scopus 로고    scopus 로고
    • Changes in the root-associated fungal communities along a primary succession gradient analysed by 454 pyrosequencing
    • Blaalid, R., Carlsen, T., Kumar, S., Halvorsen, R., Ugland, K.I., Fontana, G., and Kauserud, H. (2012) Changes in the root-associated fungal communities along a primary succession gradient analysed by 454 pyrosequencing. Mol Ecol 21: 1897-1908.
    • (2012) Mol Ecol , vol.21 , pp. 1897-1908
    • Blaalid, R.1    Carlsen, T.2    Kumar, S.3    Halvorsen, R.4    Ugland, K.I.5    Fontana, G.6    Kauserud, H.7
  • 9
    • 1642437156 scopus 로고    scopus 로고
    • Phylogeny and taxonomy of Cladosporium-like hyphomycetes, including Davidiella gen. nov., the teleomorph of Cladosporium s. str
    • Braun, U., Crous, P.W., Dugan, F., Groenewald, J.Z., and De Hoog, G.S. (2003) Phylogeny and taxonomy of Cladosporium-like hyphomycetes, including Davidiella gen. nov., the teleomorph of Cladosporium s. str. Mycol Prog 2: 3-18.
    • (2003) Mycol Prog , vol.2 , pp. 3-18
    • Braun, U.1    Crous, P.W.2    Dugan, F.3    Groenewald, J.Z.4    De Hoog, G.S.5
  • 11
    • 70349482733 scopus 로고    scopus 로고
    • 454 pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity
    • Buée, M., Reich, M., Murat, C., Morin, E., Nilsson, R.H., Uroz, S., and Martin, F. (2009) 454 pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. New Phytol 184: 449-456.
    • (2009) New Phytol , vol.184 , pp. 449-456
    • Buée, M.1    Reich, M.2    Murat, C.3    Morin, E.4    Nilsson, R.H.5    Uroz, S.6    Martin, F.7
  • 13
    • 13444304367 scopus 로고    scopus 로고
    • The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis
    • Cole, J.R., Chai, B., Farris, R.J., Wang, Q., Kulam, S.A., McGarrell, D.M., etal. (2005) The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33: D294-D296.
    • (2005) Nucleic Acids Res , vol.33
    • Cole, J.R.1    Chai, B.2    Farris, R.J.3    Wang, Q.4    Kulam, S.A.5    McGarrell, D.M.6
  • 15
    • 84897957117 scopus 로고    scopus 로고
    • Fungal high-throughput taxonomic identification tool for use with next-generation sequencing (FHiTINGS)
    • doi:10.1002/jobm.201200507.
    • Dannemiller, K., Reeves, D., Bibby, K., Yamamoto, N., and Peccia, J. (2013) Fungal high-throughput taxonomic identification tool for use with next-generation sequencing (FHiTINGS). J Basic Microbiol. doi:10.1002/jobm.201200507.
    • (2013) J Basic Microbiol
    • Dannemiller, K.1    Reeves, D.2    Bibby, K.3    Yamamoto, N.4    Peccia, J.5
  • 16
    • 77957244650 scopus 로고    scopus 로고
    • Search and clustering orders of magnitude faster than BLAST
    • Edgar, R.C. (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26: 2460-2461.
    • (2010) Bioinformatics , vol.26 , pp. 2460-2461
    • Edgar, R.C.1
  • 19
    • 84856563821 scopus 로고    scopus 로고
    • Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes
    • Gihring, T.M., Green, S.J., and Schadt, C.W. (2012) Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes. Environ Microbiol 14: 285-290.
    • (2012) Environ Microbiol , vol.14 , pp. 285-290
    • Gihring, T.M.1    Green, S.J.2    Schadt, C.W.3
  • 20
    • 66149104807 scopus 로고    scopus 로고
    • Strain-dependent variation in 18S ribosomal DNA copy numbers in Aspergillus fumigatus
    • Herrera, M.L., Vallor, A.C., Gelfond, J.A., Patterson, T.F., and Wickes, B.L. (2009) Strain-dependent variation in 18S ribosomal DNA copy numbers in Aspergillus fumigatus. J Clin Microbiol 47: 1325-1332.
    • (2009) J Clin Microbiol , vol.47 , pp. 1325-1332
    • Herrera, M.L.1    Vallor, A.C.2    Gelfond, J.A.3    Patterson, T.F.4    Wickes, B.L.5
  • 21
    • 0035921960 scopus 로고    scopus 로고
    • An arbuscular mycorrhizal fungus accelerates decomposition and acquires nitrogen directly from organic material
    • Hodge, A., Campbell, C.D., and Fitter, A.H. (2001) An arbuscular mycorrhizal fungus accelerates decomposition and acquires nitrogen directly from organic material. Nature 413: 297-299.
    • (2001) Nature , vol.413 , pp. 297-299
    • Hodge, A.1    Campbell, C.D.2    Fitter, A.H.3
  • 22
    • 78149454087 scopus 로고    scopus 로고
    • Accuracy, precision, and method detection limits of quantitative PCR for airborne bacteria and fungi
    • Hospodsky, D., Yamamoto, N., and Peccia, J. (2010) Accuracy, precision, and method detection limits of quantitative PCR for airborne bacteria and fungi. Appl Environ Microbiol 76: 7004-7012.
    • (2010) Appl Environ Microbiol , vol.76 , pp. 7004-7012
    • Hospodsky, D.1    Yamamoto, N.2    Peccia, J.3
  • 23
    • 84255189126 scopus 로고    scopus 로고
    • Phylogeny of Penicillium and the segregation of Trichocomaceae into three families
    • Houbraken, J., and Samson, R.A. (2011) Phylogeny of Penicillium and the segregation of Trichocomaceae into three families. Stud Mycol 70: 1-51.
    • (2011) Stud Mycol , vol.70 , pp. 1-51
    • Houbraken, J.1    Samson, R.A.2
  • 24
    • 84861964286 scopus 로고    scopus 로고
    • Interactions between commensal fungi and the C-type lectin receptor dectin-1 influence colitis
    • Iliev, I.D., Funari, V.A., Taylor, K.D., Nguyen, Q., Reyes, C.N., Strom, S.P., etal. (2012) Interactions between commensal fungi and the C-type lectin receptor dectin-1 influence colitis. Science 336: 1314-1317.
    • (2012) Science , vol.336 , pp. 1314-1317
    • Iliev, I.D.1    Funari, V.A.2    Taylor, K.D.3    Nguyen, Q.4    Reyes, C.N.5    Strom, S.P.6
  • 25
    • 73349110099 scopus 로고    scopus 로고
    • Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
    • Kunin, V., Engelbrektson, A., Ochman, H., and Hugenholtz, P. (2010) Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates. Environ Microbiol 12: 118-123.
    • (2010) Environ Microbiol , vol.12 , pp. 118-123
    • Kunin, V.1    Engelbrektson, A.2    Ochman, H.3    Hugenholtz, P.4
  • 26
    • 0032845186 scopus 로고    scopus 로고
    • Design of a primer for ribosomal DNA internal transcribed spacer with enhanced specificity for ascomycetes
    • Larena, I., Salazar, O., Gonzalez, V., Julian, M.C., and Rubio, V. (1999) Design of a primer for ribosomal DNA internal transcribed spacer with enhanced specificity for ascomycetes. J Biotechnol 75: 187-194.
    • (1999) J Biotechnol , vol.75 , pp. 187-194
    • Larena, I.1    Salazar, O.2    Gonzalez, V.3    Julian, M.C.4    Rubio, V.5
  • 27
    • 34548855040 scopus 로고    scopus 로고
    • Use of the ITS primers, ITS1F and ITS4, to characterize fungal abundance and diversity in mixed-template samples by qPCR and length heterogeneity analysis
    • Manter, D.K., and Vivanco, J.M. (2007) Use of the ITS primers, ITS1F and ITS4, to characterize fungal abundance and diversity in mixed-template samples by qPCR and length heterogeneity analysis. J Microbiol Methods 71: 7-14.
    • (2007) J Microbiol Methods , vol.71 , pp. 7-14
    • Manter, D.K.1    Vivanco, J.M.2
  • 28
    • 28644434509 scopus 로고    scopus 로고
    • Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus
    • Nierman, W.C., Pain, A., Anderson, M.J., Wortman, J.R., Kim, H.S., Arroyo, J., etal. (2005) Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438: 1151-1156.
    • (2005) Nature , vol.438 , pp. 1151-1156
    • Nierman, W.C.1    Pain, A.2    Anderson, M.J.3    Wortman, J.R.4    Kim, H.S.5    Arroyo, J.6
  • 31
    • 77956292565 scopus 로고    scopus 로고
    • An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology
    • Nilsson, R.H., Veldre, V., Hartmann, M., Unterseher, M., Amend, A., Bergsten, J., etal. (2010) An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology. Fungal Ecol 3: 284-287.
    • (2010) Fungal Ecol , vol.3 , pp. 284-287
    • Nilsson, R.H.1    Veldre, V.2    Hartmann, M.3    Unterseher, M.4    Amend, A.5    Bergsten, J.6
  • 33
    • 58749112527 scopus 로고    scopus 로고
    • Discovery of a sexual cycle in the opportunistic fungal pathogen Aspergillus fumigatus
    • O'Gorman, C.M., Fuller, H., and Dyer, P.S. (2009) Discovery of a sexual cycle in the opportunistic fungal pathogen Aspergillus fumigatus. Nature 457: 471-474.
    • (2009) Nature , vol.457 , pp. 471-474
    • O'Gorman, C.M.1    Fuller, H.2    Dyer, P.S.3
  • 34
    • 80052011287 scopus 로고    scopus 로고
    • Addressing current medical needs in invasive fungal infection prevention and treatment with new antifungal agents, strategies and formulations
    • Pitman, S.K., Drew, R.H., and Perfect, J.R. (2011) Addressing current medical needs in invasive fungal infection prevention and treatment with new antifungal agents, strategies and formulations. Expert Opin Emerg Drugs 16: 559-586.
    • (2011) Expert Opin Emerg Drugs , vol.16 , pp. 559-586
    • Pitman, S.K.1    Drew, R.H.2    Perfect, J.R.3
  • 35
    • 80054832176 scopus 로고    scopus 로고
    • Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons?
    • Porter, T.M., and Golding, G.B. (2011) Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons? New Phytol 192: 775-782.
    • (2011) New Phytol , vol.192 , pp. 775-782
    • Porter, T.M.1    Golding, G.B.2
  • 36
    • 0034486766 scopus 로고    scopus 로고
    • Molecular phylogenetic relationships amongst Alternaria species and related fungi based upon analysis of nuclear ITS and mt SSU rDNA sequences
    • Pryor, B.M., and Gilbertson, R.L. (2000) Molecular phylogenetic relationships amongst Alternaria species and related fungi based upon analysis of nuclear ITS and mt SSU rDNA sequences. Mycol Res 104: 1312-1321.
    • (2000) Mycol Res , vol.104 , pp. 1312-1321
    • Pryor, B.M.1    Gilbertson, R.L.2
  • 37
    • 69549112742 scopus 로고    scopus 로고
    • Accurate determination of microbial diversity from 454 pyrosequencing data
    • Quince, C., Lanzen, A., Curtis, T.P., Davenport, R.J., Hall, N., Head, I.M., etal. (2009) Accurate determination of microbial diversity from 454 pyrosequencing data. Nat Methods 6: 639-641.
    • (2009) Nat Methods , vol.6 , pp. 639-641
    • Quince, C.1    Lanzen, A.2    Curtis, T.P.3    Davenport, R.J.4    Hall, N.5    Head, I.M.6
  • 39
    • 69549129476 scopus 로고    scopus 로고
    • The 'rare biosphere': a reality check
    • Reeder, J., and Knight, R. (2009) The 'rare biosphere': a reality check. Nat Methods 6: 636-637.
    • (2009) Nat Methods , vol.6 , pp. 636-637
    • Reeder, J.1    Knight, R.2
  • 40
    • 77956304094 scopus 로고    scopus 로고
    • Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions
    • Reeder, J., and Knight, R. (2010) Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions. Nat Methods 7: 668-669.
    • (2010) Nat Methods , vol.7 , pp. 668-669
    • Reeder, J.1    Knight, R.2
  • 41
    • 33646252467 scopus 로고    scopus 로고
    • Low genetic variation and no detectable population structure in aspergillus fumigatus compared to closely related Neosartorya species
    • Rydholm, C., Szakacs, G., and Lutzoni, F. (2006) Low genetic variation and no detectable population structure in aspergillus fumigatus compared to closely related Neosartorya species. Eukaryot Cell 5: 650-657.
    • (2006) Eukaryot Cell , vol.5 , pp. 650-657
    • Rydholm, C.1    Szakacs, G.2    Lutzoni, F.3
  • 43
    • 54149097573 scopus 로고    scopus 로고
    • Intragenomic variation of fungal ribosomal genes is higher than previously thought
    • Simon, U.K., and Weiss, M. (2008) Intragenomic variation of fungal ribosomal genes is higher than previously thought. Mol Biol Evol 25: 2251-2254.
    • (2008) Mol Biol Evol , vol.25 , pp. 2251-2254
    • Simon, U.K.1    Weiss, M.2
  • 44
    • 0000909522 scopus 로고
    • Sample-size dependence of diversity indexes and the determination of sufficient sample-size in a high-diversity deep-sea environment
    • Soetaert, K., and Heip, C. (1990) Sample-size dependence of diversity indexes and the determination of sufficient sample-size in a high-diversity deep-sea environment. Mar Ecol Prog Ser 59: 305-307.
    • (1990) Mar Ecol Prog Ser , vol.59 , pp. 305-307
    • Soetaert, K.1    Heip, C.2
  • 45
    • 84858004444 scopus 로고    scopus 로고
    • One fungus=one name: DNA and fungal nomenclature twenty years after PCR
    • Taylor, J.W. (2011) One fungus=one name: DNA and fungal nomenclature twenty years after PCR. IMA Fungus 2: 113-120.
    • (2011) IMA Fungus , vol.2 , pp. 113-120
    • Taylor, J.W.1
  • 46
    • 84856448537 scopus 로고    scopus 로고
    • Assessing allergenic fungi in house dust by floor wipe sampling and quantitative PCR
    • Yamamoto, N., Shendell, D.G., and Peccia, J. (2011) Assessing allergenic fungi in house dust by floor wipe sampling and quantitative PCR. Indoor Air 21: 521-530.
    • (2011) Indoor Air , vol.21 , pp. 521-530
    • Yamamoto, N.1    Shendell, D.G.2    Peccia, J.3
  • 47
    • 84867745678 scopus 로고    scopus 로고
    • Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air
    • Yamamoto, N., Bibby, K., Qian, J., Hospodsky, D., Rismani-Yazdi, H., Nazaroff, W.W., and Peccia, J. (2012) Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air. ISME J 6: 1801-1811.
    • (2012) ISME J , vol.6 , pp. 1801-1811
    • Yamamoto, N.1    Bibby, K.2    Qian, J.3    Hospodsky, D.4    Rismani-Yazdi, H.5    Nazaroff, W.W.6    Peccia, J.7
  • 48
    • 0141726799 scopus 로고    scopus 로고
    • Carbon cycling by arbuscular mycorrhizal fungi in soil-plant systems
    • Zhu, Y.G., and Miller, R.M. (2003) Carbon cycling by arbuscular mycorrhizal fungi in soil-plant systems. Trends Plant Sci 8: 407-409.
    • (2003) Trends Plant Sci , vol.8 , pp. 407-409
    • Zhu, Y.G.1    Miller, R.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.