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Volumn 7, Issue 7, 2012, Pages

High-coverage ITS primers for the DNA-based identification of ascomycetes and basidiomycetes in environmental samples

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL DNA; INTERNAL TRANSCRIBED SPACER 1; INTERNAL TRANSCRIBED SPACER 2;

EID: 84863764544     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0040863     Document Type: Article
Times cited : (838)

References (54)
  • 1
    • 0035712954 scopus 로고    scopus 로고
    • The magnitude of fungal diversity: the 1.5 million species estimate revisited
    • Hawksworth DL, (2001) The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycol Res 105: 1422-1432.
    • (2001) Mycol Res , vol.105 , pp. 1422-1432
    • Hawksworth, D.L.1
  • 4
    • 33846995452 scopus 로고    scopus 로고
    • An estimate of the lower limit of global fungal diversity
    • Schmit JP, Mueller GM, (2007) An estimate of the lower limit of global fungal diversity. Biodiv Conserv 16: 99-111.
    • (2007) Biodiv Conserv , vol.16 , pp. 99-111
    • Schmit, J.P.1    Mueller, G.M.2
  • 5
    • 63849283004 scopus 로고
    • The ecology of mycorrhizae. New York: Cambridge University Press
    • Allen MF, (1991) The ecology of mycorrhizae. New York: Cambridge University Press. 200 p.
    • (1991) 200 P
    • Allen, M.F.1
  • 6
    • 84863771095 scopus 로고    scopus 로고
    • New York: Academic Press
    • rd ed
    • Smith SE, Read DJ, (2008) New York: Academic Press. Mycorrhizal symbiosis, 3rd ed. 800 p.
    • (2008)
    • Smith, S.E.1    Read, D.J.2
  • 7
    • 0024194334 scopus 로고    scopus 로고
    • Clay K. 1988. Fungal endophytes of grasses: a defensive mutualism between plants and fungi
    • Clay K. 1988. Fungal endophytes of grasses: a defensive mutualism between plants and fungi. Ecology 69: 10-16.
    • Ecology , vol.69 , pp. 10-16
  • 8
    • 26244452210 scopus 로고    scopus 로고
    • Fungal epiphytes and endophytes of coffee leaves (Coffea arabica)
    • Santamaría J, Bayman P, (2005) Fungal epiphytes and endophytes of coffee leaves (Coffea arabica). Microb Ecol 50: 1-8.
    • (2005) Microb Ecol , vol.50 , pp. 1-8
    • Santamaría, J.1    Bayman, P.2
  • 9
    • 70349493057 scopus 로고    scopus 로고
    • Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere
    • Jumpponen A, Jones KL, (2009) Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperate Quercus macrocarpa phyllosphere. New Phytol 184: 438-448.
    • (2009) New Phytol , vol.184 , pp. 438-448
    • Jumpponen, A.1    Jones, K.L.2
  • 10
    • 33847676398 scopus 로고    scopus 로고
    • Parasitic chytrids: their effects on phytoplankton communities and food-web dynamics
    • Kagami M, de Bruin A, Ibelings BW, Van Donk E, (2007) Parasitic chytrids: their effects on phytoplankton communities and food-web dynamics. Hydrobiologia 578: 113-129.
    • (2007) Hydrobiologia , vol.578 , pp. 113-129
    • Kagami, M.1    de Bruin, A.2    Ibelings, B.W.3    van Donk, E.4
  • 11
    • 34447306278 scopus 로고    scopus 로고
    • The parasitic chytrid, Zygorhizidium, facilitates the growth of the cladoceran zooplankter, Daphnia, in cultures of the inedible alga, Asterionella
    • Kagami M, von Elert E, Ibelings BW, de Bruin A, Van Donk E, (2007) The parasitic chytrid, Zygorhizidium, facilitates the growth of the cladoceran zooplankter, Daphnia, in cultures of the inedible alga, Asterionella. Proc R Soc Lond Ser B 274: 1561-1566.
    • (2007) Proc R Soc Lond Ser B , vol.274 , pp. 1561-1566
    • Kagami, M.1    von Elert, E.2    Ibelings, B.W.3    de Bruin, A.4    van Donk, E.5
  • 12
    • 0034904149 scopus 로고    scopus 로고
    • Cold adaptation in Arctic and Antarctic fungi
    • Robinson CH, (2001) Cold adaptation in Arctic and Antarctic fungi. New Phytol 151: 341-353.
    • (2001) New Phytol , vol.151 , pp. 341-353
    • Robinson, C.H.1
  • 13
    • 84863742756 scopus 로고    scopus 로고
    • Plant litter: decomposition, humus formation, carbon sequestration. Berlin: Springer
    • Berg B, McClaugherty C, (2003) Plant litter: decomposition, humus formation, carbon sequestration. Berlin: Springer. 300 p.
    • (2003) 300 P
    • Berg, B.1    McClaugherty, C.2
  • 14
    • 84863742755 scopus 로고    scopus 로고
    • Insect-fungal associations: ecology and evolution. New York: Oxford University Press
    • Vega FE, Blackwell M, (2005) Insect-fungal associations: ecology and evolution. New York: Oxford University Press. 333 p.
    • (2005) 333 P
    • Vega, F.E.1    Blackwell, M.2
  • 15
    • 77955482941 scopus 로고    scopus 로고
    • Negative plant-soil feedback predicts tree-species relative abundance in a tropical forest
    • Mangan SA, Schnitzer SA, Herre EA, Mack KML, Valencia MC, et al. (2010) Negative plant-soil feedback predicts tree-species relative abundance in a tropical forest. Nature 466: 752-755.
    • (2010) Nature , vol.466 , pp. 752-755
    • Mangan, S.A.1    Schnitzer, S.A.2    Herre, E.A.3    Mack, K.M.L.4    Valencia, M.C.5
  • 16
    • 33744923404 scopus 로고    scopus 로고
    • Mycorrhizas and tropical soil fertility
    • Cardoso IM, Kuyper TW, (2006) Mycorrhizas and tropical soil fertility. Agr Ecosyst Env 116: 72-84.
    • (2006) Agr Ecosyst Env , vol.116 , pp. 72-84
    • Cardoso, I.M.1    Kuyper, T.W.2
  • 17
    • 39749084540 scopus 로고    scopus 로고
    • Cereal mycorrhiza: an ancient symbiosis in modern agriculture
    • Sawers RJH, Gutjahr C, Paszkowski U, (2008) Cereal mycorrhiza: an ancient symbiosis in modern agriculture. Trends Plant Sci 13: 93-97.
    • (2008) Trends Plant Sci , vol.13 , pp. 93-97
    • Sawers, R.J.H.1    Gutjahr, C.2    Paszkowski, U.3
  • 19
    • 1442334390 scopus 로고    scopus 로고
    • Biologically active compounds from Aphyllophorales (Polypore) fungi
    • Zjawiony JK, (2004) Biologically active compounds from Aphyllophorales (Polypore) fungi. J Natur Prod 67: 300-310.
    • (2004) J Natur Prod , vol.67 , pp. 300-310
    • Zjawiony, J.K.1
  • 20
    • 0034064282 scopus 로고    scopus 로고
    • Evolution and variation of the yeast (Saccharomyces) genome
    • Mortimer RK, (2000) Evolution and variation of the yeast (Saccharomyces) genome. Genome Res 10: 403-409.
    • (2000) Genome Res , vol.10 , pp. 403-409
    • Mortimer, R.K.1
  • 21
    • 33746144422 scopus 로고    scopus 로고
    • Biosorption of heavy metals by Saccharomyces cerevisiae: a review
    • Wang J, Chen C, (2006) Biosorption of heavy metals by Saccharomyces cerevisiae: a review. Biotechnol Adv 24: 427-451.
    • (2006) Biotechnol Adv , vol.24 , pp. 427-451
    • Wang, J.1    Chen, C.2
  • 22
    • 65349088516 scopus 로고    scopus 로고
    • Progress towards DNA barcoding of fungi
    • Seifert KA, (2009) Progress towards DNA barcoding of fungi. Mol Ecol Res 9: 83-89.
    • (2009) Mol Ecol Res , vol.9 , pp. 83-89
    • Seifert, K.A.1
  • 23
    • 79952447866 scopus 로고    scopus 로고
    • Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences
    • Hibbett DS, Ohman A, Glotzer D, Nuhn M, Kirk P, et al. (2011) Progress in molecular and morphological taxon discovery in Fungi and options for formal classification of environmental sequences. Fungal Biol Rev 25: 38-47.
    • (2011) Fungal Biol Rev , vol.25 , pp. 38-47
    • Hibbett, D.S.1    Ohman, A.2    Glotzer, D.3    Nuhn, M.4    Kirk, P.5
  • 24
    • 79959874811 scopus 로고    scopus 로고
    • Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities
    • Nilsson RH, Tedersoo L, Lindahl BD, Kjøller R, Carlsen T, et al. (2011) Towards standardization of the description and publication of next-generation sequencing datasets of fungal communities. New Phytol 191: 314-318.
    • (2011) New Phytol , vol.191 , pp. 314-318
    • Nilsson, R.H.1    Tedersoo, L.2    Lindahl, B.D.3    Kjøller, R.4    Carlsen, T.5
  • 27
    • 69149084832 scopus 로고    scopus 로고
    • A DNA barcode for land plants
    • CBOL Plant Working Group
    • CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci USA 106: 12794-12797.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 12794-12797
  • 29
    • 77952765171 scopus 로고    scopus 로고
    • Current state and perspectives of fungal DNA barcoding and rapid identification procedures
    • Begerow D, Nilsson H, Unterseher M, Maier W, (2010) Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Appl Microbiol Biotechnol 87: 99-108.
    • (2010) Appl Microbiol Biotechnol , vol.87 , pp. 99-108
    • Begerow, D.1    Nilsson, H.2    Unterseher, M.3    Maier, W.4
  • 30
    • 72849126924 scopus 로고    scopus 로고
    • A PCR-based method for diet analysis in freshwater organisms using 18S rDNA barcoding on faeces
    • Corse E, Costedoat C, Chappaz R, Pech N, Martin J, Gilles A, (2010) A PCR-based method for diet analysis in freshwater organisms using 18S rDNA barcoding on faeces. Mol Ecol Res 10: 96-108.
    • (2010) Mol Ecol Res , vol.10 , pp. 96-108
    • Corse, E.1    Costedoat, C.2    Chappaz, R.3    Pech, N.4    Martin, J.5    Gilles, A.6
  • 31
    • 79957896145 scopus 로고    scopus 로고
    • DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context
    • Kelly LJ, Hollingsworth PM, Coppins BJ, Ellis CJ, Harrold P, et al. (2011) DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context. New Phytol 191: 288-300.
    • (2011) New Phytol , vol.191 , pp. 288-300
    • Kelly, L.J.1    Hollingsworth, P.M.2    Coppins, B.J.3    Ellis, C.J.4    Harrold, P.5
  • 32
    • 44949196849 scopus 로고    scopus 로고
    • Reproductive isolation among cryptic species in the ectomycorrhizal genus Strobilomyces: Population-level caps marker-based genetic analysis
    • Sato H, Murakami N, (2008) Reproductive isolation among cryptic species in the ectomycorrhizal genus Strobilomyces: Population-level caps marker-based genetic analysis. Mol Phyl Evol 48: 326-334.
    • (2008) Mol Phyl Evol , vol.48 , pp. 326-334
    • Sato, H.1    Murakami, N.2
  • 33
    • 35348971389 scopus 로고    scopus 로고
    • Cryptic species and host specificity in the ectomycorrhizal genus Strobilomyces (Strobilomycetaceae)
    • Sato H, Yumoto T, Murakami N, (2007) Cryptic species and host specificity in the ectomycorrhizal genus Strobilomyces (Strobilomycetaceae). Am J Bot 94: 1630-1641.
    • (2007) Am J Bot , vol.94 , pp. 1630-1641
    • Sato, H.1    Yumoto, T.2    Murakami, N.3
  • 34
    • 77955262221 scopus 로고    scopus 로고
    • Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land-use gradient using a pyrosequencing approach
    • Lumini E, Orgiazzi A, Borriello R, Bonfante P, Bianciotto V, (2009) Disclosing arbuscular mycorrhizal fungal biodiversity in soil through a land-use gradient using a pyrosequencing approach. Env Microbiol 12: 2165-2179.
    • (2009) Env Microbiol , vol.12 , pp. 2165-2179
    • Lumini, E.1    Orgiazzi, A.2    Borriello, R.3    Bonfante, P.4    Bianciotto, V.5
  • 35
    • 79954752208 scopus 로고    scopus 로고
    • Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing
    • Dumbrell AJ, Ashton PD, Aziz N, et al. (2011) Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing. New Phytol 190: 794-804.
    • (2011) New Phytol , vol.190 , pp. 794-804
    • Dumbrell, A.J.1    Ashton, P.D.2    Aziz, N.3
  • 36
    • 79959347335 scopus 로고    scopus 로고
    • Alien plants associate with widespread generalist arbuscular mycorrhizal fungal taxa: Evidence from a continental-scale study using massively parallel 454 sequencing
    • Moora M, Berger S, Davison J, Öpik M, Bommarco R, et al. (2011) Alien plants associate with widespread generalist arbuscular mycorrhizal fungal taxa: Evidence from a continental-scale study using massively parallel 454 sequencing. J Biogeogr 38: 1305-1317.
    • (2011) J Biogeogr , vol.38 , pp. 1305-1317
    • Moora, M.1    Berger, S.2    Davison, J.3    Öpik, M.4    Bommarco, R.5
  • 37
    • 84855289503 scopus 로고    scopus 로고
    • Multiple markers pyrosequencing reveals highly diverse and host specific fungal communities on the mangrove trees Avicennia marina and Rhizophora stylosa
    • Arfi Y, Buée M, Marchand C, Levasseur A, Record E, (2012) Multiple markers pyrosequencing reveals highly diverse and host specific fungal communities on the mangrove trees Avicennia marina and Rhizophora stylosa. FEMS Microbiol Ecol 79: 433-444.
    • (2012) FEMS Microbiol Ecol , vol.79 , pp. 433-444
    • Arfi, Y.1    Buée, M.2    Marchand, C.3    Levasseur, A.4    Record, E.5
  • 38
    • 83455224377 scopus 로고    scopus 로고
    • 454-sequencing reveals stochastic local reassembly and high disturbance tolerance within arbuscular mycorrhizal fungal communities
    • Lekberg Y, Schnoor T, Kjøller R, Gibbons SM, Hansen LH, et al. (2011) 454-sequencing reveals stochastic local reassembly and high disturbance tolerance within arbuscular mycorrhizal fungal communities. J Ecol 100: 151-160.
    • (2011) J Ecol , vol.100 , pp. 151-160
    • Lekberg, Y.1    Schnoor, T.2    Kjøller, R.3    Gibbons, S.M.4    Hansen, L.H.5
  • 39
    • 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, et al. (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
  • 40
    • 0000432452 scopus 로고
    • Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR protocols a guide to methods and applications, 315-322
    • White TJ, Bruns T, Lee S, Taylor J, (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In PCR protocols a guide to methods and applications, 315-322. Academic Press, San Diego.
    • (1990) Academic Press, San Diego
    • White, T.J.1    Bruns, T.2    Lee, S.3    Taylor, J.4
  • 41
    • 0027580147 scopus 로고
    • ITS primers with enhanced specificity for Basidiomycetes: application to the identification of mycorrhizae and rusts
    • Gardes M, Bruns TD, (1993) ITS primers with enhanced specificity for Basidiomycetes: application to the identification of mycorrhizae and rusts. Mol Ecol 2: 113-118.
    • (1993) Mol Ecol , vol.2 , pp. 113-118
    • Gardes, M.1    Bruns, T.D.2
  • 42
    • 0029513076 scopus 로고
    • Molecular analysis of ectomycorrhizal fungal communities
    • Egger KN, (1995) Molecular analysis of ectomycorrhizal fungal communities. Canadian J Bot 73: 1415-1415.
    • (1995) Canadian J Bot , vol.73 , pp. 1415
    • Egger, K.N.1
  • 43
    • 23044485088 scopus 로고    scopus 로고
    • Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts
    • Martin KJ, Rygiewicz PT, (2005) Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts. BMC Microbiol 5: 28.
    • (2005) BMC Microbiol , vol.5 , pp. 28
    • Martin, K.J.1    Rygiewicz, P.T.2
  • 44
    • 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 DK, Vivanco JM, (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
  • 45
    • 77955777197 scopus 로고    scopus 로고
    • Production of ectomycorrhizal mycelium peaks during canopy closure in Norway spruce forests
    • Wallander H, Johansson U, Sterkenburg E, Durling MB, Lindahl BD, (2010) Production of ectomycorrhizal mycelium peaks during canopy closure in Norway spruce forests. New Phytol 187: 1124-1134.
    • (2010) New Phytol , vol.187 , pp. 1124-1134
    • Wallander, H.1    Johansson, U.2    Sterkenburg, E.3    Durling, M.B.4    Lindahl, B.D.5
  • 46
    • 77956283658 scopus 로고    scopus 로고
    • 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases
    • Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, Sadam A, et al. (2010) 454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases. New Phytol 188: 291-301.
    • (2010) New Phytol , vol.188 , pp. 291-301
    • Tedersoo, L.1    Nilsson, R.H.2    Abarenkov, K.3    Jairus, T.4    Sadam, A.5
  • 48
    • 0032849859 scopus 로고    scopus 로고
    • CAP3: A DNA sequence assembly program
    • Huang X, Madan A, (1999) CAP3: A DNA sequence assembly program. Genome Res 9: 868.
    • (1999) Genome Res , vol.9 , pp. 868
    • Huang, X.1    Madan, A.2
  • 49
    • 13744252890 scopus 로고    scopus 로고
    • MAFFT version 5: improvement in accuracy of multiple sequence alignment
    • Katoh K, Kuma K, Toh H, Miyata T, (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33: 511-518.
    • (2005) Nucleic Acids Research , vol.33 , pp. 511-518
    • Katoh, K.1    Kuma, K.2    Toh, H.3    Miyata, T.4
  • 50
    • 77954695245 scopus 로고    scopus 로고
    • Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments
    • Jumpponen A, Jones KL, (2010) Seasonally dynamic fungal communities in the Quercus macrocarpa phyllosphere differ between urban and nonurban environments. New Phytol 186: 496-513.
    • (2010) New Phytol , vol.186 , pp. 496-513
    • Jumpponen, A.1    Jones, K.L.2
  • 51
    • 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 RH, et al. (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
  • 53
    • 77956373482 scopus 로고    scopus 로고
    • Indoor fungal composition is geographically patterned and more diverse in temperate zones than in the tropics
    • Amend AS, Seifert KA, Samson R, Bruns TD, (2010) 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
  • 54
    • 45749142504 scopus 로고    scopus 로고
    • Intraspecific ITS variability in the Kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification
    • Nilsson RH, Kristiansson E, Ryberg M, Hallenberg N, Larsson KH, (2008) Intraspecific ITS variability in the Kingdom Fungi as expressed in the international sequence databases and its implications for molecular species identification. Evol Bioinfo 4: 193-201.
    • (2008) Evol Bioinfo , vol.4 , pp. 193-201
    • Nilsson, R.H.1    Kristiansson, E.2    Ryberg, M.3    Hallenberg, N.4    Larsson, K.H.5


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