메뉴 건너뛰기




Volumn 10, Issue , 2010, Pages

ITS as an environmental DNA barcode for fungi: An in silico approach reveals potential PCR biases

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL DNA; INTERNAL TRANSCRIBED SPACER; INTERNAL TRANSCRIBED SPACER 1; INTERNAL TRANSCRIBED SPACER 1 F; INTERNAL TRANSCRIBED SPACER 2; INTERNAL TRANSCRIBED SPACER 3; INTERNAL TRANSCRIBED SPACER 4; INTERNAL TRANSCRIBED SPACER 5; UNCLASSIFIED DRUG; PRIMER DNA; RIBOSOMAL SPACER DNA;

EID: 77954336858     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-10-189     Document Type: Article
Times cited : (830)

References (36)
  • 1
    • 3543138422 scopus 로고    scopus 로고
    • Diversity and ecology of soil fungal communities: Increased understanding through the application of molecular techniques
    • 10.1111/j.1462-2920.2004.00675.x. 15250879
    • Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques. I Anderson J Cairney, Environmental Microbiology 2004 6 8 769 779 10.1111/j.1462-2920.2004.00675.x 15250879
    • (2004) Environmental Microbiology , vol.6 , Issue.8 , pp. 769-779
    • Anderson, I.1    Cairney, J.2
  • 2
    • 68449095065 scopus 로고    scopus 로고
    • Barcoding of plants and fungi
    • 10.1126/science.1176906. 19644072
    • Barcoding of plants and fungi. M Chase M Fay, Science 2009 325 682 683 10.1126/science.1176906 19644072
    • (2009) Science , vol.325 , pp. 682-683
    • Chase, M.1    Fay, M.2
  • 3
    • 0034843854 scopus 로고    scopus 로고
    • The molecular revolution in ectomycorrhizal ecology: Peeking into the black box
    • 10.1046/j.0962-1083.2001.01333.x. 11555231
    • The molecular revolution in ectomycorrhizal ecology: Peeking into the black box. T Horton T Bruns, Molecular Ecology 2001 10 1855 1871 10.1046/j.0962-1083.2001.01333.x 11555231
    • (2001) Molecular Ecology , vol.10 , pp. 1855-1871
    • Horton, T.1    Bruns, T.2
  • 4
    • 65349088516 scopus 로고    scopus 로고
    • Progress toward DNA barcoding of fungi
    • 10.1111/j.1755-0998.2009.02635.x
    • Progress toward DNA barcoding of fungi. K Seiffert, Molecular Ecology Resources 2009 9 Suppl 1 83 89 10.1111/j.1755-0998.2009.02635.x
    • (2009) Molecular Ecology Resources , vol.9 , Issue.SUPPL. 1 , pp. 83-89
    • Seiffert, K.1
  • 7
    • 33846184630 scopus 로고    scopus 로고
    • Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest
    • 10.1111/j.1469-8137.2006.01936.x. 17244056
    • Spatial separation of litter decomposition and mycorrhizal nitrogen uptake in a boreal forest. B Lindahl K Ihrmark J Boberg S Trumbore P Högberg J Stenlid R Finlay, New Phytologist 2007 173 611 620 10.1111/j.1469-8137.2006.01936.x 17244056
    • (2007) New Phytologist , vol.173 , pp. 611-620
    • Lindahl, B.1    Ihrmark, K.2    Boberg, J.3    Trumbore, S.4    Högberg, P.5    Stenlid, J.6    Finlay, R.7
  • 8
    • 25144516095 scopus 로고    scopus 로고
    • Fungal community analysis by large-scale sequencing of environmental samples
    • 10.1128/AEM.71.9.5544-5550.2005. 16151147
    • Fungal community analysis by large-scale sequencing of environmental samples. H O'Brien J Parrent J KJackson J Moncalvo R Vilgalys, Applied and Environmental Microbiology 2005 71 9 5544 5550 10.1128/AEM.71.9.5544-5550.2005 16151147
    • (2005) Applied and Environmental Microbiology , vol.71 , Issue.9 , pp. 5544-5550
    • O'Brien, H.1    Parrent, J.2    Kjackson, J.3    Moncalvo, J.4    Vilgalys, R.5
  • 10
    • 70149100004 scopus 로고    scopus 로고
    • Assessment of microbial communities by graph partitioning in a study of soil fungi in two alpine meadows
    • 10.1128/AEM.00748-09. 19617385
    • Assessment of microbial communities by graph partitioning in a study of soil fungi in two alpine meadows. L Zinger E Coissac P Choler R Geremia, Applied and Environmental Microbiology 2009 75 5863 5870 10.1128/AEM.00748-09 19617385
    • (2009) Applied and Environmental Microbiology , vol.75 , pp. 5863-5870
    • Zinger, L.1    Coissac, E.2    Choler, P.3    Geremia, R.4
  • 11
    • 67149109995 scopus 로고    scopus 로고
    • The ITS region as a target for characterization of fungal communities using emerging sequencing technologies
    • 10.1111/j.1574-6968.2009.01618.x. 19459974
    • The ITS region as a target for characterization of fungal communities using emerging sequencing technologies. R Nilsson M Ryberg K Abarenkov E Sjökvist E Kristiansson, FEMS Microbiology Letters 2009 296 97 101 10.1111/j.1574-6968.2009.01618.x 19459974
    • (2009) FEMS Microbiology Letters , vol.296 , pp. 97-101
    • Nilsson, R.1    Ryberg, M.2    Abarenkov, K.3    Sjökvist, E.4    Kristiansson, E.5
  • 12
    • 36049004436 scopus 로고    scopus 로고
    • Taxonomic reliability of DNA sequences in public sequence databases: A fungal perspective
    • 10.1371/journal.pone.0000059. 17183689
    • Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective. R Nilsson M Ryberg E Kristiansson K Abarenkov K Larsson U Koljalg, PLoS One 2006 1 1 59 10.1371/journal.pone.0000059 17183689
    • (2006) PLoS One , vol.1 , Issue.1 , pp. 559
    • Nilsson, R.1    Ryberg, M.2    Kristiansson, E.3    Abarenkov, K.4    Larsson, K.5    Koljalg, U.6
  • 13
    • 0025170053 scopus 로고
    • Organisation of ribosomal DNA in the basidiomycete Thanatephorus praticola
    • 10.1007/BF00318394. 2249259
    • Organisation of ribosomal DNA in the basidiomycete Thanatephorus praticola. R Vilgalys D Gonzalez, Current Genetics 1990 18 277 280 10.1007/BF00318394 2249259
    • (1990) Current Genetics , vol.18 , pp. 277-280
    • Vilgalys, R.1    Gonzalez, D.2
  • 14
    • 70349482733 scopus 로고    scopus 로고
    • 454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity
    • 10.1111/j.1469-8137.2009.03003.x
    • -454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity. M Buée M Reich C Murat E Morin R Nilsson S Uroz F Martin, New Phytologist 2009 2 449 456 10.1111/j.1469-8137.2009.03003.x
    • (2009) New Phytologist , vol.2 , pp. 449-456
    • Buée, M.1    Reich, M.2    Murat, C.3    Morin, E.4    Nilsson, R.5    Uroz, S.6    Martin, F.7
  • 15
    • 77649230349 scopus 로고    scopus 로고
    • Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals
    • 10.1371/journal.ppat.1000713. 20072605
    • Characterization of the Oral Fungal Microbiome (Mycobiome) in Healthy Individuals. M Ghannoum R Jurevic P Mukherjee F Cui M Sikaroodi A Naqvi P Gillevet, PLoS Pathogens 2010 6 1 1000713 10.1371/journal.ppat.1000713 20072605
    • (2010) PLoS Pathogens , vol.6 , Issue.1 , pp. 51000713
    • Ghannoum, M.1    Jurevic, R.2    Mukherjee, P.3    Cui, F.4    Sikaroodi, M.5    Naqvi, A.6    Gillevet, P.7
  • 16
    • 70349493057 scopus 로고    scopus 로고
    • Massively parallel 454-sequencing of Quercus macrocarpa phyllosphere fungal communities indicates reduced richness and diversity in urban environments
    • 10.1111/j.1469-8137.2009.02990.x. 19674337
    • Massively parallel 454-sequencing of Quercus macrocarpa phyllosphere fungal communities indicates reduced richness and diversity in urban environments. A Jumpponen K Jones, New Phytologist 2009 184 438 448 10.1111/j.1469-8137.2009.02990.x 19674337
    • (2009) New Phytologist , vol.184 , pp. 438-448
    • Jumpponen, A.1    Jones, K.2
  • 17
    • 77955058103 scopus 로고    scopus 로고
    • Massively parallel 454-sequencing of Quercus spp. ectomycorrhizosphere indicates differences in fungal community composition richness, and diversity among urban and rural environments
    • 20331769
    • Massively parallel 454-sequencing of Quercus spp. ectomycorrhizosphere indicates differences in fungal community composition richness, and diversity among urban and rural environments. A Jumpponen K Jones J Mattox C Yeage, Molecular Ecology 2010 20331769
    • (2010) Molecular Ecology
    • Jumpponen, A.1    Jones, K.2    Mattox, J.3    Yeage, C.4
  • 18
    • 0027580147 scopus 로고
    • ITS primers with enhanced specificity for basidiomycetes - Application to the identification of mycorrhizae and rusts
    • 10.1111/j.1365-294X.1993.tb00005.x. 8180733
    • ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. M Gardes T Bruns, Molecular Ecology 1993 2 2 113 118 10.1111/j.1365-294X.1993.tb00005.x 8180733
    • (1993) Molecular Ecology , vol.2 , Issue.2 , pp. 113-118
    • Gardes, M.1    Bruns, T.2
  • 19
    • 0000432452 scopus 로고
    • Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics
    • San Diego: Academic press Innis MA, Gelfand DH, Sninski JJ, White TJ
    • Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. T White T Bruns S Lee J Taylor, PCR-protocols a guide to methods and applications San Diego: Academic press, Innis MA, Gelfand DH, Sninski JJ, White TJ, 1990 315 322
    • (1990) PCR-protocols A Guide to Methods and Applications , pp. 315-322
    • White, T.1    Bruns, T.2    Lee, S.3    Taylor, J.4
  • 20
    • 23044485088 scopus 로고    scopus 로고
    • Fugal-specific primers developed for analysis of the ITS region of environmental DNA extracts
    • 10.1186/1471-2180-5-28. 15904497
    • Fugal-specific primers developed for analysis of the ITS region of environmental DNA extracts. K Martin P Rygiewicz, BMC Microbiology 2005 5 28 10.1186/1471-2180-5-28 15904497
    • (2005) BMC Microbiology , vol.5 , pp. 28
    • Martin, K.1    Rygiewicz, P.2
  • 22
    • 33748682933 scopus 로고    scopus 로고
    • Quantification of damage in DNA recovered from highly degraded samples - A case study on DNA in faeces
    • 10.1186/1742-9994-3-11. 16911807
    • Quantification of damage in DNA recovered from highly degraded samples - a case study on DNA in faeces. B Deagle J Eveson S Jarman, Frontiers in Zoology 2006 3 11 10.1186/1742-9994-3-11 16911807
    • (2006) Frontiers in Zoology , vol.3 , pp. 11
    • Deagle, B.1    Eveson, J.2    Jarman, S.3
  • 25
    • 33750329972 scopus 로고    scopus 로고
    • Reconstructing the early evolution of Fungi using a six-gene phylogeny
    • 10.1038/nature05110. 17051209
    • Reconstructing the early evolution of Fungi using a six-gene phylogeny. T James,, et al. Nature 2006 443 818 822 10.1038/nature05110 17051209
    • (2006) Nature , vol.443 , pp. 818-822
    • James, T.1
  • 26
    • 3042599013 scopus 로고    scopus 로고
    • The thermodynamics of DNA structural motifs
    • 10.1146/annurev.biophys.32.110601.141800. 15139820
    • The thermodynamics of DNA structural motifs. JJ SantaLucia D Hicks, Annual Review of Biophysics and Biomolecular Structure 2004 33 415 440 10.1146/annurev.biophys.32.110601.141800 15139820
    • (2004) Annual Review of Biophysics and Biomolecular Structure , vol.33 , pp. 415-440
    • Santalucia, J.J.1    Hicks, D.2
  • 27
    • 65849214907 scopus 로고    scopus 로고
    • Primerhunter: A primer design tool for pcr-based virus subtype identification
    • 10.1093/nar/gkp073. 19264805
    • Primerhunter: a primer design tool for pcr-based virus subtype identification. J Duitama D Kumar E Hemphill M Khan I Mandoiu C Nelson, Nucleic Acids research 2009 37 8 2483 2492 10.1093/nar/gkp073 19264805
    • (2009) Nucleic Acids Research , vol.37 , Issue.8 , pp. 2483-2492
    • Duitama, J.1    Kumar, D.2    Hemphill, E.3    Khan, M.4    Mandoiu, I.5    Nelson, C.6
  • 28
    • 72849150520 scopus 로고    scopus 로고
    • Potential link between plant and fungal distributions in a dipterocarp rainforest: Community and phylogenetic structure of tropical ectomycorrhizal fungi across a plant and soil ecotone
    • 10.1111/j.1469-8137.2009.03075.x. 19878464
    • Potential link between plant and fungal distributions in a dipterocarp rainforest: community and phylogenetic structure of tropical ectomycorrhizal fungi across a plant and soil ecotone. K Peay P Kennedy S Davies S Tan T Bruns, New Phytologist 2010 185 529 542 10.1111/j.1469-8137.2009.03075.x 19878464
    • (2010) New Phytologist , vol.185 , pp. 529-542
    • Peay, K.1    Kennedy, P.2    Davies, S.3    Tan, S.4    Bruns, T.5
  • 29
    • 0037492478 scopus 로고    scopus 로고
    • Can you bank on GenBank?
    • DOI 10.1016/S0169-5347(03)00150-2
    • Can you bank on GenBank? D Harris, Trends in Ecology and Evolution 2003 18 7 317 319 10.1016/S0169-5347(03)00150-2 (Pubitemid 36774619)
    • (2003) Trends in Ecology and Evolution , vol.18 , Issue.7 , pp. 317-319
    • Harris, D.J.1
  • 30
    • 0346460954 scopus 로고    scopus 로고
    • Molecular identification of ectomycorrhizal mycelium in soil horizons
    • DOI: 10.1128/AEM.1169.1121.1327-1333.2003. 10.1128/AEM.69.1.327-333.2003. 12514012
    • Molecular identification of ectomycorrhizal mycelium in soil horizons. R Landeweert P Leeflang T Kuyper E Hoffland A Rosling K Wernars E Smit, Applied and Environmental Microbiology 2003 69 1 DOI: 10.1128/AEM.1169.1121.1327-1333. 2003 10.1128/AEM.69.1.327-333.2003 12514012
    • (2003) Applied and Environmental Microbiology , vol.69 , Issue.1
    • Landeweert, R.1    Leeflang, P.2    Kuyper, T.3    Hoffland, E.4    Rosling, A.5    Wernars, K.6    Smit, E.7
  • 32
    • 72649084530 scopus 로고    scopus 로고
    • Polymerase chain reaction primers miss half of rRNA microbial diversity
    • 10.1038/ismej.2009.89
    • Polymerase chain reaction primers miss half of rRNA microbial diversity. S Hong J Bunge C Leslin J S S Epstein, The ISME shopping 2009 3 1365 1373 10.1038/ismej.2009.89
    • (2009) The ISME Shopping , vol.3 , pp. 1365-1373
    • Hong, S.1    Bunge, J.2    Leslin, C.3    Epstein, S.4
  • 33
    • 58249111615 scopus 로고    scopus 로고
    • Environmental rRNA inventories miss over half of protistan diversity
    • 10.1186/1471-2180-8-222. 19087295
    • Environmental rRNA inventories miss over half of protistan diversity. S Jeon J Bunge C Leslin T Stoeck S Hong S Epstein, BMC Microbiology 2008 8 222 10.1186/1471-2180-8-222 19087295
    • (2008) BMC Microbiology , vol.8 , pp. 222
    • Jeon, S.1    Bunge, J.2    Leslin, C.3    Stoeck, T.4    Hong, S.5    Epstein, S.6
  • 34
    • 34247098019 scopus 로고    scopus 로고
    • Effect of primer mismatch annealing temperature and PCR cycle number on 16S rRNA gene -targetting bacterial community analysis
    • 10.1111/j.1574-6941.2007.00283.x. 17343679
    • Effect of primer mismatch annealing temperature and PCR cycle number on 16S rRNA gene -targetting bacterial community analysis. R Sipos A Szekely M Palatinszky M Revesz M K M Nikolausz, FEMS Microbiology Ecology 2007 60 341 350 10.1111/j.1574-6941.2007.00283.x 17343679
    • (2007) FEMS Microbiology Ecology , vol.60 , pp. 341-350
    • Sipos, R.1    Szekely, A.2    Palatinszky, M.3    Revesz, M.4    Nikolausz, M.5
  • 36
    • 65349091290 scopus 로고    scopus 로고
    • Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure
    • 10.1111/j.1462-2920.2008.01857.x. 19220394
    • Effect of PCR amplicon size on assessments of clone library microbial diversity and community structure. J Huber H Morrison H SM P Neal M Sogin D Welch, Environmental Microbiology 2009 11 5 1292 1302 10.1111/j.1462-2920.2008. 01857.x 19220394
    • (2009) Environmental Microbiology , vol.11 , Issue.5 , pp. 1292-1302
    • Huber, J.1    Morrison, H.2    H, S.M.3    Neal, P.4    Sogin, M.5    Welch, D.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.