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Volumn 2, Issue 6, 2017, Pages

Novel ITS1 fungal primers for characterization of the mycobiome

Author keywords

Fungi; ITS1; Mycobiome; Oral; Primer design; Yeast

Indexed keywords


EID: 85041512278     PISSN: None     EISSN: 23795042     Source Type: Journal    
DOI: 10.1128/mSphere.00488-17     Document Type: Article
Times cited : (79)

References (55)
  • 2
    • 33845647653 scopus 로고    scopus 로고
    • Parallels in fungal pathogenesis on plant and animal hosts
    • Sexton AC, Howlett BJ. 2006. Parallels in fungal pathogenesis on plant and animal hosts. Eukaryot Cell 5:1941-1949. https://doi.org/10.1128/EC. 00277-06
    • (2006) Eukaryot Cell , vol.5 , pp. 1941-1949
    • Sexton, A.C.1    Howlett, B.J.2
  • 3
    • 84879786685 scopus 로고    scopus 로고
    • The emerging world of the fungal microbiome
    • Huffnagle GB, Noverr MC. 2013. The emerging world of the fungal microbiome. Trends Microbiol 21:334-341. https://doi.org/10.1016/j.tim. 2013.04.002
    • (2013) Trends Microbiol , vol.21 , pp. 334-341
    • Huffnagle, G.B.1    Noverr, M.C.2
  • 4
    • 65349088516 scopus 로고    scopus 로고
    • Progress towards DNA barcoding of fungi
    • Seifert KA. 2009. Progress towards DNA barcoding of fungi. Mol Ecol Resour 9:83-89. https://doi.org/10.1111/j.1755-0998.2009.02635.x
    • (2009) Mol Ecol Resour , vol.9 , pp. 83-89
    • Seifert, K.A.1
  • 6
    • 0002858274 scopus 로고
    • Anamorph-teleomorph relationships
    • In Barlocher F (ed) Springer, Berlin, Germany
    • Webster J. 1992. Anamorph-teleomorph relationships, p 99-117. In Barlocher F (ed), The ecology of aquatic hyphomycetes. Springer, Berlin, Germany
    • (1992) The ecology of aquatic hyphomycetes , pp. 99-117
    • Webster, J.1
  • 8
    • 52649112500 scopus 로고    scopus 로고
    • Report of the planning workshop for all fungi DNA barcoding
    • Rossman A. 2007. Report of the planning workshop for all fungi DNA barcoding. Inoculum 58:1-5
    • (2007) Inoculum , vol.58 , pp. 1-5
    • Rossman, A.1
  • 9
    • 0036176250 scopus 로고    scopus 로고
    • Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens
    • Iwen PC, Hinrichs SH, Rupp ME. 2002. Utilization of the internal transcribed spacer regions as molecular targets to detect and identify human fungal pathogens. Med Mycol 40:87-109. https://doi.org/10.1080/ mmy.40.1.87.109
    • (2002) Med Mycol , vol.40 , pp. 87-109
    • Iwen, P.C.1    Hinrichs, S.H.2    Rupp, M.E.3
  • 11
    • 0000432452 scopus 로고
    • Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics
    • In Innis MA, Gelfand DH, Sninsky JJ, White TJ (ed) Academic Press, London, United Kingdom
    • White TJ, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics, p 315-322. In Innis MA, Gelfand DH, Sninsky JJ, White TJ (ed), PCR protocols: a guide to methods and applications, vol 18. Academic Press, London, United Kingdom
    • (1990) PCR protocols: a guide to methods and applications, vol 18 , pp. 315-322
    • White, T.J.1    Bruns, T.2    Lee, S.3    Taylor, J.4
  • 12
    • 0025374564 scopus 로고
    • Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species
    • Vilgalys R, Hester M. 1990. Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species. J Bacteriol 172:4238-4246. https://doi.org/10.1128/jb.172.8.4238-4246.1990
    • (1990) J Bacteriol , vol.172 , pp. 4238-4246
    • Vilgalys, R.1    Hester, M.2
  • 13
    • 34547129847 scopus 로고    scopus 로고
    • Development of the human infant intestinal microbiota
    • Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. 2007. Development of the human infant intestinal microbiota. PLoS Biol 5:e177. https://doi.org/10.1371/journal.pbio.0050177
    • (2007) PLoS Biol , vol.5
    • Palmer, C.1    Bik, E.M.2    DiGiulio, D.B.3    Relman, D.A.4    Brown, P.O.5
  • 14
    • 0028969372 scopus 로고
    • Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes
    • Glass NL, Donaldson GC. 1995. Development of primer sets designed for use with the PCR to amplify conserved genes from filamentous ascomycetes. Appl Environ Microbiol 61:1323-1330
    • (1995) Appl Environ Microbiol , vol.61 , pp. 1323-1330
    • Glass, N.L.1    Donaldson, G.C.2
  • 15
    • 63849105333 scopus 로고    scopus 로고
    • Sufficient sampling for asymptotic minimum species richness estimators
    • Chao A, Colwell RK, Lin CW, Gotelli NJ. 2009. Sufficient sampling for asymptotic minimum species richness estimators. Ecology 90: 1125-1133. https://doi.org/10.1890/07-2147.1
    • (2009) Ecology , vol.90 , pp. 1125-1133
    • Chao, A.1    Colwell, R.K.2    Lin, C.W.3    Gotelli, N.J.4
  • 18
    • 84922479758 scopus 로고    scopus 로고
    • Host-microorganism interactions in lung diseases
    • Marsland BJ, Gollwitzer ES. 2014. Host-microorganism interactions in lung diseases. Nat Rev Immunol 14:827-835. https://doi.org/10.1038/ nri3769
    • (2014) Nat Rev Immunol , vol.14 , pp. 827-835
    • Marsland, B.J.1    Gollwitzer, E.S.2
  • 19
    • 84901296354 scopus 로고    scopus 로고
    • The mycobiota: interactions between commensal fungi and the host immune system
    • Underhill DM, Iliev ID. 2014. The mycobiota: interactions between commensal fungi and the host immune system. Nat Rev Immunol 14: 405-416. https://doi.org/10.1038/nri3684
    • (2014) Nat Rev Immunol , vol.14 , pp. 405-416
    • Underhill, D.M.1    Iliev, I.D.2
  • 20
    • 84880335170 scopus 로고    scopus 로고
    • The human mycobiome in health and disease
    • Cui L, Morris A, Ghedin E. 2013. The human mycobiome in health and disease. Genome Med 5:63. https://doi.org/10.1186/gm467
    • (2013) Genome Med , vol.5 , pp. 63
    • Cui, L.1    Morris, A.2    Ghedin, E.3
  • 21
    • 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. https://doi.org/10.1111/j.1365-294X.1993. tb00005.x
    • (1993) Mol Ecol , vol.2 , pp. 113-118
    • Gardes, M.1    Bruns, T.D.2
  • 22
    • 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. https://doi.org/10.1186/1471-2180-5-28
    • (2005) BMC Microbiol , vol.5 , pp. 28
    • Martin, K.J.1    Rygiewicz, P.T.2
  • 24
    • 38949103378 scopus 로고    scopus 로고
    • Internal transcribed spacer primers and sequences for improved characterization of basidiomycetous orchid mycorrhizas
    • Taylor DL, McCormick MK. 2008. Internal transcribed spacer primers and sequences for improved characterization of basidiomycetous orchid mycorrhizas. New Phytol 177:1020-1033. https://doi.org/10.1111/j.1469-8137.2007.02320.x
    • (2008) New Phytol , vol.177 , pp. 1020-1033
    • Taylor, D.L.1    McCormick, M.K.2
  • 28
    • 84903128093 scopus 로고    scopus 로고
    • Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies
    • Op De Beeck MO, Lievens B, Busschaert P, Declerck S, Vangronsveld J, Colpaert JV. 2014. Comparison and validation of some ITS primer pairs useful for fungal metabarcoding studies. PLoS One 9:e97629. https://doi. org/10.1371/journal.pone.0097629
    • (2014) PLoS One , vol.9
    • Op De Beeck, M.O.1    Lievens, B.2    Busschaert, P.3    Declerck, S.4    Vangronsveld, J.5    Colpaert, J.V.6
  • 31
    • 84879148662 scopus 로고    scopus 로고
    • Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents
    • Hoffmann C, Dollive S, Grunberg S, Chen J, Li H, Wu GD, Lewis JD, Bushman FD. 2013. Archaea and fungi of the human gut microbiome: correlations with diet and bacterial residents. PLoS One 8:e66019. https://doi.org/10.1371/journal.pone.0066019
    • (2013) PLoS One , vol.8
    • Hoffmann, C.1    Dollive, S.2    Grunberg, S.3    Chen, J.4    Li, H.5    Wu, G.D.6    Lewis, J.D.7    Bushman, F.D.8
  • 34
  • 35
    • 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, Kauserud H. 2010. ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases. BMC Microbiol 10:189. https:// doi.org/10.1186/1471-2180-10-189
    • (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
  • 36
    • 84938420846 scopus 로고    scopus 로고
    • Host genotype is an important determinant of the cereal phyllosphere mycobiome
    • Sapkota R, Knorr K, Jørgensen LN, O'Hanlon KA, Nicolaisen M. 2015. Host genotype is an important determinant of the cereal phyllosphere mycobiome. New Phytol 207:1134-1144. https://doi.org/10.1111/nph.13418
    • (2015) New Phytol , vol.207 , pp. 1134-1144
    • Sapkota, R.1    Knorr, K.2    Jørgensen, L.N.3    O'Hanlon, K.A.4    Nicolaisen, M.5
  • 37
    • 84875619226 scopus 로고    scopus 로고
    • MAFFT multiple sequence alignment software version 7: improvements in performance and usability
    • Katoh K, Standley DM. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30:772-780. https://doi.org/10.1093/molbev/mst010
    • (2013) Mol Biol Evol , vol.30 , pp. 772-780
    • Katoh, K.1    Standley, D.M.2
  • 38
    • 79954506754 scopus 로고    scopus 로고
    • PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
    • Walters WA, Caporaso JG, Lauber CL, Berg-Lyons D, Fierer N, Knight R. 2011. PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers. Bioinformatics 27: 1159-1161. https://doi.org/10.1093/bioinformatics/btr087
    • (2011) Bioinformatics , vol.27 , pp. 1159-1161
    • Walters, W.A.1    Caporaso, J.G.2    Lauber, C.L.3    Berg-Lyons, D.4    Fierer, N.5    Knight, R.6
  • 40
    • 84945708555 scopus 로고
    • Programming techniques: regular expression search algorithm
    • Thompson K. 1968. Programming techniques: regular expression search algorithm. Commun ACM 11:419-422. https://doi.org/10.1145/363347. 363387
    • (1968) Commun ACM , vol.11 , pp. 419-422
    • Thompson, K.1
  • 41
    • 84859972408 scopus 로고    scopus 로고
    • Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi
    • Schoch CL, Seifert KA, Huhndorf S, Robert V, Spouge JL, Levesque CA, Chen W, Fungal Barcoding Consortium, Fungal Barcoding Consortium Author List. 2012. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc Natl Acad Sci U S A 109:6241-6246. https://doi.org/10.1073/pnas.1117018109
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 6241-6246
    • Schoch, C.L.1    Seifert, K.A.2    Huhndorf, S.3    Robert, V.4    Spouge, J.L.5    Levesque, C.A.6    Chen, W.7
  • 42
    • 34547567980 scopus 로고    scopus 로고
    • OligoCalc: an online oligonucleotide properties calculator
    • Kibbe WA. 2007. OligoCalc: an online oligonucleotide properties calculator. Nucleic Acids Res 35:W43-W46. https://doi.org/10.1093/ nar/gkm234
    • (2007) Nucleic Acids Res , vol.35 , pp. W43-W46
    • Kibbe, W.A.1
  • 45
    • 84876432817 scopus 로고    scopus 로고
    • Novocraft Technologies, Pataling Jaya, Selangor, Malaysia
    • Hercus C. 2009. Novocraft short read alignment package. Novocraft Technologies, Pataling Jaya, Selangor, Malaysia. http://www.novocraft. com
    • (2009) Novocraft short read alignment package
    • Hercus, C.1
  • 46
    • 79952422304 scopus 로고    scopus 로고
    • Quality control and preprocessing of metagenomic datasets
    • Schmieder R, Edwards R. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863-864. https://doi.org/10. 1093/bioinformatics/btr026
    • (2011) Bioinformatics , vol.27 , pp. 863-864
    • Schmieder, R.1    Edwards, R.2
  • 48
    • 84994444665 scopus 로고    scopus 로고
    • VSEARCH: a versatile open source tool for metagenomics
    • Rognes T, Flouri T, Nichols B, Quince C, Mahé F. 2016. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4:e2584. https://doi. org/10.7717/peerj.2584
    • (2016) PeerJ , vol.4
    • Rognes, T.1    Flouri, T.2    Nichols, B.3    Quince, C.4    Mahé, F.5
  • 51
    • 84876427223 scopus 로고    scopus 로고
    • phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data
    • McMurdie PJ, Holmes S. 2013. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS One 8:e61217. https://doi.org/10.1371/journal.pone.0061217
    • (2013) PLoS One , vol.8
    • McMurdie, P.J.1    Holmes, S.2
  • 53
    • 85041535884 scopus 로고    scopus 로고
    • January 1903. Coin-package
    • Batdorf CS. January 1903. Coin-package. US patent US717964 A
    • Batdorf, C.S.1
  • 55
    • 84857807072 scopus 로고    scopus 로고
    • R package version. R Foundation for Statistical Computing, Vienna, Austria
    • Wickham H, Chang W. 2013. An implementation of the Grammar of Graphics. R package version. R Foundation for Statistical Computing, Vienna, Austria. https://cran.r-project.org
    • (2013) An implementation of the Grammar of Graphics
    • Wickham, H.1    Chang, W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.