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One fungus, which genes?: development and assessment of universal primers for potential secondary fungal DNA barcodes

(2015) PERSOONIA. 35. p.242-263
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Abstract
The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across > 1 500 species (1 931 strains or specimens) and the outcomes of almost twenty thousand (19 577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit (D1-D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial beta-tubulin II (TUB2); iv) gamma-actin (ACT); v) translation elongation factor 1-alpha (TEF1 alpha); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5-6). Their PCR efficiencies were compared with novel candidate primers corresponding to: i) the fungal-specific translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP; iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1 alpha. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-specific variation that make them attractive barcodes for species identification. Among these gene sections, a novel high fidelity primer pair for TEF1 alpha, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.
Keywords
phylogeny, molecular taxonomy, ITS supplement, DNA barcoding, species identification, universal primers, INTERNAL TRANSCRIBED SPACER, ELONGATION FACTOR-III, RIBOSOMAL DNA, BASIDIOMYCETOUS YEASTS, SEQUENCE-ANALYSIS, ASCOMYCETOUS YEASTS, MANTEL TEST, ACTIN GENE, IDENTIFICATION, SUBUNIT

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MLA
Stielow, JB et al. “One Fungus, Which Genes?: Development and Assessment of Universal Primers for Potential Secondary Fungal DNA Barcodes.” PERSOONIA 35 (2015): 242–263. Print.
APA
Stielow, J., Levesque, C., Seifert, K., Meyer, W., Irinyi, L., Smits, D., Renfurm, R., et al. (2015). One fungus, which genes?: development and assessment of universal primers for potential secondary fungal DNA barcodes. PERSOONIA, 35, 242–263.
Chicago author-date
Stielow, JB, CA Levesque, KA Seifert, W Meyer, L Irinyi, D Smits, R Renfurm, et al. 2015. “One Fungus, Which Genes?: Development and Assessment of Universal Primers for Potential Secondary Fungal DNA Barcodes.” Persoonia 35: 242–263.
Chicago author-date (all authors)
Stielow, JB, CA Levesque, KA Seifert, W Meyer, L Irinyi, D Smits, R Renfurm, GJM Verkley, M Groenewald, D Chaduli, A Lomascolo, S Welti, L Lesage-Meessen, A Favel, AMS Al-Hatmi, U Damm, N Yilmaz, J Houbraken, L Lombard, W Quaedvlieg, M Binder, LAI Vaas, D Vu, A Yurkov, D Begerow, O Roehl, M Guerreiro, A Fonseca, K Samerpitak, AD van Diepeningen, S Dolatabadi, LF Moreno, S Casaregola, S Mallet, N Jacques, L Roscini, E Egidi, C Bizet, D Garcia-Hermoso, MP Martin, S Deng, JZ Groenewald, T Boekhout, ZW de Beer, I Barnes, TA Duong, MJ Wingfield, GS de Hoog, PW Crous, CT Lewis, S Hambleton, TAA Moussa, HS Al-Zahrani, OA Almaghrabi, G Louis-Seize, R Assabgui, W McCormick, G Omer, K Dukik, G Cardinali, Ursula Eberhardt, M de Vries, and V Robert. 2015. “One Fungus, Which Genes?: Development and Assessment of Universal Primers for Potential Secondary Fungal DNA Barcodes.” Persoonia 35: 242–263.
Vancouver
1.
Stielow J, Levesque C, Seifert K, Meyer W, Irinyi L, Smits D, et al. One fungus, which genes?: development and assessment of universal primers for potential secondary fungal DNA barcodes. PERSOONIA. 2015;35:242–63.
IEEE
[1]
J. Stielow et al., “One fungus, which genes?: development and assessment of universal primers for potential secondary fungal DNA barcodes,” PERSOONIA, vol. 35, pp. 242–263, 2015.
@article{7170172,
  abstract     = {The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across > 1 500 species (1 931 strains or specimens) and the outcomes of almost twenty thousand (19 577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit (D1-D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial beta-tubulin II (TUB2); iv) gamma-actin (ACT); v) translation elongation factor 1-alpha (TEF1 alpha); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5-6). Their PCR efficiencies were compared with novel candidate primers corresponding to: i) the fungal-specific translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP; iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1 alpha. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-specific variation that make them attractive barcodes for species identification. Among these gene sections, a novel high fidelity primer pair for TEF1 alpha, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.},
  author       = {Stielow, JB and Levesque, CA and Seifert, KA and Meyer, W and Irinyi, L and Smits, D and Renfurm, R and Verkley, GJM and Groenewald, M and Chaduli, D and Lomascolo, A and Welti, S and Lesage-Meessen, L and Favel, A and Al-Hatmi, AMS and Damm, U and Yilmaz, N and Houbraken, J and Lombard, L and Quaedvlieg, W and Binder, M and Vaas, LAI and Vu, D and Yurkov, A and Begerow, D and Roehl, O and Guerreiro, M and Fonseca, A and Samerpitak, K and van Diepeningen, AD and Dolatabadi, S and Moreno, LF and Casaregola, S and Mallet, S and Jacques, N and Roscini, L and Egidi, E and Bizet, C and Garcia-Hermoso, D and Martin, MP and Deng, S and Groenewald, JZ and Boekhout, T and de Beer, ZW and Barnes, I and Duong, TA and Wingfield, MJ and de Hoog, GS and Crous, PW and Lewis, CT and Hambleton, S and Moussa, TAA and Al-Zahrani, HS and Almaghrabi, OA and Louis-Seize, G and Assabgui, R and McCormick, W and Omer, G and Dukik, K and Cardinali, G and Eberhardt, Ursula and de Vries, M and Robert, V},
  issn         = {0031-5850},
  journal      = {PERSOONIA},
  keywords     = {phylogeny,molecular taxonomy,ITS supplement,DNA barcoding,species identification,universal primers,INTERNAL TRANSCRIBED SPACER,ELONGATION FACTOR-III,RIBOSOMAL DNA,BASIDIOMYCETOUS YEASTS,SEQUENCE-ANALYSIS,ASCOMYCETOUS YEASTS,MANTEL TEST,ACTIN GENE,IDENTIFICATION,SUBUNIT},
  language     = {eng},
  pages        = {242--263},
  title        = {One fungus, which genes?: development and assessment of universal primers for potential secondary fungal DNA barcodes},
  url          = {http://dx.doi.org/10.3767/003158515X689135},
  volume       = {35},
  year         = {2015},
}

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