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

J B Stielow; C A Lévesque; K A Seifert; W Meyer; L Irinyi; D Smits; R Renfurm; G J M Verkley; M Groenewald; D Chaduli; A Lomascolo; S Welti; L Lesage-Meessen; A Favel; A M S Al-Hatmi; U Damm; N. Yilmaz; J. Houbraken; L. Lombard; W. Quaedvlieg; M. Binder; L.A.I. Vaas; D. Vu; A. Yurkov; D. Begerow; O. Roehl; M. Guerreiro; A. Fonseca; K. Samerpitak; A.D. van Diepeningen; S. Dolatabadi; L.F. Moreno; S. Casaregola; S. Mallet; N. Jacques; L. Roscini; E. Egidi; C. Bizet; D. Garcia-Hermoso; M.P. Martín; S. Deng; J.Z. Groenewald; T. Boekhout; Z.W. de Beer; I. Barnes; T.A. Duong; M.J. Wingfield; G.S. de Hoog; P.W. Crous; C.T. Lewis; S. Hambleton; T.A.A. Moussa; H.S. Al-Zahrani; O.A. Almaghrabi; G. Louis-Seize; R. Assabgui; W. McCormick; G. Omer; K. Dukik; G. Cardinali; U. Eberhardt; M. de Vries; V. Robert

doi:10.3767/003158515X689135

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

J B Stielow, C A Lévesque, K A Seifert, W Meyer, L Irinyi, D Smits, R Renfurm, G J M Verkley, M Groenewald, D Chaduli, A Lomascolo, S Welti, L Lesage-Meessen, A Favel, A M S Al-Hatmi, U Damm, N. Yilmaz, J. Houbraken, L. Lombard, W. QuaedvliegM. Binder, L.A.I. Vaas, D. Vu, A. Yurkov, D. Begerow, O. Roehl, M. Guerreiro, A. Fonseca, K. Samerpitak, A.D. van Diepeningen, S. Dolatabadi, L.F. Moreno, S. Casaregola, S. Mallet, N. Jacques, L. Roscini, E. Egidi, C. Bizet, D. Garcia-Hermoso, M.P. Martín, S. Deng, J.Z. Groenewald, T. Boekhout, Z.W. de Beer, I. Barnes, T.A. Duong, M.J. Wingfield, G.S. de Hoog, P.W. Crous, C.T. Lewis, S. Hambleton, T.A.A. Moussa, H.S. Al-Zahrani, O.A. Almaghrabi, G. Louis-Seize, R. Assabgui, W. McCormick, G. Omer, K. Dukik, G. Cardinali, U. Eberhardt, M. de Vries, V. Robert

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

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 β-tubulin II (TUB2); iv) γ-actin (ACT); v) translation elongation factor 1-α (TEF1α); 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 TEF1α. 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 TEF1α, 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.

Original language	English
Pages (from-to)	242-263
Number of pages	22
Journal	Persoonia
Volume	35
DOIs	https://doi.org/10.3767/003158515X689135
Publication status	Published - 2015

Keywords

DNA barcoding
ITS supplement
molecular taxonomy
phylogeny
species identification
universal primers

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10.3767/003158515X689135

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Stielow, J. B., Lévesque, C. A., Seifert, K. A., Meyer, W., Irinyi, L., Smits, D., Renfurm, R., Verkley, G. J. M., Groenewald, M., Chaduli, D., Lomascolo, A., Welti, S., Lesage-Meessen, L., Favel, A., Al-Hatmi, A. M. S., Damm, U., Yilmaz, N., Houbraken, J., Lombard, L., ... Robert, V. (2015). One fungus , which genes ? Development and assessment of universal primers for potential secondary fungal DNA barcodes. Persoonia, 35, 242-263. https://doi.org/10.3767/003158515X689135

@article{8a01046273de4310a7f51efab42b51cd,

title = "One fungus , which genes ? Development and assessment of universal primers for potential secondary fungal DNA barcodes",

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 β-tubulin II (TUB2); iv) γ-actin (ACT); v) translation elongation factor 1-α (TEF1α); 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 TEF1α. 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 TEF1α, 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 = "DNA barcoding, ITS supplement, molecular taxonomy, phylogeny, species identification, universal primers",

author = "Stielow, {J B} and L{\'e}vesque, {C A} and Seifert, {K A} and W Meyer and L Irinyi and D Smits and R Renfurm and Verkley, {G J M} and M Groenewald and D Chaduli and A Lomascolo and S Welti and L Lesage-Meessen and A Favel and Al-Hatmi, {A M S} and U Damm and N. Yilmaz and J. Houbraken and L. Lombard and W. Quaedvlieg and M. Binder and L.A.I. Vaas and D. Vu and A. Yurkov and D. Begerow and O. Roehl and M. Guerreiro and A. Fonseca and K. Samerpitak and Diepeningen, {A.D. van} and S. Dolatabadi and L.F. Moreno and S. Casaregola and S. Mallet and N. Jacques and L. Roscini and E. Egidi and C. Bizet and D. Garcia-Hermoso and M.P. Mart{\'i}n and S. Deng and J.Z. Groenewald and T. Boekhout and Beer, {Z.W. de} and I. Barnes and T.A. Duong and M.J. Wingfield and Hoog, {G.S. de} and P.W. Crous and C.T. Lewis and S. Hambleton and T.A.A. Moussa and H.S. Al-Zahrani and O.A. Almaghrabi and G. Louis-Seize and R. Assabgui and W. McCormick and G. Omer and K. Dukik and G. Cardinali and U. Eberhardt and Vries, {M. de} and V. Robert",

year = "2015",

doi = "10.3767/003158515X689135",

language = "English",

volume = "35",

pages = "242--263",

journal = "Persoonia",

issn = "0031-5850",

publisher = "National Herbarium Nederland",

}

Stielow, JB, Lévesque, CA, Seifert, KA, Meyer, W, Irinyi, L, Smits, D, Renfurm, R, Verkley, GJM , Groenewald, M, Chaduli, D, Lomascolo, A, Welti, S, Lesage-Meessen, L, Favel, A, Al-Hatmi, AMS, Damm, U, Yilmaz, N, Houbraken, J, Lombard, L, Quaedvlieg, W, Binder, M, Vaas, LAI, Vu, D, Yurkov, A, Begerow, D, Roehl, O, Guerreiro, M, Fonseca, A, Samerpitak, K, Diepeningen, ADV, Dolatabadi, S, Moreno, LF, Casaregola, S, Mallet, S, Jacques, N, Roscini, L, Egidi, E, Bizet, C, Garcia-Hermoso, D, Martín, MP, Deng, S, Groenewald, JZ , Boekhout, T, Beer, ZWD, Barnes, I, Duong, TA, Wingfield, MJ, Hoog, GSD, Crous, PW, Lewis, CT, Hambleton, S, Moussa, TAA, Al-Zahrani, HS, Almaghrabi, OA, Louis-Seize, G, Assabgui, R, McCormick, W, Omer, G, Dukik, K, Cardinali, G, Eberhardt, U, Vries, MD & Robert, V 2015, 'One fungus , which genes ? Development and assessment of universal primers for potential secondary fungal DNA barcodes', Persoonia, vol. 35, pp. 242-263. https://doi.org/10.3767/003158515X689135

TY - JOUR

T1 - One fungus , which genes ? Development and assessment of universal primers for potential secondary fungal DNA barcodes

AU - Stielow, J B

AU - Lévesque, C A

AU - Seifert, K A

AU - Meyer, W

AU - Irinyi, L

AU - Smits, D

AU - Renfurm, R

AU - Verkley, G J M

AU - Groenewald, M

AU - Chaduli, D

AU - Lomascolo, A

AU - Welti, S

AU - Lesage-Meessen, L

AU - Favel, A

AU - Al-Hatmi, A M S

AU - Damm, U

AU - Yilmaz, N.

AU - Houbraken, J.

AU - Lombard, L.

AU - Quaedvlieg, W.

AU - Binder, M.

AU - Vaas, L.A.I.

AU - Vu, D.

AU - Yurkov, A.

AU - Begerow, D.

AU - Roehl, O.

AU - Guerreiro, M.

AU - Fonseca, A.

AU - Samerpitak, K.

AU - Diepeningen, A.D. van

AU - Dolatabadi, S.

AU - Moreno, L.F.

AU - Casaregola, S.

AU - Mallet, S.

AU - Jacques, N.

AU - Roscini, L.

AU - Egidi, E.

AU - Bizet, C.

AU - Garcia-Hermoso, D.

AU - Martín, M.P.

AU - Deng, S.

AU - Groenewald, J.Z.

AU - Boekhout, T.

AU - Beer, Z.W. de

AU - Barnes, I.

AU - Duong, T.A.

AU - Wingfield, M.J.

AU - Hoog, G.S. de

AU - Crous, P.W.

AU - Lewis, C.T.

AU - Hambleton, S.

AU - Moussa, T.A.A.

AU - Al-Zahrani, H.S.

AU - Almaghrabi, O.A.

AU - Louis-Seize, G.

AU - Assabgui, R.

AU - McCormick, W.

AU - Omer, G.

AU - Dukik, K.

AU - Cardinali, G.

AU - Eberhardt, U.

AU - Vries, M. de

AU - Robert, V.

PY - 2015

Y1 - 2015

N2 - 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 β-tubulin II (TUB2); iv) γ-actin (ACT); v) translation elongation factor 1-α (TEF1α); 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 TEF1α. 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 TEF1α, 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.

AB - 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 β-tubulin II (TUB2); iv) γ-actin (ACT); v) translation elongation factor 1-α (TEF1α); 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 TEF1α. 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 TEF1α, 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.

KW - DNA barcoding

KW - ITS supplement

KW - molecular taxonomy

KW - phylogeny

KW - species identification

KW - universal primers

U2 - 10.3767/003158515X689135

DO - 10.3767/003158515X689135

M3 - Article

SN - 0031-5850

VL - 35

SP - 242

EP - 263

JO - Persoonia

JF - Persoonia

ER -

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

Abstract

Keywords

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