One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes
Stielow, J.B.; Levesque, 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, Neriman; Houbraken, J.; Lombard, L.; Quaedvlieg, W.; Binder, M.; Vaas, L.A.I.; Vu, D.; Yurkov, A.; Begerow, D.; Roehl, O.; Guerreiro, M.; Fonseca, A.; Samerpitak, K.; van Diepeningen, A.D.; Dolatabadi, S.; Moreno, L.F.; Casaregola, S.; Mallet, S.; Jacques, Noémie; Roscini, L.; Egidi, E.; Bizet, C.; Garcia-Hermoso, D.; Martin, M.P.; Deng, S.; Groenewald, Johannes Zacharias; Boekhout, T.; De Beer, Z. Wilhelm; Barnes, Irene; Duong, Tuan A.; Wingfield, Michael J.; De Hoog, G.S.; Crous, Pedro W.; Lewis, C.T.; Hambleton, S.; Moussa, T.A.A.; Al-Zahrani, H.S.; Almaghrabi, O.A.; Louis-Seize, G.; Assabgui, R.; McCormick, W.; Omer, G.; Dukik, K.; Cardinali, G.; Eberhardt, U.; De Vries, M.; Robert, V.
Date:
2015-08-28
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.
