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

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 marke...

Full description

Saved in:

Bibliographic Details
Published in:	Persoonia Vol. 35; no. 1; pp. 242 - 263
Main Authors:	Stielow, J B, Lévesque, C A, Seifert, K A, Meyer, W, Iriny, 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, 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, N, Roscini, L, Egidi, E, Bizet, C, Garcia-Hermoso, D, Martín, M P, Deng, S, Groenewald, J Z, Boekhout, T, de Beer, Z W, Barnes, I, Duong, T A, Wingfield, M J, de Hoog, G S, Crous, P 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
Format:	Journal Article
Language:	English
Published:	Netherlands Nationaal Herbarium Nederland 01-12-2015 Naturalis Biodiversity Center / Westerdijk Fungal Biodiversity Institute Naturalis Biodiversity Center & Centraallbureau voor Schimmelcultures
Subjects:	DNA BARCODING Its Supplement Life Sciences Molecular Taxonomy Phylogeny Species Identification Universal Primers phylogeny ITS supplement molecular taxonomy universal primers species identification DNA barcoding
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Description
Summary:	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.
Bibliography:	0031-5850(20151223)35:1L.242;1- ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 PMCID: PMC4713107
ISSN:	0031-5850 1878-9080
DOI:	10.3767/003158515X689135