New primers for promising single-copy genes in fungal phylogenetics and systematics - PubMed (original) (raw)

doi: 10.3767/003158509X470602. Epub 2009 Aug 4.

A Crespo, P K Divakar, J D Fankhauser, E Herman-Sackett, K Kalb, M P Nelsen, N A Nelson, E Rivas-Plata, A D Shimp, T Widhelm, H T Lumbsch

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New primers for promising single-copy genes in fungal phylogenetics and systematics

I Schmitt et al. Persoonia. 2009 Dec.

Abstract

Developing powerful phylogenetic markers is a key concern in fungal phylogenetics. Here we report degenerate primers that amplify the single-copy genes Mcm7 (MS456) and Tsr1 (MS277) across a wide range of Pezizomycotina (Ascomycota). Phylogenetic analyses of 59 taxa belonging to the Eurotiomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes and Sordariomycetes, indicate the utility of these loci for fungal phylogenetics at taxonomic levels ranging from genus to class. We also tested the new primers in silico using sequences of Saccharomycotina, Taphrinomycotina and Basidiomycota to predict their potential of amplifying widely across the Fungi. The analyses suggest that the new primers will need no, or only minor sequence modifications to amplify Saccharomycotina, Taphrinomycotina and Basidiomycota.

Keywords: Ascomycota; DNA replication licensing factor; MS277; MS456; Mcm7; Tsr1; evolution; lichenised fungi; phylogeny; pre-rRNA processing protein; protein-coding.

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Figures

Fig. 1

Fig. 1

Locations of the new primers for Mcm7 and Tsr1 using Aspergillus nidulans mRNA (XM_658504 and XM_658778) as reference sequence. Shaded areas in Tsr1 indicate regions of high sequence variability.

Fig. 2

Fig. 2

Phylogeny of Pezizomycotina (Ascomycota) based on a combined alignment of Mcm7 (MS456) and Tsr1 (MS277) sequences. Total alignment length is 1203 bp. This is a 50 % majority rule consensus tree based on a sampling of 108 000 B/MCMC trees. Bold branches indicate posterior probabilities ≥ 0.95. Numbers above branches are maximum parsimony bootstrap support values ≥ 70 based on 2 000 random addition replicates.

Fig. 3

Fig. 3

Comparison of the new primers to homologous sequences in Saccharomycotina (Ashbya, Kluyveromyces, Saccharomyces, Yarrowia), Taphrinomycotina (Schizosaccharomyces) and Basidiomycota (Coprinopsis, Cryptococcus, Ustilago). 100 % matches between primer sequence and gene sequences studied are indicated by grey shading. High sequence similarities indicate that the new primers are likely to fit in members of the analysed groups. Some primer sequences may require slight modifications.

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