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Primer sequences : RNA polymerase II largest subunit, RPB1


Stiller & Hall (1997) were the first to design primers from this molecule to resolve phylogenetic relationships. Their study focused on red algae. Matheny et al. developed one additional primer for a study of fungi in 2002.


As part of the AFToL (Assembling the Fungal Tree of Life) project, members of our lab have developed new primers for amplifying and sequencing RPB1 in Ascomycota [asc], Lecanoromycetidae [lecan], and Peltigerales [pelt] (Hofstetter et al. 2007):


Several RPB1 primers were also developed in our lab as part of a study on the systematics of the family Verrucariaceae (Gueidan et al. 2007):


References and relevant publications:

Matheny, P.B., Liu, Y.J., Ammirati, J.F., and Hall, B.D. 2002. Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe, Agaricales). Am. J. Bot. 89: 688-698.

Stiller, J.W. and Hall, B.D. 1997. The origin of red algae: Implications for plastid evolution. PNAS 94: 4520 - 4525.

Hofstetter, V., Miadlikowska, J., Kauff, F., and Lutzoni, F. 2007. Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: A case study of the Lecanoromycetes (Ascomycota). Molecular Phylogenetics and Evolution 44:412-426.
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Gueidan, C., Roux, C., and Lutzoni, F. 2007. Using a multigene phylogenetic analysis to assess generic delineation and character evolution in Verrucariaceae (Eurotiomycetes, Ascomycota). Mycological Research 111:1145-1168.
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James, T. Y., F. Kauff, C. Schoch, P. B. Matheny, V. Hofstetter, C. Cox, G. Celio, C. Gueidan, E. Fraker, J. Miadlikowska, H. T. Lumbsch, A. Rauhut, V. Reeb, A. E. Arnold, A. Amtoft, J. E. Stajich, K. Hosaka, G.-H. Sung, D. Johnson, B. O'Rourke, M. Crockett, M. Binder, J. M. Curtis, J. C. Slot, Z. Wang, A. W. Wilson, A. Schüßler, J. E. Longcore, K. O'Donnell, S. Mozley-Standridge, D. Porter, P. M. Letcher, M. J. Powell, J. W. Taylor, M. M. White, G. W. Griffith, D. R. Davies, R. A. Humber, J. B. Morton, J. Sugiyama, A. Y. Rossman, J. D. Rogers, D. H. Pfister, D. Hewitt, K. Hansen, S. Hambleton, R. A. Shoemaker, J. Kohlmeyer, B. Volkmann-Kohlmeyer, R. A. Spotts, M. Serdani, P. W. Crous, K. W. Hughes, K. Matsuura, E. Langer, G. Langer, W. A. Untereiner, R. Lücking, B. Büdel, D. M. Geiser, A. Aptroot, P. Diederich, I. Schmitt, M. Schultz, R. Yahr, D. Hibbett, F. Lutzoni, D. McLaughlin, J. Spatafora, and R. Vilgalys. 2006. Reconstructing the early evolution of the fungi using a six gene phylogeny. Nature 443:818-822.
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Download supplementary notes

Miadlikowska, J., Kauff, F., Hofstetter, V., Fraker, E., Grube, M., Hafellner, J., Reeb, V., Hodkinson, B. P., Kukwa, M., Lücking, R., Hestmark, G., Garcia Otalora, M., Rauhut, A., Büdel, B., Scheidegger, C., Timdal, E., Stenroos, S., Brodo, I., Perlmutter, G., Ertz, D., Diederich, P., Lendemer, J. C., May, P., Schoch, C. L., Arnold, A. E., Gueidan, C., Tripp, E., Yahr, R., Robertson, C., Lutzoni, F. 2006. New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes. Mycologia 98:1088-1103.
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O'Brien, H. E., Miadlikowska, J. and Lutzoni, F. 2009. Assessing reproductive isolation in highly diverse communities of the lichen-forming fungal genus Peltigera. Evolution 63:2076–2086.
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Department of Biology, Duke University, Box 90338, Durham, NC 27708
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