Finnish Museum of Natural History

DNA resources

Below you can find some of the tools for DNA and phylogenetic studies used by the Mycology Team.

Programs for phylogenetic analyses


Nuclear ITS and 5.8S rDNA primers

  • BasidLSU3-3: CGACTGACTTCAATCGT – Millanes et al. (2011)
  • ITS1F: CTT GGT CAT TTA GAG GAA GTA A – Gardes & Bruns (1993)
  • ITS4: TCC TCC GCT TAT TGA TAT GC – White et al. (1990)
  • ITS5: GGA AGT AAA AGT CGT AAC AAG G – White et al. (1990)
  • ITS1-LM: GAA CCT GCG GAA GGA TCA TT – Myllys et al. (1999)
  • ITS2-KL: ATG CTT AAG TTC AGC GGG TA – Lohtander et al. (1998)

Nucler small subunit rDNA primers

  • NS1: GTAGTCATATGCTTGTCTC – White et al. (1990)
  • NS19: CCGGAGAAGGAGCCTGAGAAAC – Gargas and Taylor (1992)
  • nu-SSU-0021-5': CTG GTT GAT TCT GCC AGT – Gargas & DePriest (1996)
  • nu-SSU-0072-5', NS17UCB: CAT GTC TAA GTT TAA GCA A – Gargas & DePriest (1996), Gargas & Taylor (1992)
  • nu-SSU-0402-5', NS19UCB: CCG GAG AAG GAG CCT GAG AAA C – Gargas & DePriest (1996), Gargas & Taylor (1992)
  • nu-SSU-0497-3', NS18UCB: CTC ATT CCA ATT ACA AGA CC – Gargas & DePriest (1996), Gargas & Taylor (1992)
  • nu-SSU-0819-5', NS21UCB: GAA TAA TAG AAT AGG ACG – Gargas & DePriest (1996), Gargas & Taylor (1992)
  • nu-SSU-0852-3', NS20UCB CGT CCC TAT TAA TCA TTA CG – Gargas & DePriest (1996), Gargas & Taylor (1992)
  • nu-SSU-1203-5': NS23UCB: GAC TCA ACA CGG GGA AAC TC – Gargas & DePriest (1996), Gargas & Taylor (1992)
  • nu-SSU-1293-3', NS22UCB: AAT TAA GCA GAC AAA TCA CT – Gargas & DePriest (1996), Gargas & Taylor (1992)
  • nu-SSU-1750-3', NS24UCB: AAA CCT TGT TAC GAC TTT TA – Gargas & DePriest (1996), Gargas & Taylor (1992)
  • nuSSU1088Rb: CGGCACCTTACGAGAAATCAAAGTC – Millanes et al. (2011)
  • SR8R: GAA CCA GGA CTT TTA CCT T – Vilgalys website
  • SR4: AAA CCA ACA AAA TAG AA – Vilgalys website
  • TnuSSU2-3: TTTTGATCCCCTAACCTTCGTTCT – Millanes et al. (2011)
  • TnuSSU1-3: CTTTCGGAATACCAAAAGGGYCAAG – Millanes et al. (2011)

Nuclear large subunit rDNA primers

  • BasidLSU1-5: TAGCGAACAAGTACCGTGAGG – Millanes et al. (2011)
  • BasidLSU3-5: ACGATTGAAGTCAGTCG – Millanes et al. (2011)
  • LR0R: ACC CGC TGA ACT TAA GC – Vilgalys website
  • LR3R: GTC TTG AAA CAC GGA CC – Rehner & Samuels (1995)
  • LR3: CCG TGT TTC AAG ACG GG – Rehner & Samuels (1995)
  • LR5: ATC CTG AGG GAA ACT TC – Vilgalys & Hester (1990)
  • LR7: TAC TAC CAC CAA GAT CT – Vilgalys & Hester (1990)
  • LR5R: GAA GTT TCC CTC AGG AT – Vilgalys website
  • nu-LSU-362-5': GCG CAC AAG TAG AGT GAT C – Döring et al. (2000)
  • nu-LSU-401-3': CCT TTC AAC AAT TTC ACG T – Döring et al. (2000)

Mitochondrial small subunit rDNA primers

  • mrSSU1: AGCAGTGAGGAATATTGGTC – Zoller et al. (1999)
  • mrSSU3R: ATGTGGCACGTCTATAGCCC – Zoller et al. (1999)
  • mtSSU1-KL: AGT GGT GTA CAG GTG AGT A – Lohtander et al. (2002)
  • mtSSU2-KL: ATG TGG CAC GTC TAT AGC CCA – Lohtander et al. (2002)

Betatubulin primers

  • Bt3-LM: GAA CGT CTA CTT CAA CGA G – Myllys et al. (2001)
  • Bt10-LM: TCG GAA GCA GCC ATC ATG TTC TT – Myllys et al. (2001)

Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) primers

  • Gpd1-LM: ATT GGC CGC ATC GTC TTC CGC AA – Myllys et al. (2002)
  • Gpd2-LM: CCC ACT CGT TGT CGT ACC A – Myllys et al. (2002)

RNA polymerase II largest subunit, RPB1 primers

  • gRPB1-Af: GAK TGT CCK GGW CAT TTT GG – Stiller & Hall (1997)
  • fRBP1-Cr: CNG CDA TNT CRT TRT CCA TRT A – Matheney et al. (2002)

RNA polymerase II 2nd largest subunit, RPB2 primers

  • fRPB2-7c: FAT GGG YAA RCA AGC YAT GGG – Liu et al. (1999)
  • fRPB2-11aR: GCR TGG ATC TTR TCR TCS ACC – Liu et al. (1999)
  • RPB2-7F: ATG GGK AAG CAR GCW ATG GG – Liu et al. (1999)
  • RPB2-3053R: TGR ATY TTR TCR TCS ACC ATR TG – Reeb et al. (2004)

MCM7 primers

  • X_mcm7_F: CGTACACYTGTGATSGATGTG – Leavitt (2010)
  • Mcm7_1348rev: GAYTTDGCDACDCCDGGRTCWCCCAT – Schmitt et al. (2009)

IGS primers

  • IGSf: TAGTGGCCGWTRGCTATCATT – Wirtz et al. (2008)
  • IGSr: TGCATGGCTTAATCTTTGAG – Wirtz et al. (2008)

TSR1 primers

  • Tsr1-1453for: GARTTCCCHGAYGARATYGARCT – Schmitt et al. (2009)
  • Tsr1-2308rev: CTTRAARTAXCCRTGXGTXCC – Schmitt et al. (2009)

References for primers:

Döring, H. & Clerc, P., Grube, M. & Wedin, M. 2000. Mycobiont-specific PCR primers for the amplification of nuclear ITS and LSU rDNA from lichenized ascomycetes. Lichenologist 32: 200–204.

Gardes, M. & Bruns, T. D. 1993. ITS primers with enhanced specificity for basidiomycetes - application to the identification of mycorrhizae and rusts. Molecular Ecology 2: 113–118.

Gargas, A. & DePriest, P. T. 1996. A nomenclature for fungal PCR primers with examples from intron-containing SSU rDNA. Mycologia 88: 745–748.

Gargas, A. & Taylor, J. W. 1992. Polymerase chain reaction (PCR) primers for amplifying and sequencing 18S rDNA from lichenized fungi. Mycologia 84: 589–592.

Leavitt, S. D. 2010. Assessing traditional morphology- and chemistry-based species circumscriptions in lichenized ascomycetes: Character evolution and species delimitation in common western North American lichens. Ph.D. dissertation, Brigham Young University, Provo, Utah, USA.

Liu Y. L., Whelen S. & Hall B. D. 1999. Phylogenetic relationships among ascomycetes: evidence from an RNA polymerase II subunit. Molecular Biology and Evolution 16: 1799–1808.

Lohtander, K., Myllys, L., Sundin, R., Källersjö, M., & Tehler, A. 1998. The species pair concept in the lichen Dendrographa leucophaea (Arthoniales): Analyses based on ITS sequences. Bryologist 101: 404–411.

Lohtander K, Oksanen I, Rikkinen J. 2002. A phylogenetic study of Nephroma (lichen-forming Ascomycota). Mycological Research 106: 777–787.

Matheny, P. B., Liu, Y. J., Ammirati, J. F. & Hall, B. D. 2002. Using RPB1 sequences to improve phylogenetic inference among mushrooms (Inocybe, Agaricales). American Journal of Botany 89: 688–698.

Millanes A. M., Diederich P., Ekman S., Wedin M. 2011. Phylogeny and character evolution in the jelly fungi (Tremellomycetes, Basidiomycota, Fungi). Molecular Phylogenetics and Evolution 61: 12–28.

Myllys, L., Lohtander, K., Källersjö, M. & Tehler A. 1999. Sequence insertions and ITS data provide congruent information on Roccella canariensis and R. tuberculata (Arthoniales, Euascomycetes) Phylogeny. Molecular Phylogenetics and Evolution 12: 295–309.

Myllys, L., Lohtander, K. & Tehler, A. 2001. β-tubulin, ITS and group I intron challenge the species pair concept in Physcia aipolia and P. caesia. Mycologia 93: 335–343.

Myllys, L., Stenroos, S. & Thell, A. 2002. New genes for phylogenetic studies of lichenized fungi: glyceraldehyde-3-phosphate dehydrogenase and beta-tubulin genes. Lichenologist 34: 237–246.

Reeb V., Lutzoni F. & Roux C. 2004. Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory. Molecular Phylogenetics and Evolution 32: 1036–1060.

Rehner, S. A. & Samuels, G. J. 1995. Molecular systematics of the Hypocreales: a teleomorph gene phylogeny and the status of their anamorphs. Canadian Journal of Botany 73: 816–823.

Schmitt, I., Crespo, A., Divakar, P. K., Fankhauser, J. D., Herman-Sackett, E., Kalb, K., Nelsen, M. P., Nelson, N. A., Rivas-Plata, E., Shimp, A. D., Widhelm, T. & Lumbsch, H. T. 2009. New primers for promising single-copy genes in fungal phylogenetics and systematics. Persoonia 23: 35–40.

Stiller, J. W. & Hall, B. D. 1997. The origin of red algae: implications for plastid evolution. Proceedings of the National Academy of Sciences USA 94: 4520–4525.

Vilgalys, R. Conserved primer sequences for PCR amplification and sequencing from nuclear ribosomal RNA. Duke University, USA. Internet address

Vilgalys, R. & Hester, M. 1990. Rapid genetic identifcation and mapping of enzymatically amplifed ribosomal DNA from several Cryptococcus species. Journal of Bacteriology 172: 4238–4246.

White, T. J., Bruns, T., Lee, S. B. & Taylor, J. W. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis, M. A., Gelfand, D. H., Sninsky, J. J. & White T. J. (eds), PCR Protocols: a Guide to Methods and Application. Academic Press, San Diego, pp. 315–322.

Wirtz, N., Printzen, C. & Lumbsch, T. 2008. The delimitation of Antarctic and bipolar species of neuropogonoid Usnea (Ascomycota, Lecanorales): a cohesion approach of species recognition for the Usnea perpusilla complex. Mycological Research 112(4): 472–484.

Zoller, S., Scheidegger, C. & Sperisen, C. 1999. PCR primers for the amplification of mitochondrial small subunit ribosomal DNA of lichen-forming. Lichenologist 31: 511–516.

Person in charge of the page: 
Saara Velmala