Francois Lutzoni's Page |  Lab Members |  Visitors |  Group Photos |  News Releases |  Publications & Data Sets |  Lichen Collection
AFToL |  Ascomycota |  Peltigera |  Teloschistales |  Lichen Evolution & Systematics |  Primers |  Downloadable Programs |  Site map

Primer sequences : Nuclear ribosomal DNA

We used the primer list from Vilgalysí lab at Duke University as the basis to which we have added primers developed in our lab. Contrary to Vilgalysí lab who are designing primers mainly for phylogenetic studies of Basidiomycota, the target organisms for our primers are typically lichenized and non-lichenized Ascomycota. Primers that work best for us are highlighted in blue. Many of these primers are likely to work more generally (e.g., for basal fungal lineages). Several of these primers work well on plants, as well as on algae found in lichens. Recently, members of our lab developed species-specific primers for nuclear ribosomal loci of Verrucariaceae (Gueidan et al. 2007).
Link to: Vilgalysí lab at Duke University


Small subunit rDNA primer sequences ssu ref. nb pb
BMB-'A' (Lan) GWA TTA CCG CGG CKG CTG 583-566 18
BMB-'B' (Lan) CCG TCA ATT CMT TTR AGT TT 1147-1128 20
BMB-'C' (Lan) ACG GGC GGT GTG TRC 1641-1637 15
BMB-BR (Lan) CTT AAA GGA ATT GAC GGA A 1131-1149 19
BMB-CR (Lan) GTA CAC ACC GCC CGT CG 1637-1643 17
nssu97a (Kau) TAT ACG GTG AAA CTG CGA ATG GC 75-97 23
nssu97b (Kau) CGG TGA AAC TGC GAA TGG C 79-97 19
nssu634 (Kau) CCC CAG AAG GAA AGI CCC GIC C 705-684 22
nssu897R (Kau) AGA GGT GAA ATT CTT GGA 897-914 18
nssu1088 (Kau) TGA TTT CTC GTA AGG TGC CG 1088-1069 20
nssu1088R (Kau) CGG CAC CTT ACG AGA AAT CA 1069-1088 20
nssu131 (Kau) CAG TTA TCG TTT ATT TGA TAG TAC C 107-131 25
NS1 (Whi) GTA GTC ATA TGC TTG TCT C 20-38 19
NS2 (Whi) GGC TGC TGG CAC CAG ACT TGC 573-553 21
NS3 (Whi) GCA AGT CTG GTG CCA GCA GCC 553-573 21
NS4 (Whi) CTT CCG TCA ATT CCT TTA AG (sim. to BMB-b) 1150-1131 20
NS5 (Whi) AAC TTA AAG GAA TTG ACG GAA G (sim. to BMB-BR) 1129-1150 22
NS6 (Whi) GCA TCA CAG ACC TGT TAT TGC CTC 1436-1413 24
NS7 (Whi) GAG GCA ATA ACA GGT CTG TGA TGC 1413-1436 24
NS8 (Whi) TCC GCA GGT TCA CCT ACG GA 1788-1769 20
NS17 (Gar) CAT GTC TAA GTT TAA GCA A 54-72 19
NS18 (Gar) CTC ATT CCA ATT ACA AGA CC 516-497 20
NS19 (Gar) CCG GAG AAG GAG CCT GAG AAA C 381-402 22
NS20 (Gar) CGT CCC TAT TAA TCA TTA CG 871-852 20
NS21 (Gar) GAA TAA TAG AAT AGG ACG 802-819 18
NS22 (Gar) AAT TAA GCA GAC AAA TCA CT 1312-1297 20
NS23 (Gar) GAC TCA ACA CGG GGA AAC TC 1184-1203 20
NS24 (Gar) AAA CCT TGT TAC GAC TTT TA 1769-1750 20
SR1 (VilU) ATT ACC GCG GCT GCT (similar to BMB-'A') 581-567 15
SR1R (Vil0) TAC CTG GTT GAT TCT GC 21-1 21
SR2 (Elw) CGG CCA TGC ACC ACC 1277-1263 15
SR3 (VilU) GAA AGT TGA TAG GGC T 321-306 16
SR4 (VilU) AAA CCA ACA AAA TAG AA 841-825 17
SR5 (VilU) GTG CCC TTC CGT CAA TT 1155-1139 17
SR6 (VilU) TGT TAC GAC TTT TAC TT 1763-1747 17
SR7 (VilU) GTT CAA CTA CGA GCT TTT TAA 637-617 21
SR7R (VilU) TTA AAA AGC TCG TAG TTG AAC 617-637 21
SR8R (VilU) GAA CCA GGA CTT TTA CCT T 732-750 19
SR9R (Elw) YAG AGG TGA AAT TCT 896-910 15
SR10R (VilU) TTT GAC TCA ACA CGG G 1181-1196 16
SR11R (Spa) GGA GCC TGA GAA ACG GCT AC 389-408 20
1 (DeP) GCT CTT TCT TGA TTT TGT 1241-1258 18
3 (DeP) TTT GAG GCA ATA ACA GGT 1410-1427 18
4 (DeP) CAT CTA AGG GCA TCA CAG 1445-1428 18
5 (DeP) TTG TCT CTG TCA GTG TAG 1482-1465 18
6 (DeP) CAA CGA GGA ATT CCT AGT 1566-1583 18
9 (DeP) AAT GAT CCT TCC GCA GGT 1797-1780 18


Large subunit rDN primer sequences lsu ref. nb pb
GUADET P1 (Gua) GAG TCG AGT TGT TTG GGA ATG CAG C 275-300 25
GUADET P2 (Gua) GAA AAG AAC TTT GAA AAG AGA GTG AA 379-403 26
GUADET P3 (Gua) CCC GTC TTG AAA CAC GGA CCA AGG 661-685 24
P2R (Reh) CTC TCT TTT CAA AGT TCT TTT CAT CT 1412-1396 17
LR0R (VilU) ACC CGC TGA ACT TAA GC 26-42 17
LR0R (Reh) GTA CCC GCT GAA CTT AAG C 24-42 19
LR1R (Mon) AGG AAA AGA AAC CAA CC 57-73 17
LR2 TTT TCA AAG TTC TTT TC 395-379 17
LR2R AAG AAC TTT GAA AAG AG 382-398 17
LR3 (Vil0) GGT CCG TGT TTC AAG AC 677-661 17
LR3R GTC TTG AAA CAC GGA CC 664-680 17
LR4 ACC AGA GTT TCC TCT GG 887-871 17
LR5 (Vil0) ATC CTG AGG GAA ACT TC 997-981 17
LR5R (VilU) GAA GTT TCC CTC AGG AT 981-997 17
LR6 (Vil0) CGC CAG TTC TGC TTA CC 1173-1157 17
LR7 (Vil0) TAC TAC CAC CAA GAT CT 1483-1467 17
LR7R (Vil0) AGA TCT TGG TGG TAG TA 1465-1481 17
LR8 CAC CTT GGA GAC CTG CT 1917-1901 17
LR8R AGC AGG TCT CCA AGG TG 1901-1917 17
LR9 AGA GCA CTG GGC AGA AA 2292-2276 17
LR10 AGT CAA GCT CAA CAG GG 2508-2492 17
LR10R GAC CCT GTT GAG CTT GA 2490-2506 17
LR11 GCC AGT TAT CCC TGT GGT AA 2919-2900 20
LR12 (Vil0) GAC TTA GAG GCG TTC AG 3221-3204 17
LR12R (VilU) CTG AAC GCC TCT AAG TCA GAA 3205-3225 21
LR13 CAT CGG AAC AAC AAT GC 3464-3448 17
LR14 AGC CAA ACT CCC CAC CTG 2701-2694 18
LR15 TAA ATT ACA ACT CGG AC 161-145 17
LR16 (Mon) TTC CAC CCA AAC ACT CG 716-700 17
LR17R TAA CCT ATT CTC AAA CTT 1066-1083 18
LR20R GTG AGA CAG GTT AGT TTT ACC CT 3058-3080 23
LR21 ACT TCA AGC GTT TCC CTT T 442-424 19
LR22 CCT CAC GGT ACT TGT TCG CT 371-352 20
F377 AGA TGA AAA GAA CTT TGA AAA GAG AA 375-400 26
R377 CTC TCT TTT CAA AGT TCT TTT CAT CT 400-375 26
LIC15R (Mia2) GGA GGA AAA GAA ACC AAC AG 55-74 20
* LIC24R (Mia1) GAA ACC AAC AGG GAT TG 64-80 17
LIC2044 (Kau) ACG CCT GCC TAC TCG CC 26-42 17


IGS and 5S rDNA p rimer sequences
5S RNA (VilU) ATC AGA CGG GAT GCG GT 17
5S RNAR (VilU) ACQ GCA TCC CGT CTG AT 17
NS1R GAG ACA AGC ATA TGA CTA C 38-20 (SSU) 19
LR13R GCA TTG TTG TTC CGA TG 3448-3464(lsu) 17


ITS and 5.8S rDNA primer sequences
ITS1 (Whi) TCC GTA GGT GAA CCT GCG G 1769-1787(ssu) 19
ITS1F (Gad) CTT GGT CAT TTA GAG GAA GTA A 22
ITS2 (Whi) GCT GCG TTC TTC ATCG ATG C (sim. to 5.8S) 20
ITS3 (Whi) GCA TCG ATG AAG AAC GCA GC (sim. to 5.8SR) 20
ITS4 (Whi) TCC TCC GCT TAT TGA TAT GC 60-41(lsu) 20
ITS4B (Gad) CAG GAG ACT TGT ACA CGG TCC AG 23
ITS4S (Kre) CCT CCG CTT ATT GAT ATG CTT AAG 59-36 (lsu) 24
ITS5 (Whi) GGA AGT AAA AGT CGT AAC AAG G (sim. to SR6R) 1745-1766(ssu) 22
ITS5R CCT TGT TAC GAC TTT TAC TTC C 1766-1745 (ssu) 22
5.8S (Vil0) CGC TGC GTT CTT CAT CG 17
5.8SR (Vil0) TCG ATG AAG AAC GCA GC 18
SR6R (VilU) AAG TAP AAG TCG TAA CAA GG 1747-1766(ssu) 20
LR1 (Vil0) GGT TGG TTT CTT TTC CT 73-57(lsu) 17
SLG-1 (Gro) TTG CGC AAC CTG CGG AAG GAT 1773-1793(ssu) 21
NS24R TAA AAG TCG TAA CAA GGT TT 1750-1769(ssu) 20
ssu ref. Mankin et al., 1986. Gene 44:143-145
lsu ref. Lapeyre et al., 1993. Nucleic Acids Res. 21:3322-3322


* Primers designed in Lutzoni's lab
(DeP) DePriest,1993. Gene 134:67-74
(Elw) Elwood et al., 1985. Mol. Biol. Evol. 2:399-410
(Gad) Gardes and Bruns, 1993. Mol. Ecol. 2:113-118
(Gar) Gargas and Taylor, 1992. Mycologia 84(4): 589-592
(Gro) Groner and LaGreca, 1997. Lichenologist 29(5):441-454
(Gua) Guadet et al., 1989. Mol. Biol. Evol. 6:227-242
(Kau) Kauff and Lutzoni, 2002. Mol. Phylogen. Evol. 25:138-156
(Kre) Kretzer et al., 1996. Mycologia 88(5): 776-785
(Lan) Lane et al., 1985. PNAS USA 82:6955-6959
(Mia1) Miadlikowska and Lutzoni, 2000. Int. J. Plant Sci. 161(6)
(Mia2) Miadlikowska, McCune, Lutzoni,2001. Bryologist 105:1-10
(Mon) Moncalvo et al., 1993. Mycologia 85(5):788-794
(Reh) Rehner and Samuels, 1994. Mycol. Res. 98(6):625-634
(Spa) Spatafora et al, 1995. J. Clinical Microbiol. 33:1322-1326
(Vil0) Vilgalys and Hester, 1990. Journal of bacteriology 172:4238-4246
(VilU) Vilgalys unpublished [http://www.botany.duke.edu/fungi/mycolab]
(Whi) White et al., 1990. pp 315-322 in PCR protocols: A guide to methods and applications

New Primers for Verrucariaceae

Species-specific primers for nuclear ribosomal loci of Verrucariaceae (Gueidan et al. 2007):
Download list (PDF file)


Department of Biology, Duke University, Box 90338, Durham, NC 27708
Database driven website by J. Bélisle