Primer sequences : Nuclear ribosomal DNA

We used the primer list from Vilgalys’ lab at Duke University as the basis to which we added primers developed in our lab. We update this list as new primers are published. Please let us know if new primers that we are not aware of should be included here. Contrary to Vilgalys’ lab who are designing primers mainly for phylogenetic studies of basidiomycota, the target organisms for our primers are lichenized and non-lichenized Ascomycota. Primers that work best for us are highlighted in blue. Many of these primers are likely to work on Zygomycetes or Chytridiomycetes. Several of these primers work well on plants, as well as on algae found in lichens.
Link to: Vilgalys’ 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


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