Oligonucleotide Primers - Plastid Genome

By placing these primer sequences on the web, I am making them available for general use. Thus, you have my permission to use these sequences and order primers for your own use. Some of the primers here have not been published in the literature. For those that have, please see references listed at end for proper citation. Given the low cost of primers these days, I prefer that you do not request aliquots of these (except under special circumstances).

Small Subunit (SSU) rDNA

Name Primer Sequence 5'-3' Length Position on Nicotiana Comments  Ref.
8 for GGA GAG TTC GAT CCT GGC TCA G 22 7 - 27 cp & bac  1
63 for CGG GAA GTG GTG TTT CCA GT 20 68-87 cp specific  1
261 for AGC TAG TTG GTG GGG T 16 217-232 2 mismatches; one at 3' C  
281 for GAT CAG TAG CTG GTC CGA GA 20 252-271 cp (& bac)  1
282 for CCA CAC TRG GAC TG 14 281-294 cp & mt & bac  
323 for CAG CAG TGG GGA ATT TTC CG 20 323-343 cp specific  1
530 for GTG CCA GCA GCC GCG G 16 462-477 cp & mt & bac  1
717 for CGA GAC GGG TGA ATG GG 17 717-733 Pilostyles, Bdallophyton  
802 for ATT AGA TAC CCT GGT A 16 734-749 2 mismatches  
756 for GCC GTA AAC GAT G 13 756-768 cp & mt & bac  1
856 for AAC TCA AAG GAA TTG 15 856-870 cp & mt & bac  1
1240 for CCT CAG TTC GGA TTG 15 1241-1255 cp  
1457 for CTG GAA GGT GCG GCT GGA TCA CC 23 1461-1483 cp specific  
7 rev TGA GCC AGG ATC GAA CTC TCC 21 7 - 27 cp  
343a rev CTG CTG CCT CCC GTA 15 314-328 cp & bac  1
321 rev AAG ATT CCC CAC TGC TGC C 19 321-339 cp  
374 rev ACG ACT CTT TAG CCT 15 385-399 Corynaea spec  1
517 rev ACC GCG GC(TG) GCT GGC 15 464-478 cp? & bac  
705 rev TGA TAC CCC AAC TTT CGT CGT TG 23 705-727 Corynaea spec  1
915 rev GCC CCC GYC AAT TCC T 16 863-878 cp & mt & bac  1
993 rev CCA TGC ACC ACC TG 14 993-1006 cp & mt? & bac  1
1037 rev CGA GGG TTG CGC TCG TTG 18 1048-1065 cp & bac  1
1149 rev AGG GGC ATG ATG ACT TGA CG 20 1139-1158 cp & mt & bac  1
1259 rev TTC ATG YAG GCG AGT TGC AGC 21 1259-1280 cp specific  1
1284 rev GCG ATT ACT AGC GAT T 16 1285-1300 cp  
1289 rev CAA TCC GAA CTG AGG A 16 1289-1304 cp & bac  
1392 rev ACG GGC GGT GTG TRC 15 1339-1353 cp & mt & bac  1
1461 rev GGT GAT CCA GCC GCA CCT TCC AG 23 1461-1483 cp & bac  1
1461 rev GGT GAT CCA GCC GCA CCT TCC AG 23 1461-1483 cp & bac  
1525 rev AAG GAG GTG ATC CAG CC 17 1472-1488 cp & bac  1

Large Subunit (LSU) rDNA

Name Primer Sequence 5'-3' Length Position on Nicotiana Comments Ref.
23S-42 for GGT GGA TAC CTA GGC ACC CAG AG 23 cp specific
23S-66 for GAC GAA ATG CTT CGG GGA G 19 cp specific
23S-420 for CAA GGA CCA CCT TGC AAG GCT 21 cp specific
23S-481 for TGA GGG AAA GGT GAA AG 17 cp specific
23S-815 for TGG TTC TCC CCG AAA TGC GTT 21 cp specific
23S-821 for CTG GTT CTC CCC GAA A 16 cp specific
23S-1294 for CAT TGG TGA GAA TCC AAT GCC 21 cp specific
23S-1686 for AAC TCT CTC TAA GGA ACT CGG 21 cp specific
23S-2044 for GCG GAC TAC CTG CAC CTG GA 20 cp specific
23S-2437 for CGG ATA AAA GTT ACT CTA GGG 21 cp specific
23S-2749 for CCT ATT GAC GAC TTT CGT AG 20 cp specific
23S-2759 for GCT GAA AGC ATC TAA G 16 cp specific
23S-35 rev CTT CCT CGT CTC TGG GTG CCT 21 cp specific
23S-42 rev CTG GGT GCC TAG GTA TCC ACC 21 cp specific
23S-245 rev TCC CAT TTC GCT CGC CGC TAC 21 cp specific
23S-459 rev CTT TCC CTC ACG GTA 15 cp specific
23S-2672 rev GGT GCG TCC TTC CCG GTC CTC T 22 cp specific
23S-2744 rev CTT AGA TGC TTT CAG C 16 cp specific
23S-2749 rev GAT GCT TTC AGC AGT TAT CC 20 cp specific

tRNA Genes

Name Primer Sequence 5'-3' Length Position on Nicotiana Comments Ref.
trnE rev TTC AAG GAG GCG ACG GGG ATT CG 23 cp specific
trnH for AAC GAC GGG AAT TGA ACC CGC GC 23 cp specific
trnP for GTA CCC AAA ACA AAC GCG CTA CC 23 cp specific
trnQ rev CGG AGG TTC GAA TCC TTC CGT CC 23 cp specific
trnK 17 for (5') GGT AGA GTA GTC GGC TTT TAA 21 cp specific

Ribosomal Protein Genes

Name Primer Sequence 5'-3' Length Position on Nicotiana Comments Ref.
rps2-47 for ACC CTC ACA AAT AGC GAA TAC CAA 24 47-70 cp specific 1
rps2-661 rev CTC GTT TTT TAT CTG AAG CCT G 22 661-682 cp specific 1
rps4 32 for AGC AAT TCA TTT ATT TKA RAC CGA 24 32-55 cp specific 1
rps4 585 rev ATG TCR CGT TAC CGR GGA CCT M 22 585-606 cp specific 1
rps7 1 for ATG TCA CGT CGA GGT ACT GC 20 1 - 20 cp specific 1
rps7 446 rev TAA CGA AAA TGT GCA AMA GCT C 22 446 - 467 cp specific 1
rpl16 29 for GGC ATT TTA GAT GCT GCT AKT GAA A 25 29 - 54 cp specific 1
rpl16 351 rev AAA CAA CAT AGA GGA AGA ATG AAG G 25 351- 375 cp specific 1
rpl16 110 for GGT TTA AYA ACA GCT ACC CAA 21 cp specific
rpl16 302 for TGA AGA GCA TAT TTA CC 17 cp specific

ndhF Gene

Name Primer Sequence 5'-3' Length Position on Nicotiana Comments Ref.
ndhF (-52) for 5' flanking AGG TAA GAT CCG GTG AAT CGG AAA C 25 3
ndhF 1 for (5' PCR) ATG GAA CAK ACA TAT SAA TAT GC 23 2
ndhF 274 for CTT ACT TCT ATT ATG TCA ATA TTA AT 26 2
ndhF 536 for TTG TAA CTA ATC GTG TAG GGG A 22 2
ndhF 803 for CTA TGG TAG CGG CGG GAA TTT TTC 24 2
ndhF 972 for GTC TCA ATT GGG TTA TAT GAT G 22 2
ndhF 1318 for GGA TTA ACY GCA TTT TAT ATG TTT CG 26 2
ndhF 1603 for CCT YAT GAA TCG GAC AAT ACT ATG C 25 2
ndhF 1655 for TTA CTT TGT TTG TTG GAT HTM TAG G 25 2
ndhF 1955 for TAT ATG ATT GGT CAT ATA ATC G 22 2
ndhF (+ 607) for 3' flanking ACC AAG TTC AAT GTT AGC SAG ATT AGT C 23 3
ndhF 274 rev ATT AAT ATT GAC ATA ATA GAA GTA AG 26 2
ndhF 536 rev TCC CCT ACA CGA TTA GTT ACA A 22 2
ndhF 803 rev GAA AAA TTC CCG CCG CTA CCA TAG 24 2
ndhF 972 rev CAT CAT ATA ACC CAA TTG AGA C 22 2
ndhF 1318 rev CGA AAC ATA TAA AAT GCR GTT AAT CC 26 2
ndhF 1603 rev GCA TAG TAT TGT CCG ATT CAT RAG G 25 2
ndhF 1955 rev CGA TTA TAT GAC CAA TCA TAT A 22 2
ndhF 2110 rev (3' PCR) CCC CCT AYA TAT TTG ATA CCT TCT CC 26 2

matK Gene

Name Primer Sequence 5'-3' Length Position on Nicotiana Comments Ref.
5' trnK 3914 for GGG GTT GCT AAC TCA ACG G 19 dicot spec. (1 m/d mism) 5
trnK 17 for (5') GGT AGA GTA GTC GGC TTT TAA 21 cp specific
matKintron1 253 for TTG GGT CGA GTC AAT AAA T 19 dicot spec (13 indels m/d) 5
matKintron1 582 for CTA ACC ATC TTG TTA TCC T 19 mism. 3/ Sinapis, 16 indels m/d 5
matKintron1 710 for GTA TCG CAC TAT GTW TCA TTT GA 23 dicot spec. (8 indels m/d) 5
934 for ATT TTG GTT ATG ACA ATA A 19 140-158 9 m/d mismatches 5
173 rev AAT TAA RCG TTT CAC AA 17 173-189 1 m/d mismatches
1168 rev ATT GAA TGA ATT GAT CGT A 19 389-407 4 m/d mismatches 5
1176 for CAA TTC ATT CAM TAT TTC CTT 21 395-415 4 m/d mismatches 5
1235 rev GGR GTG GGG TAT TAG TAT A 19 456-473 7 m/d mismatches 5
1402 for TYT TGT TTY TAT ATA ATT 18 635-652 6 m/d mismatches
1412 for ATA TAA TTC TTA TGT ATG TG 20 635-652 6 m/d mismatches 5
1412 rev CAC ATA SAT AAG AAT TAT AT 20 635-652 6 m/d mismatches 5
1470 rev AAG ATG TTG ATY GTA AAT GA 20 705-724 9 m/d mismatches 5
1506 rev TTC CAT AGA AAT ATA TTC G 19 742-760 9 m/d mismatches 5
matK 5 for GGA TCC TTT CAT GCA TT 18 1036-1053 9 m/d mismatches 6
matK 6 for TCA AGG GTA CGT AGT CAA 18 1036-1053 9 m/d mismatches 6
1848 rev TAT CGA ACT TCT TAA TAG C 19 1084-1102 9 m/d mismatches 5
matK 7 for GTA TTA GGG CAT CCC ATT 18 1159-1176 7 m/d mismatches 6
2000 rev ATT TCT GCA TAT GCG CAC AAA TC 23 1223-1244 7 m/d mismatches 5
matK 8 for CTT CGA CTT TCT TGT GCT 18 1306-1323 6 m/d mismatches 6
1326 rev TGT TTA CGA GCY AAA GTT 18 1326-1353 no mismatches
2200 rev TCT GTA TAA CCT CCA CAA AG 20 1454-1463 15 m/d mismatches 5
1481 rev CAA ATA ATA TCM AAA TAC CAA 21 1481-1502 4 m/d mismatches
trnK 2 rev AAC TAG TCG GAT GGA GTA G 19 rev. compl. of primer seq. shown in publ, but no mismatches 6

rbcL Gene

Name Primer Sequence 5'-3' Length Position on Nicotiana Comments Ref.
1 for ATG TCA CCA CAA ACA GAR AC 20
Z-1 for ATG TCA CCA CAA ACA GAR ACT AAA GC 26 4
Z-234 for CGT TAC AAA GGG CGA TGC TAC CGC ATC GAG 30 4
414 for CGA ATY CCW CCT GCT TAT 18
Z-427 for GCT TAT GTT AAA ACT TTC CAA GGT CCG CC 29 4
Z-523 for TAA ACC TAA ATT GGG GTT ATC TGC TAA AAA CTA 33 4
Z-674 for TTT ATA AAG CAC AGG CTG AAA CAG GTG AAA TC 32 4
Z-895 for GCa GTT ATT GAT AGA CAG AAA AAT CAT GGT 30 4
Z-967 for GGA GAT CAT ATT CAC TCT GGT ACC GTA GTA 30 4
Z-1020 for ACT TTA GGT TTT GTT GAT TTA TTG CGC GAT GAT T 34 4
Z-1204 for TTT GGT GGA GGA ACT TTA GGA CAC CCT TGG GG 32 4
Z-1264 for GTA GCT AAT CGA GTA GCT CTA GAA GCA TGT GTA A 34 4
Z-153 rev GAA GCA GGG GCC GCG GTA GCT GCC GAA TCT TCT A 34 4
Z-346 rev ATG TTT ACT TCC ATT GTA GGT AAC GTA TTT GG 32 4
Z-674 rev TTT ATA AAG CAC AGG CTG AAA CAG GTG AAA TC 32 4
Z-895 rev ACC ATG ATT CTT CTG CCT ATC AAT AAC TGC 30 4
Z-1020 rev ATC ATC GCG CAA TAA ATC AAC AAA ACC TAA AGT 34 4
Z-1204 rev CCC TAA GGG TGT CCT AAA GTT TCT CCA CC 32 4
Z-1375 rev GTG AAG TAT GGA AAG AGA TCG TAT TTA ATT TTG 33 4
3' rbcL (in atpB) CTC GGA GCT CCT TTT AGT AAA AGA TTG GGC CGA G 20

Other Plastid Genes

Name Primer Sequence 5'-3' Length Position on Glycine Comments Ref.
ndhD 1062 rev ATG TGG GAG TTA GAA TTA ATT CCT G 25 cp specific
5S 22 for GAG GAA CCA CAC CAA TCC ATC CCG 24 cp specific
5S 22 rev GGA TGG ATT GGT GTG GTT CCT C 22 cp specific

References

  1. Nickrent, D. L., Y. Ouyang, R. J. Duff & C. W. dePamphilis. 1997. Do nonasterid holoparasitic flowering plants have plastid genomes? Plant Mol. Biol. 34: 717-729.
  2. Olmstead, R. G. & J. A. Sweere. 1994. Combining data in phylogenetic systematics - an empirical approach using three molecular data sets in the Solanaceae. Syst. Biol. 43: 467-481.
  3. K.-J. Kim and R. Jansen, unpublished.
  4. G. Zurawski, unpublished.
  5. Johnson, L. A. & D. E. Soltis. 1995. Phylogenetic inference in Saxifragaceae sensu stricto and Gilia (Polemoniaceae) using matK sequences. Annals of the Missouri Botanical Gardens 82: 149-175.
  6. Steele, K. P. & R. Vilgalys. 1994. Phylogenetic analyses of Polemoniaceae using nucleotide sequences of the plastid gene matK. Syst. Bot. 19: 126-142.

SIUC / Plant Biology / Faculty/ Dan Nickrent
URL: http://www.plantbiology.siu.edu/nickrent/primer.plastid.html
Last updated: 25-Sept-07 / dln