Oligonucleotide Primers - Mitochondrial 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 Zea Comments Ref.
9 for GAG TTT GAT CCT GGC TCA GA 20 9 - 28 mt specific 1, 2
282 for CCA CAC TRG GAC TG 14 322-335 mt, cp & bac 2
434 for GCC GCT TGT AAA GCT C 16 434-450 mt specific 1, 2
530 for GTG CCA GCA GCC GCG G 16 505-520 mt, cp & bac 2
707 for CCA AAA GCG AAG GCA 15 707-721 mt specific 2
756 for GCC GTA AAC GAT G 13 797-809 mt, cp & bac 2
856 for AAC TCA AAG GAA TTG 15 893-907 mt, cp & bac 2
1090 for CTG CAT GGC TGT CGT C 16 1035-1050 mt specific 1, 2
1622 for CAC ACG TGC TAC AAT 15 1622-1636 mt specific 2
1787 for GTA CAC ACC GCC CGT CAC ACC 21 1787-1807 mt specific 2
318 rev AGT YGC AGT GTG GCT G 16 318-333 mt specific 1, 2
558 rev CCT ACG TGC CCT TTA CGC 18 558-575 mt specific 1, 2
658 (685) rev CAC ACG AAA TTC CAC T 16 658-673 mt specific 2
857 rev CCA GGC GGA GTG TTT 15 857-871 mt specific 2
898 rev GCC CCC GTC AAT TCC TT 17 898-915 cp and mt
915 rev GCC CCC GYC AAT TCC T 16 900-915 mt, cp & bac 2
957 rev GCT GGT AAG GTT TTG CG 17 957-973 mt specific 2
993 rev CCA TGC ACC ACC TG 14 1029-1042 mt, cp & bac 2
1567 rev CCA CCT TCC TCC AGT 15 1567-1581 mt specific 1, 2
1585 rev CAT GCG GAC TTG ACG TCA 18 1585-1602 mt specific 2
1149 rev AGG GGC ATG ATG ACT TGA CG 20 1588-1607 mt, cp & bac
1392 rev ACG GGC GGT GTG TRC 15 1787-1801 mt, cp & bac
1949 (1454) rev GCC ACA GGT TCC CCT ACG GCT 21 1949-1969 mt specific 1, 2
5S-100 rev GAC CAT GTC TCC CGA A 16 xxx mt specific
Moss 1 for GCR AGG TCA GAG TGT G 16 in the intron mt spec. - moss V7
Moss 1 rev CCA GCG TTG TTG AAT 15 in the intron mt spec. - moss V7

matR

Name Primer Sequence 5'- 3' Length Position on Arabidopsis Comments Ref.
matR-F1 (ZP-1) GAC CGC TNA CAG TAG TTC T 19 14-32 3
matR-F12 (ZP-41) TTT AGA YCG CTY ACA GTA GT 20 10-29 3
matR-F13 (ZP-42) TTT AGA YCG CTR ACA GTA GT 20 10-29 3
matR-F14 (ZP-46) ATC CCG AGT TTC MRG ACA C 19 89-107 3
matR-F15 (ZP-47) ATC CCG AGT TTC MRG ACG C 19 89-107 3
matR-F16 (ZP-59) TCG GGT CGA GGC WGC CAC T 19 121-139 3
matR-LPF 420 (ZP 64) GAT CCG RCA RRA GCA CG 17 417-432 3
matR Raff459Forward GAT CGT TCA TGA CAG GTC GT 20 458-476 Rafflesia specific 4
matR Tetra459Forward GAT CGG TTC TAT TAA GGG CAG 21 458-476 Tetrastigma specific 4
matR-LPF 520 (ZP 103) CTC TRG AGA AGA RGC AAG C 19 504-522 3
matR-F2 (ZP-2) CAT TCC CTT RTT TCG TCG TG 20 595-614 3
matR Raff742Forward CAT GGA ATC CGT GAC CCT TA 20 741-759 Rafflesia specific 4
matR Tetra741Forward TCA TAG AAG CCG CCG GGT TGA 21 740-759 Tetrastigma specific 4
matR-F4 (ZP-7) ACG TAT CGC CCA CTT CCT AC 20 1023-1040 3
matR-LPF 1230 (ZP 66) GAG YRA AGC ACC RTA TCC 18 1190-1207 3
matR-F3 (ZP-3) CTA CGC TCC GCC ATC CAT T 19 1225-1243 3
matR-LPF 1400 (ZP 78) ACC GCC AAG GAC ATM CRG C 19 1392-1410 3
matR-MF1 (ZP 75) GTG CCG CGA CAA CCT TTA CC 20 1767-1786 3
matR-R450 (ZP-51) ATT TCG TRC TTC TGY CGG A 19 419-467 3
matR-R3 (ZP-6) CAC GAC GAA AYA AGG GAA TG 20 595-614 3
matR-R870 (ZP-50) CCG CCC AGC TCT ATM WG 17 850-866 3
matR-R4 (ZP-8) TCT CTC TGA CCT GAT AAC TAG 21 877-897 3
matR-R980 (ZP-61) AGT CGT CGG CAT ATC GCG C 19 955-973 3
matR-LPR 1270 (ZP 67) GAA TKG ATG GCR GAR CG 17 1228-1244 3
matR-R2 (ZP-5) AAT GGA TGG CGG AGC GTA G 19 1225-1243 3
matR-LPR 1250 (ZP 104) TGG AAT GGA TGG CRG ARC G 19 1228-1244 3
matR Raff1558Reverse TGA TAG ATC CCG CTC CTC CT 20 1557-1575 Rafflesia specific 4
matR-R15 (ZP-60) TCT YCG GCT AAT GAKACC TCG 21 1645-1665 3
matR Tetra1663Reverse ATA GAT CCC GCC CAG TGT C 19 1562-1579 Tetrastigma specific 4
matR-R13 (ZP-48) TGR TAR AGG TTG TCG CGG CA 20 1768-1787 3
matR-R14 (ZP-49) TGR TAR AGG TTG TCG CAG CA 20 1768-1787 3
matR-R1 (ZP-4) TGC TTG TGG GCY RGG GTG AA 20 1831-1850 3
matR-R12 (ZP-19) CGC GYC GAR GAT TTG TGC T 19 1847-1865 3

atp1

atpA-F1 (ZP-20) ATG AGA TCG GTC GAG TGR T 19 83-101 3
atpA-F2 (ZP-21) GTG GTC AAC GAG AAC TTM T 19 488-506 3
atpA-F3 (ZP-22) TCA TTA TTG TTA CGC CGA CC 20 853-872 3
atpA-R1 (ZP-23) CCY TTG ACA GCH GCR TAA A 19 1343-1361 3
atpA-R12 (ZP-24) CCR TTG ACA GCH GCR TAA A 19 1343-1361 3
atpA-R2 (ZP-25) ACG TCT CCK GCT TGT GTT TC 20 981-1010 3
atpA-R3 (ZP-26) RGC WAC ATA GAC ACA ATA CA 20 605-624 3

References

  1. Duff, R. J. & D. L. Nickrent. 1997. Characterization of mitochondrial small-subunit ribosomal RNAs from holoparasitic plants. J. Mol. Evol. 45: 631-639.
  2. Duff, R. J. & D. L. Nickrent. 1999. Phylogenetic relationships of land plants using mitochondrial small-subunit rDNA sequences. Amer. J. Bot. 86: 372-386.
  3. Y.-L. Qiu. Cited in several publications, but never published per se. Listed as "available upon request from author." They are being posted on this web page for the first time.
  4. Nickrent, D.L., A. Blarer, Y.-L. Qiu, R. Vidal-Russell, F.E. Anderson. 2004. Phylogenetic inference in Rafflesiales: the influence of rate heterogeneity and horizontal gene transfer. BMC Evolutionary Biology in press.