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Primer sequence table

This table contains primer sequences, together with their names (in most cases, I tried to retain the name chosen in the original publication), gene locations, and locations of their 5' ends in some of the published chloroplast DNA sequences (e.g., Nicotiana tabacum, Atropa belladonna, Spinacia oleracea etc). Please cite the original publications when using these primers!

primer name gene forward-plus/reverese-minus Nicotiana Atropa Spinacia Arabidopsis Populus Oryza Pinus Marchantia length sequence references additional remarks

16S-F F 102853 103161 98039 101104 102489 91391 84432 82209 20 ACGGGTGAGTAACGCGTAAG Tsumura et al. 1995

16S-R R 104228 104537 99415 102480 103865 92767 85808 83582 20 CTTCCAGTACGGCYACCTTG Tsumura et al. 1995

3'rps12-15R (trnL) 96469 96735 91703 94315 95753 84750 111974 3714 22 GAGATTTTGAGTCTCGCGTGTC second match Spinacea 141742; second match Nicotiana 146157; Zea 134114; Oryza 130368; Oenothera 153707; Arabidopsis 144334;

3'rps12-1F 3'rps12 141781 142440 137347 82919 141933 125854 109716 94 23 ccmaaaaaaccmaactctgcctt Graham and Olmstead 2000 second match Spinacia 96098;Nicotiana 100845; Zea 93092; Oryta 89264; Oenothera 104123; Arabidopsis ???

3'rps12-2F 141983 142642 137549 140067 142135 126056 109918 296 24 atcgtcaacaagggcgttctagtg Graham and Olmstead 2000 2nd Spin 95896; Nicot 100643; Zea 92890; Oryza 89062; Oenothera 103921; Arabi 98582;

3'rps12-3R 142374 143032 95505 98191 142526 126451 110305 78158 23 gatyggaaatcctgtattttmca Graham and Olmstead 2000 2nd Spin 137940; Nicot 100252; Oryza 88667; Oenothera 149804; Arabi 140458; Zea 130234; Medicago 111832 ????; Marchantia ???

3'rps12-4F 100100 143184 138092 140611 142678 126603 110466 803 23 gagatccaccctacaatMtgggg Graham and Olmstead 2000 2nd Spin 95353; Nicot 142526; Zea 92343; Oryza 88515; Oenothera 149960; Ara 98038; Pinus is partial; modif 3'most C; Marchantia???

3'trnG(UUC) trnG(UCC) exon1 R 10255 10036 8929 9426 8474 13008 9651 42100 23 GTAGCGGGAATCGAACCCGCATC Shaw et al. 2005 second match Pinus: 79094, Oryza: 36079

3'trnG(UUC) 2 trnG R 38123 37862 35224 36555 36760 36079 79094 21389 23 GTAGCGGGAATCGAACCCGCATC Shaw et al. 2005

5'rpoC1 exon 85345 20 GGTCTTCCTAGYTAYATHGC Downie, Katz-Downie, and Cho, 1996

5'-rps12 Hamilton rps12 exon1 R 72246 72503 68357 69632 70488 67415 20 GTCGAGGAACATGTACTAGG Hamilton 1999

5'rpS12 Shaw rps12 exon1 R 72313 72570 68426 69703 70555 67482 30402 23 ATTAGAAANRCAAGACAGCCAAT modified from Hamilton (1999)

5'trnG2G trnG(UCC) exon2 9499 9281 8156 8646 7710 13752 8845 22047 23 GCGGGTATAGTTTAGTGGTAAAA Shaw et al. 2005

5'trnG2G 2 29392 42035 23 GCGGGTATAGTTTAGTGGTAAAA Shaw et al 2005

5'trnG2S trnG(UCC) exon2 R 9521 9303 8178 8668 7732 13730 8867 22025 23 TTTTACCACTAAACTATACCCGC Shaw et al. 2005

5'trnG2S 2 42035 42057 23 TTTTACCACTAAACTATACCCGC Shaw et al 2005

accD M accD=ORF512 R 60544 60201 56694 58508 23 amr caa kts tcg cat tga acc ca ?? this publication

accD M2 accD=ORF512 R 60684 60339 57909 58648 42124 58370 21 MCA TGT CTT CAT CCA TAG GAT this publication

accD-769F accD=ORF512 60963 60618 58925 25 GGAAGTTTGAGCTTTATGCAAATGG T. Barkman and B. Simpson, University of Texas, Austin, personal communication to small et al. (1998)

accD-f accD=ORF512 F 61140 60795 57288 58365 59102 41632 101465 22 GCA GGT AAA AGA GTA ATT GAA C this publication

ALS-11F 2069 2267 104588 19 ATCTTTCGCATTATTATAG M. Nepokroeff, University of South Dakota, personal communication - Shaw et al 2005

atpA-f1 atpA F 11047 10815 35311 23 CCACTCTGGAAACGGAGATACCC this publication

atpA-f2 atpA F 11059 10827 9615 10372 9354 35299 10495 44495 25 CGGAGATACCCACATTAATAGCAGG this publication

atpA-f3 atpA F 12009 11777 10565 11322 10304 11445 23 TCATCAAGACCGTGAATACGAGC this publication

atpA-f4 atpA F 12016 11784 10572 10311 11452 23 GAC CGT GAA TAC GAG CAA TGC CG this publication

atpA-P3MD atpA R 10686 10454 9242 9999 8981 35672 30 TCA (tA)AT AAA AGC (Ct)AT GAA A(aC)A (gA)GT AGCTGG this publication

atpA-r1 atpA R 10459 24 CCC TTT TGA AAG AAG CTA TTC AGG this publication

atpA-r2 atpA R 12037 11805 10593 10332 11473 25 GGCATTGCTCGTATTCACGGTCTTG this publication

atpB 3' 1460R Rydin atpB 55312 54968 46600 19 TTAATAGCCTTCGCGGTAG Rydin et al. 2002

atpB 5' Hoot atpB 57633 57286 53861 54988 55754 54133 44435 56393 25 GAATCCAACACTTGCTTTAGTCTCT Hoot et al. 1995

atpB Fofana atpB F 56497 56153 52759 54641 53030 45421 20 GTGTCAATCACTTCCATTCC Fofana et al. 1997

atpB Hodges atpB F 56737 56393 52999 53270 26 GTGGAAACCCCGGGACGAGAAGTAGT Hodges and Arnold, 1994

atpB Samuel atpB F 56755 56411 53017 54134 54899 53288 21 GAA GTA GTA GGA TTG ATT CTC Samuel et al. 1997.

atpB-r1 atpB R 55393 55049 51655 52772 53537 51926 46525 54468 21 TTTCCGGAGAATTAGATGGTC this publication

atpB-r2 atpB R 55729 55385 51991 53108 53873 24 CCGTACTATCAAGAGGATTGGCTG this publication

atpE-f (r*) atpE F 54941 54597 51203 26 GCCTCAATTTTTTGTCTCCTTCCTTC this publication

atpE-r atpE R 54966 54622 51228 26 GAAGGAAGGAGACAAAAAATTGAGGC this publication

atpE-r2 atpE R 55254 54910 52633 53398 46664 26 AATCGARTYRTTTGGGATTCAGAAGT this publication

atpF1-f1 atpF exon1 F 13301 13089 11938 12647 11629 32892 12821 18617 20 CTC GCA CAC ACT CCC TTT CC this publication

atpF1-r1 atpF exon1 R 13318 13106 11955 12664 11646 32875 12838 18602 21 AAA GGG AGT GTG TGC GAG TTG this publication

atpF2-f1 atpF exon2 F 12546 12314 11113 11872 10844 33780 25 CGC AGT TCT TCT GAA TTT CGA ATA G this publication

atpF2-r1 atpF exon2 R 12537 12305 33789 25 CTA TTG AAC AAC TCG AAA AAG CTC G this publication

atpHf atpH F 14016 13822 12647 13424 32122 18097 20 TTG ACC AAC TCC AGG TCC AA Tsumura et al. 1996

atpH-P atpH F 14059 13865 12690 13467 12426 32079 13494 18054 20 cca gca gca ata acg gaa gc Grivet et al. 2001

atpHr atpH R 14081 13887 12712 13489 12448 32057 13516 18035 23 GCC GCT TCC GTT ATT GCT GCT GG Grivet et al. 2001

atpI-f atpI F 15262 15044 13481 31239 14231 22 GAT GRC CCT CCA TGG ATT CAC C Grivet et al. 2001

atpI-M atpI R 15286 15068 13505 31215 14255 20 ata ggt gaa tcc atg gag gg Grivet et al. 2001

atpIr atpI R 15297 15079 13463 20 CCG CAG CTT ATA TAG GCG AA Tsumura et al. 1996

ccmp10-f rps19 F 86660 22 TTTTTTTTTAGTGAACGTGTCA Weising & Gardner 1999

ccmp10R - F 155864 156536 150498 154293 20 TTCGTCGDCGTAGTAAATAG Weising & Gardner 1999

ccmp10-r rpl2 exon2 R 86762 87021 82947 84356 69889 20 TTCGTCGDCGTAGTAAATAG Weising & Gardner 1999

ccmp1f intron trnK F 3767 3724 20 CAGGTAAACTTCTCAACGGA Weising & Gardner 1999

ccmp1r intron trnK R 3905 3862 3550 3822 20 CCGAAGTCAAAAGAGCGATT Weising & Gardner 1999

ccmp2f F 8476 8396 7265 7661 7686 7774 23029 19 GAT CCC GGA CGT AAT CCT G Weising & Gardner 1999

ccmp2r trnS(GCU) R 8664 8596 7513 7817 6908 7861 7924 22947 20 ATC GTA CCG AGG GTT CGA AT Weising & Gardner 1999

ccmp3f trnG(UCC) intron F 10037 9820 8709 20 CAG ACC AAA AGC TGA CAT AG Weising & Gardner 1999

ccmp3r trnG(UCC) intron R 10148 9929 8822 9311 8367 13115 9550 21496 20 GTT TCA TTC GGC TCC TTT AT Weising & Gardner 1999

ccmp4-F - R 12943 12708 11233 20 AAT GCT GAA TCG AYG ACC TA Weising & Gardner 1999

ccmp4-R - F 12808 21 CCA AAA TAT TBG GAG GAC TCT Weising & Gardner 1999

ccmp5-F rps2 F 16916 16698 15060 15702 15117 29561 15946 24 TGT TCC AAT ATC TTC TTG TCA TTT Weising & Gardner 1999

ccmp5-R - R 17036 16813 15787 15226 29409 21 AGG TTC CAT CGG AAC AAT TAT Weising & Gardner 1999

ccmp6-f - F 45078 44848 43434 43544 72427 20 CGA TGC ATA TGT AGA AAG CC Weising & Gardner 1999

ccmp6-r ycf3 exon2 R 45180 44945 42065 43529 43644 42744 72346 20 CAT TAC GTG CGA CTA TCT CC Weising & Gardner 1999

ccmp7-f - F 57284 56940 53511 20 CAA CAT ATA CCA CTG TCA AG Weising & Gardner 1999

ccmp7-r - R 57416 57069 53650 54782 55540 53785 56232 23 ACA TCA TTA TTG TAT ACT CTT TC Weising & Gardner 1999

ccmp8-f - F 71536 71794 68983 69768 20 TTGGCTACTCTAACCTTCCC Weising & Gardner 1999

ccmp8-r - R 71612 71869 80260 22 TTCTTTCTTATTTCGCAGTGAA Weising & Gardner 1999

ccmp9-f - F 74011 74245 71312 20 GGATTTGTACATATAGGACA Weising & Gardner 1999

ccmp9-r - R 74108 21 CTCAACTCTAAGAAATACTTG Weising & Gardner 1999

CHTRN F 110670 110975 105997 109051 110706 99254 92626 90299 25 ACAGCCGACCGCTCTACCACTGAGC this publication

CHTRN-r R 131956 132582 127448 129598 131457 115864 92626 111821 25 ACAGCCGACCGCTCTACCACTGAGC this publication

CLPP Goulding F 73995 74229 17 AAGATCCGCCCGATTTG Goulding et al. 1996

clpP pr1 clpP ex2 F 73527 30 atcytckryactsamatataccatsagacc this publication fits for tobacco and pine

clpP1-f clpP exon1 F 74447 25 YCCAADHYGMWYYWTCHTCTCCRGG

clpP1-r clpP exon1 R 74471 24 CCYGGAGADGASRRSDCRDHTTGG

clpP2-f clpP exon2 F 73604 73846 69669 70919 71898 29707 68026 26 GTAATCTYTCWCGATAAAGTCGRTTG

clpP-3'ex2r clpP exon2 R 73406 73647 69471 71700 113209 29905 20 GCNGCNYCAATGGGATCTTT Downie

clpP-3'ex3 clpP exon3 F 72527 72784 68637 69964 70828 67752 30147 67205 21 CAT AAA AAC ATC RTC CAT Downie

clpP-5'ex1 clpP exon1 F 74507 74741 70604 71882 72808 68640 20 ATGCCTATTGGTGTNCCNAA Downie

clpP-5'ex2r - R 74110 20 TCYTCWATACTAAGATATAC Downie some mismatches

clpP-f F 72665 72922 84084 67890 30009 67343 20 ataawaagaactagcaggtt Grivet et al. 2001

clpP-r R 72684 72941 84070 67909 29990 67362 20 aacctgctagttcttwttat Grivet et al. 2001

JSB-f1 F 111852 112157 107150 110183 111895 21 GGACTAAACAGGAACAAGAGG this publication

JSB-f1-R R 130774 131400 126295 128466 130268 21 GGACTAAACAGGAACAAGAGG this publication

JSB-r1 R 112164 112911 110495 24 TAGGGGGCGGACGCATCTCTTCTT this publication

matK-1 trnK exon F 1835 1795 1513 1742 1706 1398 1531 19 AACTAGTCGGATGGAGTAG Johnson and Soltis, 1994

matK-5 3360 262 20 TGTCATAACCTGCATTTTCC Panero and Crozier, 2003

matK-59R F 3570 3509 3212 4079 29 GCATAAATATAYTCCYGAAARATAAGTGG Johnson and Soltis, 1994

matK-5-PSI-F 110946 3692 20 CTATGGCTCCAATTCTGGT Shaw et al 2005

matK-5-PSI-R F 4026 3983 3958 3905 3587 20 CCGCATCAGGCACTAATCTA Shaw et al 2005

matK-5r matK-intron trnK R 2837 17 GGATCCTTTCATGCATT Hilu & Liang 1997

matK-6 trnK exon R 4408 4361 4056 4348 4310 3932 26039 19 TGGGTTGCTAACTCAATGG Johnson and Soltis, 1994

matK-7Br matK-intron trnK R 2500 2439 2154 2427 18 GTATTAGGGCATCCCATT Hilu & Liang 1997

matK-8F R 2351 2290 2005 2203 1896 27854 24 TCGACTTTCTTGTGCTAGAACTTT Steele and Vilgalys, 1994

matK-AR F 3452 3391 3103 3307 3000 87998 16 CTGTTGATACATTCGA Kazempour Osaloo et al., 1999

matKf1 matK-intron trnK F 3578 3517 3220 3427 3123 21 ATACTCCTGAAAGATAAGTGG this publication

matKf2 matK-intron trnK F 3543 3482 3185 3455 3147 22 CTATTTAAACCATGATCATGAG this publication

ndhAF-Small R 123504 124194 119339 121580 123192 101768 26 GGwCTTCTyATGkCrGGATATrgmTC Small et al. 1998

ndhAR-Small F 122192 122880 118096 120336 121903 111129 100892 26 CTGyGCTTCmACTATATCAACTGTAC Small et al. 1998

ndhB 7R ndhB F 99155 99421 60057 97078 98502 87533 23 cattctgggaaaatsaaacttcc Graham and Olmstead 2000

ndhB 7RR R 143471 144136 115479 141591 143681 127585 23 cattctgggaaaatsaaacttcc Graham and Olmstead 2000

ndhB-10R ndhB F 98486 98752 93726 96389 97813 86864 0 ccttcgtagacgtcaggagtccattg Graham and Olmstead 2000

ndhB-10RR R 144140 144805 139719 142260 144350 128254 26 ccttcgtagacgtcaggagtccattg Graham and Olmstead 2000

ndhB-11F ndhB R 98010 95908 93256 95908 97334 86367 24 gaaggattcctcgaaaagttaagg Graham and Olmstead 2000 2nd Spin 140189, Nicot 144616, Zea 132529, Oryca 128751, Oehn 152109, Arabi 142741,

ndhB-11FF F 144616 145281 140189 142741 144829 128751 24 gaaggattcctcgaaaagttaagg Graham and Olmstead 2000

ndhB-11R ndhB F 97987 98253 93233 95885 97311 86344 24 ccttaacttttcgaggaatccttc Graham and Olmstead 2000 2nd Spinacea 140212, Nicot 144639; Zea 132552, Oryza 128774, Oenothera 152132, Arabidopsis 142764, Medicago mm, Marchantia mm

ndhB-11RR R 144639 145304 140212 142764 144852 128774 24 ccttaacttttcgaggaatccttc Graham and Olmstead 2000

ndhB-12F ndhB R 97781 98047 93026 95678 97105 86126 2800 0 ctttctgttacttcgaaagtagc Graham and Olmstead 2000 2nd Spin 140419, Nicot 144845, Zea 132770, Oen 152340, Arabi 142971, Oryza 128992,

ndhB-12FF F 144845 145510 140419 142971 145058 128992 23 ctttctgttacttcgaaagtagc Graham and Olmstead 2000

ndhB-13F ndhB R 97636 97902 92881 95533 96960 85981 19 ctcaaacaagcatgaaacgatgc Graham and Olmstead 2000 2nd Spinacea 140564, Nicot 144990, Zea 132915, Oryza 129137, Oenothera 152485, Arabi 143116

ndhB-13FF F 144990 145655 140564 143116 145203 129137 19 ctcaaacaagcatgaaacg Graham and Olmstead 2000

ndhB-13R ndhB F 97613 97879 92858 95510 96937 85958 0 gcatacgtttcatgcttgtttgag Graham and Olmstead 2000 2nd Spin 140587, Nicot 145013, Zea 132938, Oryza 129160, Oenothera 152508, Arabi 143139,

ndhB-13RR R 145013 145678 140587 143139 145226 129160 24 gcatacgtttcatgcttgtttgag Graham and Olmstead 2000

ndhB-14R ndhB F 97102 97368 92347 94999 96426 85447 23 ggtatagtagatgctatcacaca Graham and Olmstead 2000 2nd Spin 141098; Nicot 145524, Zea 133449, Oryca 129671, Arabi 143650,

ndhB-14RR R 145524 146189 141098 143650 145737 129671 23 ggtatagtagatgctatcacaca Graham and Olmstead 2000

ndhB-7F ndhB R 99175 99441 60077 97069 98502 45287 21 ggaagtttstttcccagaatg Graham and Olmstead 2000

ndhB-7FF F 143451 144116 115459 141571 143661 87553 21 ggaagtttstttcccagaatg Graham and Olmstead 2000

ndhB-7R ndhB F 99155 99421 97058 98482 87533 23 cattctgggaaaatsaaacttcc Graham and Olmstead 2000 2nd Nicot 99155; Zea 91366; Oryza 127585; Ara 97058; Oenothera 150962;

ndhB-8R ndhB F 98918 99184 94158 96821 98245 87296 25 gatagaggaatacatagagttgaac Graham and Olmstead 2000

ndhB-8RR R 143708 144373 139287 141828 143918 127822 25 gatagaggaatacatagagttgaac Graham and Olmstead 2000

ndhB-9F ndhB R 98675 98941 93915 96578 98002 87053 22 atggtttctcttggctatatgg Graham and Olmstead 2000

ndhB-9FF R 143951 144616 139530 142071 144161 128065 22 atggtttctcttggctatatgg Graham and Olmstead 2000

ndhB-B10R ndhB F 98528 98794 93768 96431 97855 86906 23 gaaagcttgaacccaattcctac Graham and Olmstead 2000

ndhB-B10RR R 144098 144763 139677 142218 144308 128212 23 gaaagcttgaacccaattcctac Graham and Olmstead 2000

ndhB-C11R ndhB F 98170 98436 93416 96069 97497 86527 21 ttacactcgtagtctctgaag Graham and Olmstead 2000

ndhB-C11RR R 144456 145121 140029 142580 144666 128591 21 ttacactcgtagtctctgaag Graham and Olmstead 2000

ndhC-f ndhC F 52645 52285 50341 50511 49640 23 TCATATTCGTRAAGCAGAAACAT

ndhF+607 F 111463 111768 106788 109848 111515 28 ACCAAGTTCAATGTTAGCCAGATTAGTC Neyland & Urbatsch 1996

ndhF+607-R R 131163 131789 126657 128801 130648 28 ACCAAGTTCAATGTTAGCCAGATTAGTC Neyland & Urbatsch 1996

ndhF-1259 ndhF 113034 113781 108740 111380 113909 102379 91921 26 atttcatctttggaccaraarcaagc Neyland & Urbatsch 1996

ndhF-52 R 114344 115091 25 AGGTAAGATCCGGTGAATCGGAAAC Neyland & Urbatsch 1996

ndhf-523 ndhF 113770 114517 109476 112116 114651 103115 92657 26 tgtcaaaaagcttttgtawcwaatcg Neyland & Urbatsch 1996

ndhF-803 F 113467 114214 109173 111813 114342 24 GAAAAATTCCCGCCGCTACCATAG Neyland & Urbatsch 1996

ndhF-803R R 113490 114237 109196 111836 114365 24 CTATGGTAGCGGCGGGAATTTTTC Neyland & Urbatsch 1996

ndhF-f1 F 112141 112888 110472 24 AAGAAGAGATGCGTCCGCCCCCTA this publication

ndhF-r1 R 114267 115014 109973 112613 25 GGATCATACCTTTCATTCCACTTCC this publication

ndhJ-r ndhJ R 51016 50656 47691 48704 48873 48019 23 TTTTYATGAAATACAAGATGCTC

NTCP10-f F 12931 12706 33293 99665 11231 18 TGCTGAATCGACGACCTA Bryan et al. 1999 atpF intron

NTCP10-r R 12812 12590 11390 12173 11125 21 AATATTCGGAGGACTCTTCTG Bryan et al. 1999 atpF intron

NTCP11-f F 15006 14789 13196 22 AGTGAATATTCATTGAGACGAACG Bryan et al. 1999 ars2

NTCP11-r R 15139 14922 20 ATCTAGAGTGATAGCAAAAA Bryan et al. 1999 ars2

NTCP12-f rps2 F 16892 16674 15036 15678 15922 19 CCTCCATCATCTCTTCCAA Bryan et al. 1999 rps2/RF862 intergenic region

NTCP12-r rps2 R 16892 19 CCTCCATCATCTCTTCCAA one of them wrong Bryan et al. 1999 rps2/RF862 intergenic region

NTCP13-f F 19094 18862 17384 19 TTTCCTGTTCCTGGTGGTA Bryan et al. 1999 rpoC2 exon

NTCP13-r R 19271 19039 17545 22 TTGGGGTAGATACACAAATCAC Bryan et al. 1999 rpoC2 exon

NTCP14-f F 31580 22 AATCCGTAGCCAGAAAAATAAA Bryan et al. 1999 psbM/trnD intergenic region

NTCP14-r R 31730 31506 20 CCGATGCATGTAATGGAATC Bryan et al. 1999 psbM/trnD intergenic region

NTCP15-f F 32662 32458 19 TGCAAAAATCCTACTCTTC Bryan et al. 1999 trnE/trnT intergenic region

NTCP15-r R 32543 32321 23 TCTTTCGATTATTTTAGTTTAGA Bryan et al. 1999 trnE/trnT intergenic region

NTCP16-f F 32565 32343 23 TCTAAACTAAAATAATCGAAAGA Bryan et al. 1999 trnE/trnT intergenic region

NTCP16-r R 32381 32158 29852 30588 31073 15575 21 TGAAATTGTCAATATAATCGA Bryan et al. 1999 trnE/trnT intergenic region

NTCP18-f F 36872 36627 35113 35177 11302 80170 21 CTGTTCTTTCCATGACCCCTC Bryan et al. 1999 psbC/trnS intergenic region

NTCP18-r R 37057 36809 18 CCACCTAGCCAAGCCAGA Bryan et al. 1999 psbC/trnS intergenic region

NTCP19-f F 45063 44833 43528 21 AATCGTTGTTTTAGACGATGC Bryan et al. 1999 ycf3 intron

NTCP19-r R 45227 44992 42112 43691 42791 72299 21 GAAACCCATTCTTACCACAAG Bryan et al. 1999 ycf3 intron

NTCP20-f F 46079 45850 22 TCCTCGTAAGACTGAGAGAAAT Bryan et al. 1999 ycf3 intron

NTCP20-r R 46200 45966 43125 44525 44651 43771 22 TTACGAGTAATTCCGACAACTT Bryan et al. 1999 ycf3 intron

NTCP21-f F 46311 46077 21 AAAAAGATCCCACAAAGAAAA Bryan et al. 1999 ORF74A exon

NTCP21-r R 47007 46675 19 GTCAAAGCAAAGAACGATT Bryan et al. 1999 ORF74A exon

NTCP22-f F 46876 46550 22 TATCAGAAAAAGAAAAAGAAGG Bryan et al. 1999 ORF74A/trnS intergenic region

NTCP22-r R 47007 46675 19 GTCAAAGCAAAGAACGATT Bryan et al. 1999 ORF74A/trnS intergenic region

NTCP23-f F 48457 48120 22 CAAAGGAACATTATCAATCATC Bryan et al. 1999 rps4/trnT intergenic region

NTCP23-r trnT R 48578 48238 45568 46278 46547 45780 69182 50326 21 TAGCTCAGAGGTTAGAGCATC Bryan et al. 1999 rps4/trnT intergenic region

NTCP24-f atpB F 56685 56349 19 GACCGATGATTTGGACGAC Bryan et al. 1999 atpB exon

NTCP24-r R 56849 56505 22 GCTAGCGGACATTTATTTTGAA Bryan et al. 1999 atpB exon

NTCP25-f F 57326 56982 21 TTAGTCAGGTATTTCCATTTC Bryan et al. 1999 atpB/rbcL intergenic region

NTCP25-r R 57515 57168 54862 55636 22 CTTTTCATAGGAATCTTTCACA Bryan et al. 1999 atpB/rbcL intergenic region

NTCP26-f F 62140 61806 58144 59307 60068 57279 21 GCAATTGCAATGGCTTCTTTA Bryan et al. 1999 psaI/ORF184 intergenic region

NTCP26-r R 62307 61971 22 TTTATGTTCGGTGGAAATCACA Bryan et al. 1999 psaI/ORF184 intergenic region

NTCP27-f F 69322 69570 22 ATAAATACAGAACCCGTCGTAA Bryan et al. 1999 trnP/psaJ intergenic region

NTCP27-r R 69487 69734 22 TGCTTAGAGTTGGACACAGAAT Bryan et al. 1999 trnP/psaJ intergenic region

NTCP28-f F 71526 71784 67680 68973 66819 31104 17 TCCAATGGCTTTGGCTA Bryan et al. 1999 rpl20/rps12 intergenic region

NTCP28-r R 71695 71951 67857 18 AGAAACGAAGGAACCCAC Bryan et al. 1999 rpl20/rps12 intergenic region

NTCP29-f F 73621 73863 69686 70936 71915 22 AGTCGGTTGATTAGGGTAAAAT Bryan et al. 1999 clpP intron

NTCP29-r R 73777 74016 22 AAAGCCCTTTCGTTAGAAGTAA Bryan et al. 1999 clpP intron

NTCP2-f F 83 84 18 CTCGCCTACTTACATTCC Bryan et al. 1999 trnH/psbA intergenic region

NTCP2-r R 376 10945 20 AAGGAGAGGTTATTTTCTTG Bryan et al. 1999 trnH/psbA intergenic region

NTCP30-f F 72945 73195 69050 70339 71242 19 GATGGCTCCGTTGCTTTAT Bryan et al. 1999 clpP intron

NTCP30-r R 73106 73349 22 TGCCGGAGAGTTCTTAACAATA Bryan et al. 1999 clpP intron

NTCP32-f F 73958 74192 71252 64941 22 TGTTTCATCTTTTTAGGTTTAT Bryan et al. 1999 clpP intron

NTCP32-r R 74122 74356 20 TCAAGCAAAGTTATCTCAAC Bryan et al. 1999 clpP intron

NTCP33-f F 80561 80794 76557 77977 79060 47827 20 TGGCTGTTATTCAAAAGGTC Bryan et al. 1999 rpoA exon

NTCP33-r R 80709 80942 79208 22 CATGATAAATTGGCTAAACTCA Bryan et al. 1999 rpoA exon

NTCP34-f F 82949 83197 79029 80415 81512 22 GATCCATATCAGCATTTCGTAT Bryan et al. 1999 rps8/rpl14 intergenic region

NTCP34-r R 83160 83406 22 CTGTTTCTAGTGGGGTATTTGA Bryan et al. 1999 rps8/rpl14 intergenic region

NTCP36-f F 86753 87012 82938 84347 85699 76552 24 GTAGTAAATAGGAGAGAAAATAGA Bryan et al. 1999 rps19/rpl2 intergenic region; second match in Populus at 156466

NTCP36-ff F 155873 156545 150507 154302 156466 24 GTAGTAAATAGGAGAGAAAATAGA Bryan et al. 1999

NTCP36-r R 86654 86900 82835 85599 79072 21 TTGTAGCCAATCATTTATTAA Bryan et al. 1999 rps19/rpl2 intergenic region

NTCP36-rr F 156657 150610 156564 21 TTGTAGCCAATCATTTATTAA

NTCP37-f F 109856 110153 105191 108191 98771 18 TTCCGAGGTGTGAAGTGG Bryan et al. 1999 rrn5/trnR intergenic region

NTCP37-ff R 132770 133404 128254 130458 116347 18 TTCCGAGGTGTGAAGTGG Bryan et al. 1999

NTCP37-r R 109714 110007 105060 108064 109651 98629 91714 23 CAGGATGATAAAAAGCTTAACAC Bryan et al. 1999 rrn5/trnR intergenic region

NTCP37-rr F 132912 133550 128385 130585 132512 116489 23 CAGGATGATAAAAAGCTTAACAC Bryan et al. 1999

NTCP38-f F 127389 128078 22 AATTTCGAGGTTCTTATTTACT Bryan et al. 1999 ycf1/oriR intergenic region

NTCP38-r R 127541 128230 22 GATTCTGAGCTCTATTCATTAG Bryan et al. 1999 ycf1/oriR intergenic region

NTCP39-f F 109826 110123 108162 109749 22 GTCACAATTGGGGTTTTGAATA Bryan et al. 1999 trnR/rrn5 intergenic region

NTCP39-ff 132800 133434 130482 132414 22 GTCACAATTGGGGTTTTGAATA Bryan et al. 1999

NTCP39-r R 109671 109964 105017 108021 109608 98586 91671 21 GACGATACTGTAGGGGAGGTC Bryan et al. 1999 trnR/rrn5 intergenic region

NTCP39-rr 132955 133593 128428 130628 132555 116532 21 GACGATACTGTAGGGGAGGTC Bryan et al. 1999

NTCP3-f F 3902 3859 3547 3819 3441 0 AAGTCAAAAGAGCGATTAG Bryan et al. 1999 trnK intron

NTCP3-r F 3707 3645 3360 3629 3566 20 TGATACATAGTGCGATACAG Bryan et al. 1999 trnK intron

NTCP40-f F 86773 87032 84367 85719 19 TAATTTGATTCTTCGTCGC Bryan et al. 1999 rp12/trnH intergenic region

NTCP40-ff 155853 156525 154281 156444 19 TAATTTGATTCTTCGTCGC Bryan et al. 1999

NTCP40-r R 76 77 71 73 74 81054 49959 29599 19 GATGTAGCCAAGTGGATCA Bryan et al. 1999 rp12/trnH intergenic region

NTCP40-rr 134064 119062 19 GATGTAGCCAAGTGGATCA Bryan et al. 1999

NTCP4-f F 4692 56328 18 TTGGATTAGATTTGTAGTTCCA Bryan et al. 1999 trnK/rps16 intergenic region

NTCP4-r R 4536 4513 22 ATCCACTTCATTTATCACAATG Bryan et al. 1999 trnK/rps16 intergenic region

NTCP5-f F 6881 6824 21 CGAATTGATAGATACGAAACC Bryan et al. 1999 rps16/trnQ intergenic region

NTCP5-r R 6732 6679 21 AATACACCAAACAACAAATCC Bryan et al. 1999 rps16/trnQ intergenic region

NTCP6-f trnQ F 7437 7381 6233 6637 5607 6637 6624 23854 18 GGTTCGAATCCTTCCGTC Bryan et al. 1999 rps16/trnQ intergenic region

NTCP6-r R 7262 7208 21 GATTCTTTCGCATCTCGATTC Bryan et al. 1999 rps16/trnQ intergenic region

NTCP7-f F 8475 8395 7660 7685 7773 23030 18 TGATCCCGGACGTAATCC Bryan et al. 1999 ORF98/trnS intergenic region

NTCP7-r trnS R 8649 8581 7498 7802 6893 7846 7909 22962 18 cgaatccctctctttccg Bryan et al. 1999 ORF98/trnS intergenic region

NTCP7-rr trnS 47188 46849 44093 44896 45347 44507 70457 48915 18 cgaatccctctctttccg Bryan et al. 1999 further occurrence in Pinus 51819, Nicotiana 104500, 138126 and elsewhere

NTCP8-f F 9895 9677 8562 9053 8114 20 ATATTGTTTTAGCTCGGTGG Bryan et al. 1999 trnG intron

NTCP8-r trnG(UCC) intron R 10145 9926 8819 9308 8364 13118 9547 21499 18 TCATTCGGCTCCTTTATG Bryan et al. 1999 trnG intron

NTCP9-f F 10220 10001 8894 9391 8439 13043 9616 21424 18 CTTCCAAGCTAACGATGC Bryan et al. 1999 trnG/trnR intergenic region

NTCP9-r trnR R 10456 10227 9068 9615 8732 35911 9906 21295 18 CTGTCCTATCCATTAGACAATG Bryan et al. 1999 trnG/trnR intergenic region

ORF106 Rieseberg (ORF106-r) accD=ORF512 R 60868 60523 69242 58093 58830 56593 22 actacagatctcatactacccc Rieseberg et al. 1992

ORF184 Grivet ycf4=ORF184 R 63082 62749 87081 60200 60989 58146 39834 22 ggccycggatttccatataaag Grivet et al. 2001

ORF184-f ycf4=ORF184 F 62644 62311 58559 59778 60551 57708 68439 19 tggcgatcagaacayatatggatag Grivet et al. 2001

ORF2280-f Katayama 127325 0 TATTGATATGAAGATTGCCG Katayama & Ogihara 1996

ORF2280-r Katayama R 128833 129528 124426 126681 20 TGAAACCTTGGCATAsATCT Katayama & Ogihara 1996 t->S

ORF315 F 117225 117913 113228 115394 106144 104976 26 GGTCAATCTTTTAGGAATAGGGTTAC this publication

ORF512-f accD=ORF512 F 60852 60507 57000 58077 58814 58533 20 agtatgggatcYgtagtmgg Grivet et al. 2001 cc->cY

ORF62-M - R 37809 37548 19 ttggttttgggtctgcgac Heinze 1998 only matches Nicotiana

ORF62-P ycf9 F 37600 37339 34650 35757 35913 11943 79571 41653 20 cttgctttccaattggctgt Heinze 1998

petA-f(FOF) petA F 65214 65415 61529 63287 60480 20 gcatctgttattttggcaca Fofana et al. 1997

petA-f0 petA F 64443 64644 62516 59709 37936 25 CCCATTTTTGCACAGCAGGGTTATG this publication

petA-r petA R 65092 65293 61407 62414 63165 60358 19 ccctckgaaacaagaagtt Grivet et al. 2001

petA-r0 petA R 64467 25 CATAHYCYTGYTGBGCRAAAATDGG this publication

petB3-r petB exon2 R 78628 78868 74696 77068 72466 77069 25 grtcccaagggaargaataaccagt Grivet et al. 2001

petB-f psbH F 77209 77443 73252 75587 70989 54537 71200 20 TGGGGAACTACTCCTTTGAT Tsumura et al. 1996

petB-f (BD-B) petB exon2 F 78375 25 ctatcgtccraccgttacwgaggct Grivet et al. 2001

petB-r petB exon2 R 78842 79082 74910 76282 77282 72680 72556 21 CCCGAAATACCTTGCTTACG Tsumura et al. 1996

petD-f F 79904 80144 80144 73747 57279 20 tccagtagtaattctaggta Grivet et al. 2001

petD-r (BD-D) petD exon2 R 79992 77397 78521 73415 22 caaayggataygcaggttcacc Grivet et al. 2001

psaA-B1 psaA R 38851 38599 35918 37449 36590 18 tctccctctgaatcaaac Schaffner et al. 1995

psaA-f psaA F 43458 43206 40524 41829 42052 41222 73847 47179 22 acttctggttccggcgaacgaa Demesure et al. 1995

psaA-f Tsumura psaA F 41262 41010 38328 39633 39856 39026 76052 44983 20 aagaatgcccatgttgtggc Tsumura et al. 1996

psaA-r psaA R 43480 43228 40546 41851 42074 41244 73825 47201 23 attcgttcgccggaaccagaagt Dumolin-Lapegue et al. 1997

psaA-r Tsumura psaA R 43479 43227 40545 41850 42073 41243 73826 47200 20 ttcgttcgccggaaccagaa Tsumura et al. 1996

psaA-ycf3 PG1f psaA F 43410 43158 40476 41781 42004 30 CATTCCTCGAACGAAGTTTTTACGGGATCC Huang & Shi 2002

psaA-ycf3 PG2r ycf3 exon3 R 44296 44081 41198 42641 42755 47542 0 TCCCGGTAATTATATTGAAGCGCATAATTG Huang & Shi 2002

psaB (PSAB3) psaB F 40816 40564 37882 39187 18 agtgcgtaaaccgattg Schaffner et al. 1995

psaB (PSAB4) psaB R 40834 0 TAC AAT CCG TTT ACG CAC Schaffner et al. 1995

psaB 10 psaB R 39823 18 GATACAATCSGCTCATGG Schaffner et al. 1995

psaB 11 psaB R 39404 39152 37775 37998 18 ggcagggtaacgtttcac Schaffner et al. 1995

psaB 5 psaB F 40655 40403 37721 76658 18 ACRCCRAAGAGTCCTGAC Schaffner et al. 1995

psaB 8 psaB F 40123 39871 37887 77190 18 TGC TAT GAA TGC ATA AGC Schaffner et al. 1995

psaB 9 psaB R 40000 39748 37066 38594 37764 77313 18 tgaagataatgtattggc Schaffner et al. 1995

psaB-FOF psaB R 39210 38958 36276 37581 37804 36974 78103 42930 20 tggcgtggatattggcagga Fofana et al. 1997

psaI-75R 62157 61823 58161 59324 60085 57296 40816 24 AGAAGCCATTGCAATTGCCGGAAA T. Barkman and B. Simpson, University of Texas, Austin, personal communication to small et al. (1998)

psaI-r psaI R 62147 61813 58151 59314 60075 57286 22 gcaattgccggaaamactargc

psbA Hamilton psbA R 558 518 240 403 342 425 21 CGAAGCTCCATCTACAAATGG Hamilton 1999

psbA Sang psbA R 608 568 291 457 392 156 65708 29355 22 GTTATGCATGAACGTAATGCTC Sang et al., 1997 second match in Pinus: 119696

psbA-3' psbA F 1531 1491 1214 1380 1315 1079 912 28432 20 ctagcactgaaaaccgtctt Tsumura et al. 1995

psbA-5' psbA F 593 553 276 442 377 65723 29370 20 TACGTTCRTGCATAACTTCC Tsumura et al. 1995

psbA-5'-2 psbA 20288 119681 20 TACGTTCRTGCATAACTTCC Tsumura et al. 1995

psbA59R psbA F 1498 1458 1181 1347 1282 1046 879 28465 24 AACCATCCAATGTAAAGACGGTTT M. Nepokroeff, University of South Dakota, personal communication - Shaw et al 2005

psbAf1 psbA F 1279 1239 1128 1063 723 28684 23 AACCATTCATCAACGGATGCCGC this publication

psbAf2 psbA F 1342 1302 1025 1191 1126 890 28621 20 GTAGGAATAATGGCACCGGA this publication

psbAr1 psbA R 758 718 441 607 542 139 24 GTAGTAGGTATCTGGTTTACCGCT this publication

psbAr2 psbA R 780 740 463 563 328 161 24 CTTCTTCCTAGCTGCTTGGCCTGT this publication

psbAr2-2 psbA 114690 24 CTTCTTCCTAGCTGCTTGGCCTGT this publication

PSBB Goulding psbB R 74971 75201 71065 72389 73352 68817 52442 17 GATACCAAGGCAAACCC Goulding et al. 1996

psbB Hamilton psbB F 76302 76532 72396 74683 53773 70375 22 GTTTACTTTTGGGCATGCTTCG Hamilton 1999

psbB1-f (B1B2-B1) psbB F 74960 75190 71054 72378 73341 68806 52431 69033 22 tgccttggtatcgtgttcatac Grivet et al. 2001

psbB2-f (B2B3-B2) psbB F 75848 76078 71942 73266 74229 69694 53319 69921 22 cagaagcttggtctaaaattcc Grivet et al. 2001

psbB2-r (B1B2-B2) psbB R 76470 76701 72565 73889 74852 21 cytgtcttyttgtagttggat Grivet et al. 2001

psbB-60F psbB F 74953 75183 71047 72371 73334 68799 52424 69026 29 atgggtttgccttggtatcgtgttcatac Graham and Olmstead 2000

psbB-61R psbB R 75308 75538 71402 72726 73689 69154 52779 69381 25 tcccaatayacccaatgccagatag Graham and Olmstead 2000

psbB-63F psbB F 75634 75864 73052 74015 69480 53105 26 ggattrcgtatgggmaatattgaaac Graham and Olmstead 2000

psbB-65F psbB F 76028 25 tgcctactttttttgaaacatttcc Graham and Olmstead 2000

psbB-66R psbB R 76313 76543 72407 74694 70159 53784 25 ccaaaagtraaccaaccccttggac Graham and Olmstead 2000

psbB-67F psbB F 76379 76609 72473 73797 74760 70225 53850 70452 22 gagatgtttttgctggtattga Graham and Olmstead 2000

psbB-B60F psbB F 75028 75258 71122 52499 24 CATACAGCTCTRGTTKCTGGTTGG Graham and Olmstead 2000 slightly modified from original

psbB-B61F psbB F 75215 22 cgggtmtttggagttaygargg Graham and Olmstead 2000

psbB-B66R psbB R 76298 76528 72392 73713 74679 70144 53769 70368 0 ccccttggactrctacgaaaaacacc Graham and Olmstead 2000

psbB-B68R psbB R 76460 76690 72554 73878 74841 70306 53931 24 gtagttggatctccaagtttttgg Graham and Olmstead 2000

psbB-M1 psbB R 75791 76021 71885 73209 69637 53262 28 aagtayccctgatcccaytgrtaacgag this publication minor mismatches with tobacco

psbB-r psbB R 75303 75533 71397 72721 73684 69149 52774 69376 20 atayacccaatgccaratag Grivet et al. 2001

psbC2-P psbC F 36235 35990 34540 10665 80807 20 ttaaccaaacccttcgcatg

psbC2r psbC R 35819 20 AGC ACT AAA GCT TGG ACA GG Ziegenhagen et al. 1996 Abies sp.

psbC-46F psbC F 35572 35327 32609 33813 33877 10002 81470 39957 26 ggtttygcttggtgggcygggaatgc Graham and Olmstead 2000

psbC-47R psbC R 35926 35681 32963 34167 34231 10356 81116 40311 25 cataaccraagaakggaaaagattc Graham and Olmstead 2000

psbC-48F psbC R 35959 35714 33399 34264 10792 40344 26 ttaggtattcacytaatyttgttagg Graham and Olmstead 2000

psbC-49R psbC R 36362 36117 34603 34667 80680 36117 29 gtattattgaaccagacaaaacaacaagc Graham and Olmstead 2000

psbC-50F psbC F 36413 36168 33450 34654 10843 28 ctcaagcatttacttttytagttagaga Graham and Olmstead 2000

psbC-51R psbC R 36758 36513 35065 34999 35063 11188 41143 25 gctaaccaacttctaggrgaracat Graham and Olmstead 2000

psbC-B47F psbC F 35930 22 GGAAAGATMGRAAYAAAATGAC Graham and Olmstead 2000 modified from original

psbC-B47R psbC R 35951 22 GTCATTTTRTTYCKATCTTTCC Graham and Olmstead 2000 modified from original

psbC-B51R psbC R 36795 36550 33832 35036 11225 80247 24 tacgaagaagaaraatcctagaac Graham and Olmstead 2000

psbCf psbC F 35551 35306 32588 33792 33856 9981 81491 39936 20 ggtcgtgaccaagaaaccac Demesure et al. 1995

psbC-r psbC R 36415 36170 33452 34656 34720 10845 20 gagcttgagaagcttctggt Dumolin-Lapegue et al. 1997

psbD 3' Tsumura psbD R 35510 35265 32547 33751 33815 9940 81532 39895 20 tagaacctcctcagggaat Tsumura et al. 1995

psbD 5' Tsumura psbD F 34469 34224 31506 32710 32774 8899 82573 38854 20 tatgactatagcccttggta Tsumura et al. 1995

psbD Doyle psbD R 34488 34243 31525 32729 32793 8918 82556 38873 19 taccaagggctatagtcat Doyle et al. 1992

psbD-40F psbD F 34528 34283 31565 32769 32833 8960 22 atgactggttacgragggaccg Graham and Olmstead 2000

psbD-41R psbD R 34791 34546 31828 33032 33096 9221 39176 22 attgasaccaacgagtaaaatc Graham and Olmstead 2000

psbD-42F psbD F 34837 24 taataggtttyatgytacgtcaat Graham and Olmstead 2000

psbD-44F psbD F 35244 34999 32281 33485 33549 9674 81798 39629 23 ggkgttgctttttccaataaacg Graham and Olmstead 2000

psbD-B44R psbD R 35266 35021 32303 33507 33571 9696 81776 39651 23 cgtttattggaaaaagcaacccc Graham and Olmstead 2000

psbDC-45R psbC, psbD R 35505 35260 32542 33746 33810 9935 81537 27 cctcctcagggaatataagrttttcat Graham and Olmstead 2000

psbE-55F psbE R 67129 67381 63209 64322 65189 62334 23 atgtctggaagcacrggagaacg Graham and Olmstead 2000

psbE-B55F psbE R 67069 67321 63149 64262 65129 62274 23 gtyattcatagyattactatacc Graham and Olmstead 2000

psbE-r(FOF) psbE R 67050 67302 63130 64243 65110 62255 35379 20 taccttccctattcattgcg Fofana et al. 1997

psbF Hamilton psbH R 77154 77387 75529 20 CGCAGTTCGTCTTGGACCAG Hamilton 1999

psbF-56F psbF R 66783 67035 62864 63976 64838 61987 35646 63208 25 grtcaatatcagcaatgcagttcat Graham and Olmstead 2000

psbF-56R psbF F 66759 67011 62840 63952 64814 61963 35670 63184 22 atgaactgcattgctgatattg Graham and Olmstead 2000

psbH-71R R 77231 77465 73274 75609 71011 22 cccatmaaaggagtagtycccc Graham and Olmstead 2000

psbH-B71R R 77207 77441 73250 77491 75585 70987 54535 23 ccaggagctactttaccatattc Graham and Olmstead 2000

psbJ-58R psbJ F 66370 25 GATGAACCYAATCCRGAATAYGAAC Graham and Olmstead 2000 modified from original

psbJ-B58R psbJ F 66453 66705 62514 63628 64413 61655 35981 26 ccaaagaggaatccttccagtrgtat Graham and Olmstead 2000

psbK-P1 psbK-ORF98 F 7985 7927 6749 7167 6165 7183 7173 26 gcctttgtttggcaagctgctgtaag this publication

psbL-B57F psbL R 66659 66911 62735 63853 64704 61863 35781 15369 22 TACTCATTTTTGTACTTGSYGT Graham and Olmstead 2000 modified from original

psbL-f Grivet psbL F 66629 66881 62705 63823 64674 61833 35811 63055 20 GAAAATAAAACAGCAAGTAC Grivet et al. 2001

psbMF Shaw psbM F 30832 30591 28341 28782 29007 16714 27841 4030 30 AGCAATAAATGCRAGAATATTTACTTCCAT Shaw et al. 2005

psbM-f1 psbM F 30821 30580 28330 28771 28996 16725 27830 4041 23 aatagtgcagtagcaataaatgc this publication

psbM-f2 psbM F 30836 30595 28345 28786 29011 27845 24 ataaatgcaagaatatttacttcc this publication

psbMR Shaw psbM R 30861 30620 28811 29036 16685 27870 4001 30 ATGGAAGTAAATATTCTYGCATTTATTGCT Shaw et al. 2005

psBM-r1 psbM R 30855 30614 28364 28805 29030 16694 27864 4007 23 gtaaatattcttgcatttattgc this publication

psbN-70R R 76958 77192 73010 74349 75326 70746 54318 28 tatctggtttacttgtaagytttactgg Graham and Olmstead 2000

psbT-68R R 76702 76936 72765 74104 75080 70512 54052 70691 23 aaygtataaaccaatgcttccat Graham and Olmstead 2000

psbT-69F psbT F 76735 24 tcgctatcttyttycgagaaccrc Graham and Olmstead 2000

rbcL 1360R Reeves rbcL R 58975 58626 55205 56338 57096 43093 57735 22 cttcacaagcagcagctagttc Reeves et al. 2001 Reeves, G., et al. Molecular systematics of Iridaceae: evidence from four plastid DNA regions. American Journal of Botany 88(11): 2074-2087. 2001

rbcL 1368R Reeves rbcL R 58984 58637 55214 56347 57105 43084 57744 23 ctttccawayttcacaagcagca Reeves et al. 2001 W and Y as required from tobacco sequence

rbcL 3' Tsumura rbcL R 58982 58635 55212 56345 57103 110331 43086 20 ttccatacttcacaagcagc Tsumura et al. 1995

rbcL 3' ZC rbcL R 59154 58807 55320 57215 42994 24 CTTTTAGTAAAAGATTGGGCCGAG Zurawski & Clegg 1987; Rydin et al. 2002

rbcL 5' Tsumura rbcL F 57596 57249 53826 54959 55717 44472 20 tgtcaccamaaacagagact Tsumura et al. 1995

rbcL 5"F-PCR rbcL F 57592 57245 53822 54955 55713 54092 44476 56352 29 TTTATGTCACCACAAACAGAGACTAAAGC 5' mismatches (linker?)

rbcL C34 (M34) rbcL F 57628 57281 53858 54991 55749 54128 44440 56388 21 GGATTCAAAGCTGGTGTTAAA M34 mismatches!

rbcL Dumolin rbcL R 57620 57273 53850 54983 55741 54120 44448 56380 20 gctttagtctctgtttgtgg Dumolin-Lapegue et al. 1997

rbcL F259R rbcL R 57872 57525 54423 54693 20 TCTCCAACAACACGCTCGAT

rbcL Fofana rbcL R 58193 57846 55556 56314 56953 20 gtaaaatcaagtccaccgcg Fofana et al. 1997

rbcL H1f rbcL F 57601 57254 53831 54964 55722 54101 44467 56361 20 CCACAAACAGAGACTAAAGC this publication mismatches!

rbcL H201F rbcL F 57794 57447 54024 55157 44274 19 CAACTGTATGGACCGATGG

rbcL Heinze f rbcL F 58873 58526 43195 57633 22 tgtgtamaagcwcgtaatgaagg this publication

rbcL Hodges R 57624 57277 53854 54987 55745 54124 56384 27 ACTTGCTTTAGTTTCTGTTTGTGGTGA Hodges and Arnold, 1994

rbcL K286 R (H286R) rbcL R 57899 57552 56020 54399 56659 20 GCTACATAAGCAATATATTG also M305R closely overlapping; H286R mism

rbcL K32F rbcL F 57626 57279 53856 54989 54126 44442 56386 20 TTGGATTCAAAGCTGGTGTT mismatches/deletions

rbcL M286 rbcL F 57880 57533 56001 54380 56640 20 CAATATATTGCTTATGTAGC

rbcL M288 rbcL F 57882 57535 56003 56642 17 ATATATTGCTTATGTAG

rbcL M288R rbcL R 57898 57551 50788 56019 56658 17 CTACATAAGCAATATAT

rbcL M313 rbcL F 57907 57560 54137 55270 56028 55564 44161 20 TTAGACCTTTTTGAAGAAGG

rbcL P1R rbcL R 57911 57564 56032 62566 44157 17 TCTAAAGGGTAAGCTAC

rbcL PR1f rbcL 57595 57248 53825 54958 55716 54095 44473 56355 21 ATGTCACCACAAACAGAGACT- Huang & Shi 2002

rbcL PR2r rbcL 58895 58548 55125 56258 57016 55395 43173 57655 22 ccttcattacgagcttgcacac Huang & Shi 2002

rbcL PR3r rbcL 58344 57997 56465 54844 43724 57104 0 CATTTCTTCACATGTACCTGC Huang & Shi 2002

rbcL RH1 rbcL F 57595 57248 53825 54958 55716 54095 44473 56355 26 ATGTCACCACAAACAGAGACTAAAGC Rydin et al. 2002; Zurawski & Clegg 1987

rbcL Rieseberg (rbcL2f) rbcL F 57595 57248 53825 54958 55716 54095 44473 56355 29 atgtcaccacaaacagaaactaagcaagt Rieseberg et al. 1992

rbcL Samuel rbcL R 57586 57239 55707 54086 21 ccctacaactcatgaattaag Samuel et al. 1997.

rbcL Savolainen rbcL R 57801 57454 54031 55164 55922 54301 44267 56561 20 tacagttgtccatgtaccag Savolainen et al. 1995

rbcL TWNP1 rbcL F 57900 57553 54134 55263 56021 44168 30 TTACCCTTTAGACCTTTTTGAAGAAGGTTC mismatches to tobacco

rbcL W296R rbcL R 57910 57563 56031 54410 44158 56670 21 CTAAAGGGTAAGCTACATAAG mismatches viz. tobacco

rbcL Z1 rbcL F 57595 57248 53825 54958 55716 54095 44473 56355 30 ATGTCACCACAAACAGAGACTAAAGCAAGT = F1F (1F-ANGIO)

rbcL Z153R rbcL R 57778 57431 54008 55141 55899 54278 31 AAGATTCGGCAGCTACCGCGGCCCCTGCTTC

rbcL Z1R rbcL R 57624 57277 53854 54987 55742 54124 44444 56384 30 ACTTGCTTTAGTCTCTGTTTGTGGTGACAT

rbcL Z234 rbcL F 57829 57482 54059 55192 54329 44239 30 CGTTACAAAGGGCGATGCTACCGCATCGAG includes K234

rbcL Z346R (&K) mims rbcL R 57969 57622 54199 56090 54469 44099 56729 30 AAATACGTTACCTACAATGGAAGTAAACAT

rbcL-1382R rbcL R 58975 58628 55205 56338 57096 55475 43093 57735 30 CTTCACAAGCAGCAGCTAGTTCAGGACTCC Wolfe et al. 1997

rp116 F71 Small rpl16 exon1 85098 85345 81101 82655 83840 79201 62282 77688 25 GCTATGCTTAGTGTGTGACTCGTTG Jordan, Courtney, and Neigel, 1996; Kelchner and Wendel, 1996

rpl14-r (B) rpl14 F 83511 83754 79569 77592 76586 36 ATCTGCAGCATTTAAAAGGGTCTGAGGTTGAACAT Nakamura 1997

rpl16-f rpl16 exon2 F 84041 84289 81562 82688 78105 61417 20 TGTTTACGAAATCTGGTTCT Grivet et al. 2001

rpl16-f (A) rpl16 exon2 R 84062 81583 78173 78126 9710 21 AAAGATCTAGATTTCGTAAAC Nakamura 1997

rpl16-F71 rpl16 exon1 R 85100 85347 81103 82657 83842 79203 62284 77690 23 ttgctatgcttagtgtgtgactc

rpl16-r rpl16 exon2 R 84058 81579 78122 61434 77133 20 AACCAGATTTCGTAAACAAC Grivet et al. 2001

rpl16-R1516 rpl16 exon2 F 84020 84268 80089 82670 78084 61396 23 CCCTTCATTCTTCCTCTATGTTG Jordan et al. 1996, Kelchner and Wendel 1996

rpl16-R1661 rpl16 exon2 F 83876 84124 79945 81397 82523 77940 61252 25 CGTACCCATATTTTTCCACCACGAC Jordan et al. 1996, Kelchner and Wendel 1996

RPL2 Goulding R 86775 87034 84369 85721 81209 22 GATAATTTGATTCTTCGTCGCC Goulding et al. 1996

RPL2 Goulding 2 155851 156523 154290 156442 133909 22 GATAATTTGATTCTTCGTCGCC Goulding et al. 1996

rpl20 Hamilton rpl20 F 71363 71621 68819 69591 20 TTTGTTCTACGTCTCCGAGC Hamilton 1999

rpL20 Shaw rpl20 F 71372 71630 67528 68828 69600 66677 31246 0 CGYYAYCGAGCTATATATCC modified from Hamilton (1999)

RPL22 Goulding F 86274 86521 20 ACTCTTCGTGCTTTGTCAGC Goulding et al. 1996

rpl2-20f rpl2 F 88119 88376 83638 85729 82550 65177 23 aaaggtcgtaatgccagaggaat Graham and Olmstead 2000

rpl2-20ff 154507 155181 149807 152920 132568 23 aaaggtcgtaatgccagaggaat Graham and Olmstead 2000

rpl2-21F rpl2 F 87854 88111 85464 86802 82285 64912 80129 24 ccctacctttgagtgcggtttgaa Graham and Olmstead 2000

rpl2-21FF 154772 155446 153185 155361 132833 24 ccctacctttgagtgcggtttgaa Graham and Olmstead 2000

rpl2-22R rpl2 R 154989 85246 86585 82068 64695 23 gtcttctccatattacyatatct Graham and Olmstead 2000 has two binding sites because within inv. repeat

rpl2-22R-f F 87637 87894 153403 155578 133050 23 gtcttctccatattacyatatct Graham and Olmstead 2000 other inverted repeat

rpl2-23F F 87422 87679 85031 86370 81858 64443 79740 26 gctacatgaAgaacataagccagatg Graham and Olmstead 2000 2nd Ara 85031; Oen 90244; Ory 81858; Zea 83608; Nicot 87422;

rpl2-23FF 155204 155878 153618 155793 133260 26 gctacatgaAgaacataagccagatg Graham and Olmstead 2000

rpl2-24F F 87178 87437 83358 84772 86124 81612 6431 21 caacratatgcccttaggcac Graham and Olmstead 2000

rpl2-24FF 155448 156120 150082 153877 156049 133506 21 caacratatgcccttaggcac Graham and Olmstead 2000

rpl2-24R R 87158 87417 83343 84752 86104 81592 64211 21 gtgcctaagggcatatyggtg Graham and Olmstead 2000

rpl2-24RR 155468 156140 150102 153897 156059 133526 21 gtgcctaagggcatatyggtg Graham and Olmstead 2000

rpl2-25R R 86805 87064 82990 84399 85751 81239 22 ttccaagygcaggataacccca Graham and Olmstead 2000 2nd Spin 150455, Nicot 155821, Zea 139748, Oryca 133879, Arabi 154250

rpl2-25R-f F 155821 156493 150455 154250 156412 133879 22 ttccaagygcaggataacccca Graham and Olmstead 2000

rpl2-3' rpl2 exon2 R 86933 87192 83118 84527 85879 81367 26 AGCCAACGCTTAGATCCGGCTCTACC Doyle et al. 1995

rpl2-3' 2 155693 156365 150327 154122 156284 133751 26 AGCCAACGCTTAGATCCGGCTCTACC Doyle et al. 1995

rpl23p46 rpl23 F 88441 88698 83940 86051 87389 82872 43540 29 taagacagaaataaagcattgcgtcgaac Heinze 1998

rpl23p46-2 154185 154859 149505 152598 154774 132246 29 taagacagaaataaagcattgcgtcgaac Heinze 1998

rpl23r rpl23 R 88367 88624 83880 85977 4775 22 GGAAGTCGATGACTATTCATAG this publication

rpl23rr 154259 154933 149565 152672 22 GGAAGTCGATGACTATTCATAG this publication

rpl2-5' rpl2 F 88074 88331 83593 85684 87022 82505 23 GGAGGTCATAAGCGTCTATACCG Doyle et al. 1995

rpl2-5'-2 154552 155226 149852 152965 155141 132613 23 GGAGGTCATAAGCGTCTATACCG Doyle et al. 1995

rpl2-B20F rpl2 F 88005 88262 83524 85615 86953 82436 65063 20 gtaaccatagaatacgaccc Graham and Olmstead 2000

rpl2-B20FF 154621 155295 149921 153034 155210 132682 20 gtaaccatagaatacgaccc Graham and Olmstead 2000

rpl2-B25R R 86894 87153 83079 84488 85840 63947 23 gggttcatarctactcctcttac Graham and Olmstead 2000

rpl2-B25RR 155732 156404 150366 154161 156323 23 gggttcatarctactcctcttac Graham and Olmstead 2000

rpl2f rpl2 F 87177 87436 83362 84771 86123 81611 64230 23 ACCGATATGCCCTTAGGCACGGC this publication

rpl2ff 155449 156121 150083 153878 156040 133507 23 ACCGATATGCCCTTAGGCACGGC Heinze 1998

rpl2m1 rpl2 R 87994 88251 83513 85604 86942 82425 30 TTCTATGGTTACGATTCTACCATATATGTC this publication

rpl2m1-2 154632 155306 149932 153045 155221 132693 30 TTCTATGGTTACGATTCTACCATATATGTC Heinze 1998

rpl2-r rpl2 exon1 R 88001 88258 83520 85611 86949 82432 65059 20 CCATAGAATACGACCCTAAT Grivet et al. 2001

rpl2-r-F rpl2 exon1 F 154625 155299 149925 153038 155214 132686 20 CCATAGAATACGACCCTAAT Grivet et al. 2001

rpl32 R 115086 24 GAAGTGCGTTTTTTTGGAACTGCC

rpoB-f(1) rpoB F 24588 24355 22695 23400 22936 22152 23023 8766 20 ctaaggggttgttgtgtaac Tsumura et al. 1996

rpoB-f2 rpoB F 25856 25623 23963 24668 24204 20893 24291 7499 23 TGCTTGACGTTGCATATTAGAAC this publication

rpoB-f3 rpoB F 27437 27194 25534 22 gatcaatgaacctmcaaaatcc this publication

rpoB-r(2) rpoB R 25873 25640 23980 24685 24221 24308 7482 20 aatatgcaacgtcaagcagt Tsumura et al. 1996

rpoB-r1 rpoB R 24607 24374 22714 23419 22955 22133 23042 8748 23 GTTACACAACAACCCCTTAGAGG Grivet et al. 2001

rpoB-r3 rpoB R 27466 27233 25573 26284 25814 20 aatcagatacartttgaagg this publication 6 bases at 3' truncated ??

rpoC1 exon 2 rpoC1 exon2 F 23032 21122 21339 4621 20 ATTTCATATTCGAAYAANCC Downie, Katz-Downie, and Cho, 1996

rpoC1 Tsumura rpoC1 R 17450 17227 15598 16203 15725 28982 16453 15670 20 gcagtttcttgaaaactcgc Tsumura et al. 1996

rpoC1-br(Liston) rpoC1 exon1 R 24078 23845 22186 22426 22673 9281 20 aagcggaatttgtgcttgtg Liston 1992

rpoC1-f rpoC1 exon1 F 24064 23831 22172 22412 9295 23 gcacaaattccrctttttatrgg Dumolin-Lapegue et al. 1997

rpoC1-f1 rpoC1 exon2 F 21649 21417 19742 20411 24367 37081 64298 23 CCTAAAGATTCATAGTGAACTTC this publication

rpoC1-f2 rpoC1 exon2 F 21950 21718 24063 24 AAATGGGATCCCCAATAGCCGGAG this publication

rpoC1-f3 rpoC1 exon2 F 22523 22291 20613 21282 20830 23490 25 TATCAAGAAGTGTATCCACGGCTTC this publication

rpoC1-f4 rpoC1 exon2 F 22705 22473 20795 21464 21012 23299 21169 23 CTCAACTCAGGAGGAAGAACTGG this publication

rpoC1-f5 rpoC1 exon2 F 22724 22492 20816 23289 24 CTG GTA ATA RRC ACA AAA CCA TCC Grivet et al. 2001

rpoC1-r1 rpoC1 exon2 R 21740 21508 19833 20502 24276 62893 23 TTAGATAGTCCTTTGTGGCTCCG this publication

rpoC1-r2 rpoC1 exon2 R 22052 21820 20142 20811 20359 23961 20510 11165 23 ATGGCTGTTCATGTACCTTTATC this publication

rpoC1-r3 rpoC1 exon2 R 22394 20484 20701 23619 23 CGTTCTGTCATTGTCGTGGGTCC this publication

rpoC1-r4 rpoC1 exon2 R 22550 22318 20640 21309 20857 23463 22 CAAGAAGCCGTGGATACACTTC this publication

rpoC1-r5 rpoC1 exon2 R 22736 22504 20826 21495 21043 23277 21191 23 tgtctattaccwgttcttcctcc Grivet et al. 2001

rpoC1-r6 rpoC1 exon2 R 23104 22872 21863 21411 22909 21 ATTTTTCTTTTGCTAGGCCCA this publication

rpoC2 Tsumura rpoC2 F 21061 20829 19161 19799 24996 20 tgtacacgcggtagaaaaat Tsumura et al. 1996

rpoC2-bf rpoC2 F 19967 19735 18067 18699 18248 26105 18445 21 TAG ACA TCG GTA CTC CAG TGC Liston 1992 Liston, A. Variation in the chloroplast genes rpoC1 and rpoC2 of the genus Astralagus (Fabaceae): evidence from restriction site mapping of a PCR-amplified fragment. Am. J. Bot. 79, 953-961. 1992.

rpoC2-f1 rpoC2 F 17447 17224 15595 16200 15722 28985 16450 22 CGAGCAGTTTCTTGRAAACTCGC Grivet et al. 2001

rpoC2-f2 rpoC2 F 18002 17779 16150 16277 28430 17005 22 GTGGCCAAATAAGGCTTAGCTG this publication

rpoC2-f3 rpoC2 F 18814 18582 16944 17546 17104 27 CCAATTTAATACTAAACAAGTCCGAAC this publication

rpoC2-f4 rpoC2 F 19965 19733 18065 18697 18246 26107 18443 23 GATAGACATCGGTACTCCAGTGC this publication

rpoC2-f5 rpoC2 F 20858 20626 18958 19596 19139 25199 19342 12283 25 ccttgwggatcygmcattaatcctc Grivet et al. 2001

rpoC2-f6 rpoC2 F 21045 20813 19145 19783 19326 25012 19529 23 TTTCTACCGCGTGTACATTCCCA this publication

rpoC2-r1 rpoC2 R 17469 17246 15617 16222 15744 28963 16472 15651 23 GCGAGTTTTCAAGAAACTGCTCG Grivet et al. 2001

rpoC2-r2 rpoC2 R 18026 17803 16174 28406 17029 22 GATCAGCTAAGCCTTATTTGGC this publication

rpoC2-r3 rpoC2 R 18850 18618 16980 17582 17140 21 TATTCAATTAGTTCGGACTTG this publication

rpoC2-r4 rpoC2 R 19995 19763 18095 18727 18276 26077 18473 21 GGAGAAATGCACTGGAGTACC this publication

rpoC2-r5 rpoC2 R 20882 20650 18982 19620 19163 25175 19366 12259 22 gaggattaatgkcrgatccwcaagg Grivet et al. 2001

rpoC2-r6 rpoC2 R 21073 20841 19173 19811 19354 19557 22 TCATTATGGGAATGTACACGCG this publication

rpoC2-rc1F rpoC2 R 17393 17170 16977 21 AAGAGAACGTTGTTTTGGGGG Graham 1994 (3 minor mismatches to tobacco)

rpoC2-rc2F rpoC2 R 17267 17044 15415 16011 15542 29165 28212 16294 22 TGAGAGATATTTTGTTCCACCA Graham 1994 (2 minor mismatches to tobacco)

rps14 (psaB2) rps14 F 38851 38599 35918 37449 36590 18 TCTCCCTCTGAATCAAAC Schaffner et al. 1995

rps14 Doyle rps14 R 38650 38398 37248 36380 78685 20 cta tcc gga cac ata ctt cg Doyle et al. 1992

rps14-FOF rps14 F 38624 38372 35691 37227 36354 78711 42378 22 catttcacgaagtatgtgtccg Fofana et al. 1997

rps15-r R 125387 126027 121195 123405 100990 24 AAATTTTGGGAAAACGTCAACGAC this publication second fit Oyza - 114128

rps16 F Downie rps16 ex2 F 5158 20 cct gta ggy tgn gcn ccy tt Downie 2001 ??? S. Downie, in: Lee, K. and Theodore Hymowitz. A Molecular Phylogenetic Study Of The Subtribe Glycininae (Leguminosae) Derived From The Chloroplast DNA rps16 Intron Sequences. American Journal of Botany 88(11): 206-–2073. 2001.

rps16 R Downie rps16 ex1 R 6193 6120 5788 6170 5535 20 aaacgatgtggnagnaarca Downie 2001

rps16-4547F rps16 exon2 R 5175 5140 4755 4568 55535 22 AGGGGCTCAACCTACAGGAACT Learn

rps16-5' rps16 exon1 F 6162 6089 5757 6139 5504 32 CAAGTCGCACGTTGCTTTCTACCACATCGTTT Hahn

rps16-F rps16 exon1 R 6186 6113 5781 6163 5528 32 GTGGTAGAAAGCAACGTGCGACTT Oxelman et al. 1997, Wallander & Albert 2000

rpS16-F Shaw rps16 exon1 R 6193 6120 5788 6170 5535 22 AAACGATGTGGTARAAAGCAAC modified from Oxelman et al. (1997) by Shaw et al (2005)

rps16-R2 rps16 exon2 F 5271 5236 4851 5243 4666 24 TCGGGATCGAACATCAATTGCAAC Oxelman et al. 1997, Wallander & Albert 2000

rps18-f Grivet rps18 F 70722 70975 66830 68121 68887 65926 31869 23 GCTCGTATTTTATCTTTGTTACC Grivet et al. 2001

rps18-r Grivet rps18 R 70744 70997 66852 68143 68909 65948 31847 23 GGTAACAAAGATAAAATACGAGC Grivet et al. 2001

rps2-1 F 16254 16036 6341 15040 30221 15939 16730 24 TCCCTCACAAATAGCGAATACCAA Wolfe et al. 1997 3' mismatches?

rps2-4C rps2 R 16909 16691 15053 15695 75524 15939 28136 19 TGGAAGAGATGATGGGGGC Wolfe et al. 1997

rps2-f rps2 F 16751 16533 14895 15537 28137 15781 16241 24 CAAAAACTAAATCACAAGCTTCTG Graham 1994

rps2-r rps2 R 16786 16568 14930 15572 14987 29691 15816 69909 24 CTCGTTTTTTATCAGAAGCTTGTG Graham 1994 not perfect, but acceptable fit to tobacco sequence

rps2-rs1R rps2 F 16657 16439 14801 29820 22 TGACACCGGGCCCTTATTGCAG Graham 1994

rps2-rs2R rps2 F 16882 16664 22 TGAACTCCTGCCTCCATCATCT Graham 1994 not a perfect fit for tobacco

rps3 Campagna Downie rps3 R 85483 85730 81495 83067 15020 20 tttcctttcgaaaagcaatg Campagna & Downie 1998 Campagna, M. L., Stephen R. Downie . The Intron in Chloroplast Gene rpl16 is Missing From the Flowering Plant Families Geraniaceae, Goodeniaceae, and Plumbaginaceae. Transactions of the Illinois State Academy of Science (1998), Volume 91, 1 and 2, pp.1-11

rps4-3' rps4 F 47554 47224 29338 45241 45057 21 ATATTCTACGACTAGCAATTC Souza-Chies et al. 1997 (mismatches close to 3' end!)

rps4-5' rps4 R 48141 21 ATG TCS CGT TAY CGA GGA CCT Souza-Chies et al. 1997

rps4-M rps4 F 47783 47453 44721 45470 45900 54127 20 ccattaactaaaatatgtYG Souza-Chies et al. 1997 second-most 3' site C->T in original primer - use Y or shorten primer

rpS4R2 Shaw rps4 F 47958 47628 44897 45645 46075 45232 69711 49847 22 CTGTNAGWCCRTAATGAAAACG Shaw et al. 2005

rps7-5R 66733 21 gaaagccaatgatttttttcc Graham and Olmstead 2000 3' mism even in Pinus

rps7-6F rps7 99586 99859 94839 97524 98966 87990 110975 25 ctcatagaatggcagaggcaaatag Graham and Olmstead 2000

rps7-6FF 143040 143698 138606 141125 143197 127128 25 ctcatagaatggcagaggcaaatag Graham and Olmstead 2000

rps7-6R rps7 99562 99835 94815 97500 98942 87966 110999 25 ctatttgcctctgccattctatgag Graham and Olmstead 2000

rps7-6RR 143064 143722 138630 141149 143221 127152 25 ctatttgcctctgccattctatgag Graham and Olmstead 2000

rps8-f Grivet rps8 F 82897 83145 76999 32175 20 TGAACAATATTTTCGGTAAT Grivet et al. 2001

rps8-r Grivet rps8 R 82899 83147 78977 80365 81462 60300 20 TCAAATACTTTTACGAGAAG Grivet et al. 2001

trnC-f trnC F 28841 28634 26765 27420 27125 18082 67748 5673 20 ccagttcaaatctgggtgTC Demesure et al. 1995 second fit Marchantia 51047, Oryza 47474 usw.

trnC-r trnC R 28861 21 CGA CAC CCR GAT TYG AAC TGG Dumolin-Lapegue et al. 1997

trnD(GUC)R Shaw trnD F 46998 46666 42277 33834 87997 20 GGGATTGTAGYTCAATTGGT modified from Demesure et al., 1995, by Shaw et al. 2005

trnD+420 f trnY F 32134 31911 29601 30341 30826 15849 28748 20 AACCAGCGTAGACATATTGC Bill Hahn (pers. comm.)

trnD-M trnD R 32007 31784 29178 29874 30343 16231 36484 20 gggattgtagttcaattggt Demesure et al. 1995

trnD-P trnD F 31988 31765 29159 29855 30324 16250 36465 20 accaattgaactacaatccc Demesure et al. 1995

trnE Doyle trnE F 32287 32064 29759 30494 30979 15694 28896 36743 20 gcctccttgaaagagagatg Doyle et al. 1992

trnE R trnE R 32306 32083 29778 30513 30998 15675 28915 36762 20 CATCTCTCTTTCAAGGAGGC this publication

trnE(UUC) Shaw trnE R 32310 32087 29782 30517 31002 15671 28919 36766 22 AGGACATCTCTCTTTCAAGGAG Shaw et al. 2005

trnET-F - F 32916 32713 26 gtatgtacatgtatmaatsaartkaa this publication

trnET-R - R 32956 27 CRA AAT TMA YTT WAT TKA TAC ATG TAC this publication

trnF-f trnF F 50280 49927 46977 48215 48061 47465 67757 51038 20 ctcgtgtcaccagttcaaat Dumolin-Lapegue et al. 1997

trnfM Doyle trnfM F 38380 38128 35444 36728 36962 12863 78935 42180 20 TGACCTCAAGGTTATGAGCC Doyle et al. 1992

trnfM-f trnfM F 38373 38121 35437 36721 36955 12856 78942 42173 23 gaacccgtgacctcaaggttatg Dumolin-Lapegue et al. 1997

trnfM-M trnfM R 38395 38143 35459 36743 36977 12878 78920 42195 20 cataaccttgaggtcacggg Demesure et al. 1995

trnG Doyle trnG F 38088 37827 35189 36520 36726 12361 79129 42065 19 TTGCCAAGGAGAAGATGCG Doyle et al. 1992

trnG(UCC) Hamilton trnG(UCC) exon2 R 9534 9316 8191 8681 7745 13717 8880 22012 22 GAACGAATCACACTTTTACCAC Hamilton 1999 second match in Pinus: 29426

trnG(UCC)-3' trnG(UCC) exon1 F 10243 10024 8917 9414 8462 13020 9639 21401 20 GAACCCGCATCGTTAGCTTG Doyle et al. 1992

trnG1f trnG(UCC) exon1 F 10237 10018 8911 9408 8456 13026 9633 42082 20 cgggttcgattcccgctacc this publication

trnG1ff trnG 38105 37844 35206 36537 36743 36097 21407 20 cgggttcgattcccgctacc this publication

trnG1-r trnG(UCC) exon2 R 10239 10020 8913 9410 8458 13024 9635 21405 22 ccgcatcgttagcttggaaggc this publication

trnG2-f trnG(UCC) exon2 F 9508 9290 8165 8655 7719 13743 8854 22038 26 gtttagtggtaaaagtgtgattcgtt this publication second match in Pinus: 29401

trnG2-r trnG(UCC) exon2 R 9519 9301 8176 8666 7730 13732 8865 22027 21 ttaccactaaactatacccgc this publication second match in Pinus: 29412; Marchantia: 42055

trnG-M trnG R 38110 37849 35211 36542 36748 12383 79107 20 aacccgcatcttctccttgg Heinze 1998

trnG-P trnG F 38090 37829 35191 36522 36728 12363 79127 42067 19 gccaaggagaagatgcggg Heinze 1998

trnG-UCC 5' trnG(UCC) exon2 R 9519 9301 8176 8666 7730 13732 8865 22027 19 TTACCACTAAACTATACCC Doyle et al. 1992 second match Pinus: 29412; Marchantia: 42055

TRNH Goulding R 78 79 73 75 76 81052 49957 29597 20 CGGATGTAGCCAAGTGGATC Goulding et al. 1996 second match Oryza: 134066; Pinus: 119064

trnH(GUG) Hamilton trnH F 51 52 46 48 49 81079 29624 20 ACTGCCTTGATCCACTTGGC Hamilton 1999 second match Oryza: 134039

trnH(GUG) Tate trnH F 28 29 23 30 26 81102 50007 23 CGCGCATGGTGGATTCACAATCC Tate and Simpson, 2003 second match in Orza: 134016; Pinus: 119014

trnHf trnH F 14 15 9 12 12 81116 50021 29661 20 ACGGGAATTGAACCCGCGCA Demesure et al. 1995 second match Oryza: 134002; Pinus: 119000

trnHM trnH R 45 46 43 81085 49990 20 GTGAATCCACCAYGCGCGGG this publication second match Oryza: 134033; Pinus: 119031

trnIf trnI F 88761 89018 84260 86374 87709 83201 66000 81046 22 TGAATGGTTAAAGCGCCCAACT this publication

trnIff 153865 154539 149185 152275 154454 131917 119404 22 TGAATGGTTAAAGCGCCCAACT this publication

trnK F Tsumura trnK ex1 F 1828 1788 4044 1735 1699 1391 28204 20 AACCCGGAACTAGTCGGATG Tsumura et al. 1995

trnK R Tsumura trnK ex2 R 4396 4349 4044 4336 4298 3920 4069 26051 20 TCAAYGGTAGAGTACTCGGC Tsumura et al. 1995 "Y" is introduced (polymorphism)

trnK-19 trnK exon R 4397 4350 4045 4337 4299 3921 4068 26050 19 CTCAAyGGTAGAGTACTCG Wolfe et al. 1997 3rd C->Y

trnK1f trnK exon2 F 1811 1771 1490 1718 1682 1374 1507 28221 20 GGGTTGCCCGGGACTCGAAC Demesure et al. 1995

trnK1r trnK exon2 R 1844 1804 1751 1715 1407 1540 28188 20 CCGACTAGTTCCGGGTTCGA Demesure et al. 1995

trnK-20 trnK exon F 1825 1785 1732 1696 1388 1521 28207 23 TCGAACCCGGAACTAGTCGGATG Wolfe et al. 1997

trnK2f trnK exon1 F 4372 4325 4020 4312 4274 3896 4043 26075 24 TAAAAGCCGAGTACTCTACCGTTG Dumolin-Lapegue et al. 1997

trnK2r trnK exon1 R 4395 4348 4043 4335 4297 3911 4062 26052 24 caacggtagagtactcggctttta Demesure et al. 1995

trnM-f trnM F 54616 54272 50886 52083 52705 51246 47201 53829 20 TGCTTTCATACGGCGGGAGT Demesure et al. 1995

trnM-r trnM R 33242 33039 30322 31431 31326 15191 95156 21 ttggatttgaaccaaygactc

trnM-rr trnM 54652 54308 50922 52119 52741 51282 47165 53865 21 ttggatttgaaccaaygactc

trnQ Hahn trnQ R 7442 7386 6238 6642 5612 6642 6629 23849 27 TCGGAGGTTCGAATCCTTCCGTCCCAG Hahn

trnQf trnQ F 7418 7362 6214 6618 5588 6618 6605 23873 20 gggacggaaggattcgaacc Dumolin-Lapegue et al. 1997 minor matches in Spinacia: 78347, 105969, 127476; also in others …

trnQr trnQ R 7446 7390 6242 6646 5616 6646 6632 23845 24 ctattcggaggttcgaatccttcc Dumolin-Lapegue et al. 1997

trnR Doyle trnR R 10454 10225 9066 9614 8730 35913 9904 21 GTCCTATCCATTAGACAATGG Doyle et al. 1992

trnR-f trnR F 10474 10245 9086 9634 8750 35893 9924 21277 25 ggtataggttcaaatcctattggac Grivet et al. 2001

trnR-f1 trnR F 10439 10210 9051 9599 8715 35928 9889 21312 21 gtctaatggataggacagagg this publication

trnR-f2 trnR F 10474 10245 9086 9634 8750 35893 9924 21277 25 ggtataggttcaaatcctattggac this publication

trnRr trnR R 10503 10274 9115 9663 8779 35864 9953 22 attgcgtccaataggatttgaa Dumolin-Lapegue et al. 1997

trnS Doyle trnS(GCU) F 8672 8604 7521 7825 6916 7869 7932 22939 19 TACAACGGATTAGCAATCC Doyle et al. 1992 second (also not perfect) match in Pinus: 51796

trnS(GCU) Hamilton trnS(GCU) F 8691 8623 7540 7844 6935 7888 20 GCCGCTTTAGTCCACTCAGC Hamilton 1999

trnS(GCU) Shaw trnS 8637 8569 7486 7790 6881 7834 7897 22974 23 AGATAGGGATTCGAACCCTCGGT Shaw et al. 2005

trnS(GCU) Shaw 2 trnS 47200 46861 44105 44908 45359 44519 51831 48923 23 AGATAGGGATTCGAACCCTCGGT Shaw et al. 2005

trnS(GCU) Shaw 3 trnS F 37144 36896 34193 35317 35446 11508 70445 23 AGATAGGGATTCGAACCCTCGGT Shaw et al. 2005

trnS(GGA) Shaw trnS 47176 46837 44081 44884 45335 44495 70469 22951 22 TTACCGAGGGTTCGAATCCCTC Taberlet et al., 1991

trnS(GGA) Shaw 2 trnS 8661 8593 7510 7814 6905 7858 7921 48903 22 TTACCGAGGGTTCGAATCCCTC Shaw et al. 2005

trnS(GGA) Shaw 3 37169 36920 34217 35341 35470 11532 51807 22 TTACCGAGGGTTCGAATCCCTC Shaw et al. 2005

trnS0f trnS(GCU) F 8690 8622 7843 6934 7887 19 cgccgctttagtccactca Grivet et al. 2001

trnS0r trnS(GCU) R 8720 8652 7569 7873 6964 7917 7980 22892 21 gggagagatggctgagtggac Grivet et al. 2001

trnS0rr 37232 36984 34281 35404 35531 11591 51748 41495 21 gggagagatggctgagtggac Grivet et al. 2001

trnS0rrr trnS 47118 46779 44023 44826 45277 79864 21 gggagagatggctgagtggac Grivet et al. 2001

trnS1-M trnS R 47138 46799 44043 44846 45297 44457 79884 41475 22 aaccactcggccatctctccta Demesure et al. 1995

trnS1-MM 37212 36964 34261 35384 35511 11571 70507 22909 22 aaccactcggccatctctccta Demesure et al. 1995

trnS1-MMM trnS 8700 8632 7549 7853 6944 7897 22 aaccactcggccatctctccta Demesure et al 1995

trnS1-P trnS F 47180 46841 44085 44888 45339 44499 70465 22954 20 cgagggttcgaatccctctc Demesure et al. 1995 further match Pinus: 79927

trnS1-PP 37165 36916 34213 35337 35466 11528 51811 48907 20 cgagggttcgaatccctctc Demesure et al. 1995

trnS1-PPP trnS 8657 8589 7506 7810 6901 7854 7917 20 cgagggttcgaatccctctc Demesure et al. 2005

trnS-M trnS R 37161 36912 34209 35333 35462 11524 51815 41428 20 ggttcgaatccctctctctc Demesure et al. 1995

trnS-MM trnS 8653 8585 7502 7806 6897 7850 7913 22958 20 ggttcgaatccctctctctc Demesure et al. 1995

trnS-MMM trnS 47184 46845 44089 44892 45343 44503 79931 48911 20 ggttcgaatccctctctctc Demesure et al. 1995

trnS-P trnS F 37142 36893 34190 35314 35443 11505 51834 41409 20 gagagagagggattcgaacc Demesure et al. 1995

trnS-PP trnS 8634 8566 7483 7787 6878 7831 7894 22977 20 gagagagagggattcgaacc Demesure et al. 1995

trnS-PPP trnS 47203 46864 44108 44911 45362 44522 79950 48930 20 gagagagagggattcgaacc Demesure et al. 1995

trnS-SC-F trnS F 8660 8592 7509 7813 6904 7857 7920 22951 20 taccgagggttcgaatc Souza-Chies et al. 1997

trnS-SC-FF 37168 36919 34217 35340 35469 11528 51808 48904 20 taccgagggttcgaatc Souza-Chies et al. 1997

trnS-SC-FFF trnS 47177 46838 44082 44885 45336 44496 70468 20 taccgagggttcgaatc Souza-Chies et al. 1997

trnT(UGU)2F-trnA2 trnT F 48551 48211 45541 46251 46520 45753 69209 20 CAAATGCGATGCTCTAACCT Cronn et al., 2002

trnT(UGU)R Shaw trnT R 48570 48230 45560 46270 46539 45772 69190 20 AGGTTAGAGCATCGCATTTG Shaw et al. 2005

trnT-f trnT F 33180 32977 30262 31369 31264 15060 50236 38367 20 gcccttttaactcagtggta Dumolin-Lapegue et al. 1997 second match Pinus: 83939

trnT-M trnT R 48565 48225 45555 46265 46534 45767 69195 20 agagcatcgcatttgtaatg Demesure et al. 1995

trnT-M(P*) trnT R 33200 32997 30282 31389 31284 15080 50216 38387 20 ctaccactgagttaaaaggg Demesure et al. 1995 second match Pinus: 83919

trnV1-r trnV exon2 R 53790 53436 50046 51234 51873 50402 48013 53086 20 ccgagaaggtctacggttcg Dumolin-Lapegue et al. 1997

trnV2-f trnV exon2 F 53771 53417 50027 51215 51854 50383 48032 53067 20 cgaaccgtagaccttctcgg Dumolin-Lapegue et al. 1997

trnV-P5 trnV intron R 53855 53501 50111 51299 51938 50467 47948 53137 29 aaatgcatgttgggttcttkraacagttc this publication minor mismatches with tobacco as indicated

trnY(GUA) Shaw trnY F 32120 31897 29587 30327 30812 15863 28734 36566 19 CCGAGCTGGATTTGAACCA Shaw et al. 2005

ucp-a/trnT-f trnT F 48546 48206 45536 46246 46515 45748 69214 20 cattacaaatgcgatgctct Taberlet et al. 1991

ucp-b/trnL-r trnL exon1 R 49318 48965 46234 47050 46580 2417 50544 20 tctaccgatttcgccatatc Taberlet et al. 1991 second match Atropa: 116874; Populus:115766

ucp-c trnL exon1 F 49306 48953 46222 46904 47038 46568 68739 20 cgaaatcggtagacgctacg Taberlet et al. 1991

ucp-d trnL exon2 R 49882 49523 46599 47489 47707 47181 68178 50920 20 ggggatagagggacttgaac Taberlet et al. 1991

ucp-e trnL exon2 F 49862 49503 46579 47469 47687 47161 68198 50900 20 ggttcaagtccctctatccc Taberlet et al. 1991

ucp-f/trnF-r trnF R 50299 49946 46996 48234 48080 47484 67738 51057 20 atttgaactggtgacacgag Taberlet et al. 1991

ycf10-f1 ycf4=ORF184 F 63509 63710 59780 23 AATCTTGGGTTACCAATTGGTGG this publication

ycf10-f2 ycf4=ORF184 F 63987 24 CKKKTYTTGTTTCNAYHTTKCCAG this publication

ycf10-r1 ycf4=ORF184 R 63533 21 TTCCACCAATYNDTAAHCCAA this publication

ycf3-3f ycf3 exon3 F 44366 23 CCCTGTHGAATSGCYTGTTCTCC this publication

ycf3-3r ycf3 exon3 R 44352 23 GCRGARGCTTGGTTYGATCAAGC this publication

ycf4-f2 ycf4=ORF184 F 62957 24 GGGGATTYCCKGGAAWAARHCGTC this publication

ycf4-f3 ycf4=ORF184 F 63163 22 TTCTTGCGYGTAYCMATKGAAG this publication

ycf4-r1 ycf4=ORF184 R 62749 62416 59883 51457 22 ctaataagaagcctaatgaacc this publication

ycf4-r2 ycf4=ORF184 R 62685 62352 59819 23 agaccccgttataagwtctatcc this publication

ycf4-r3 ycf4=ORF184 R 63184 62851 59099 60318 61091 39732 22 CTTCAATTGGTACACGCAAGAA this publication

ycf6 f ycf6 F 29554 29358 27304 28108 27560 17626 26797 5238 18 CTTGGGCTGCTTTAATGG this publication

ycf6 r1 ycf6 R 29570 29374 27320 28124 27576 17610 26813 5222 18 CATTAAAGCAGCCCAAGC this publication

ycf6 r2 ycf6 R 29573 29377 27323 28127 27579 17607 26816 5219 20 TACCATTAAAGCAGCCCAAG this publication

ycf6F Shaw ycf6 F 29535 29339 28370 28089 27541 17645 26 ATGGATATAGTAAGTCTYGCTTGGGC Shaw et al. 2005

ycf6R Shaw ycf6 R 29560 29364 28114 27566 17620 26 GCCCAAGCRAGACTTACTATATCCAT Shaw et al. 2005

ycf9-M ycf9 R 37624 37363 34674 35781 35937 11967 41677 22 caaamacagccaattggaaagc this publication

ycf9-P ycf9 F 37619 24 TTGCYTCTCCYGATGGYTGG this publication

A data base for PCR primers in the chloroplast genome
Primer sequence data