Supplementary Figure 1. HPLC chromatograms of the authentic standards (A) and the methanol extracts from the dried latex of P. somniferum WT plant (B) and the representative transformants (C to F).

0.20

32.913

29.861

27.001

27.893

33.899 36.868

20.854

–

–

–

–

– – –

0.15 11.972

– Thebaine

0.10 Coptisine

Palmatine Palmatine Berberine

Papaverine -24.958

AU

Morphine- 7.308

Columbamine Columbamine

Oripavine

Sanguinarine Sanguinarine

Isothebaine -18.134

[AU]

Jateorrhizine Jateorrhizine - 14.262

0.05

Noscapine- 26.093

Methylcodeine- 15.384

Magnoflorine- 13.756 - 9.847

0.00 0.00 2.00 4.00 6.00 8.00 10.00 12.00 14.00 16.00 18.00 20.00 22.00 24.00 26.00 28.00 30.00 32.00 34.00 36.00 38.00 40.00 [min][min]分 (A) Standards

0.08

0.06

0.04

AU [AU]

0.02 Noscapine- 26.016

Morphine- 7.294

Papaverine -25.093 Codeine- 9.843

0.00

0.00 2.00 4.00 6.00 8.00 10.00 12.00 14.00 16.00 18.00 20.00 22.00 24.00 26.00 28.00 30.00 32.00 34.00 36.00 38.00 40.00 [min]分 (B) WT1

0.14

0.12 20.732 – 0.10

0.08

Thebaine Thebaine AU

[AU] 0.06

0.04

0.02 Papaverine -25.051

Noscapine- 25.992

Codeine- 9.821 Morphine- 7.246 0.00 0.00 2.00 4.00 6.00 8.00 10.00 12.00 14.00 16.00 18.00 20.00 22.00 24.00 26.00 28.00 30.00 32.00 34.00 36.00 38.00 40.00 [min]分 (C) T1 #1-27(HT) PCR Inverse Method PCR

[AU]AU [AU]AU [AU]AU 0.030 0.040 0.050 0.000 0.010 0.020 0.00 0.05 0.10 0.15 0.20 0.00 0.02 0.04 0.06 0.08 0.10 0.12 0.14 and obtained amplified DNA in analyses of the fragments T TableSupplementary 0.00 0.00 0.00

RB RB RB RB LB LB LB Region 2.00 2.00 2.00

4.00 4.00 4.00

Kpn Eco Eco Bam Kpn Kpn Hae Library * 6.00 6.00 6.00 RV RV III I I I HI Morphine - 7.264 8.00 Morphine - 7.178 Morphine - 7.295 8.00

8.00

1 10.00 10.00 10.00 . 14997S 14997S 14 14738S 490S 75S 490S Codeine - 9.854 Codeine - 9.836

Summary of the used PCR methods, DNA libraries, primer sets, sets, primer DNA libraries, methods, PCR used the of Summary Codeine - 9.822 738S 12.00 12.00

12.00

1st PCR 1st

14.00 14.00 14.00 14981A 14981A 14408A 12909A 401A 58A 401A ( D ( ( E 16.00 16.00 F

16.00 ) Primer Set

) ) T

T T 1 1 1

18.00 18.00 18.00 #

# # 2 2 2 15011S 15011S 14765S 14765S 510S 80S 510S - - [min] - [min] 1 [min] 6(LT) 1(LT) 20.00 20.00 20.00 7(HT) 分 分 分

Thebaine – 20.744 PCR 2nd Thebaine - 20.907 Thebaine - 20.898 22.00 22.00

22.00

14960A 14960A 14307A 12878A 368A 52A 368A 24.00 24.00 24.00 -

DNA loci. insertion

Papaverine - 25.076 Papaverine - 25.063 26.00 Papaverine - 25.112 26.00 26.00

Noscapine - 26.055 Noscapine - 25.976 Noscapine - 26.009 Tandem 1 riorf13 3; 2, RB1, Tandem 1 RB4 LB1; Tandem 1 Tandem 2 Tandem riorf13 5,6; 2, 1, 28.00 28.00 28.00 Description

30.00 30.00 30.00 - 3

32.00 32.00 32.00 Product(s)

34.00 34.00 34.00

of of Amplified

36.00 36.00 36.00

- 38.00 1, 2 1, 38.00 38.00

40.00 40.00 40.00

Supplementary Table 1. Cont.

PCR Primer Set Description of Amplified Region Library * Method 1st PCR 2nd PCR Product(s) RB PvuII 14738S 12909A 14765S 12878A RB4 Inverse RB SspI 14738S 14408A 14765S 14307A RB4; Tandem 1, 4 PCR RB StuI 14738S 14408A 14765S 14307A RB4; Tandem 5 LB EcoRV AP1 401A AP2 368A Tandem 2; riorf13-1, 2 LB HaeIII AP1 401A AP2 368A LB2, 3, 4; Tandem 5 LB PvuII AP1 401A AP2 368A LB2; Tandem 1, 2; riorf13-1, 2 Adaptor- LB SspI AP1 237A AP2 226A LB2; Tandem 1, 2, 5; riorf13-1, 2 ligation LB StuI AP1 401A AP2 368A Tandem 4, 6; riorf13-1 PCR RB EcoRV 14738S AP1 14765S AP2 RB1, 2, 3; Tandem 1; riorf13-3 RB HaeIII 14963S AP1 14997S AP2 RB5, 6; Tandem 6; riorf13-4 RB PvuII 14738S AP1 14765S AP2 RB3, 4; riorf13-4 Genome RB, LB un cut 14738S 401A 14765S 368A Tandem 1 direct RB, LB un cut 14738S 401A ** Tandem 1, 3, 4 PCR * Restriction enzymes used for library construction are shown; ** 1st PCR only, anneal 62 °C .

Supplementary Table 2. List of the sequences (from 5' to 3') of the primers and the oligo-DNAs used for IPCR, AL-PCR, and genome direct PCR. Left Border Primers Sense Primers Anti-Sense Primers 75S ATT ACC AGA TGG TGT CCG GG 52A TCG CTT CAA AGC TCT TGT AC 80S CAG ATG GTG TCC GGG TAT G 58A CGA AAA TCG CTT CAA AGC TC 490S GAG CAA CGA CGT TTC AGT GC 226A TTG TTG CAC GGC GAC GAT TGG 510S ATT CCT GTA CTC GCT TTC CG 237A AGG CTC ACG TAT TGT TGC ACG 368A AAC TCG TAC GGC ATA GTC GG 401A TCA ACT TGT GGC GAG TCT CC Right Border Primers Sense Primers Anti-Sense Primers 14738S TAA CCT CGC ACG TAT GGT GC 12878A CAT GCT CAT GCT TTA GCA GG 14765S GAC GTC GAT TTC GAT GTG G 12909A TGC CTT CCA ATT GAC GCT C 14963S AGC CGA CAA CGT GCA ATT TGC 14307A CAA TTT TCT TGA CCG AAG CC 14997S GAG CCA CCT GCC TTC AGA CC 14408A AGG TGC CAC AGT CCG ACT G 15011S CAG ACC TAC TGT TTG CTG CG 14960A ATA ATT TAG AGC ATT GCG GG 14981A AAA TTG CAC GTT GTC GGC TG Adaptor Oligo DNAs AP-LS CGTTGAGAGGCATTATCTTCGGGCTAAGGCGTCGTCGCGACGTCACGC

AP-SS * (PO4)-GCGTGACGTC-(NH2) Adaptor Specific Primers AP1 CGT TGA GAG GCA TTA TCT TCG G AP2 TTA TCT TCG GGC TAA GGC G * AP-SS: 5'-end phosphorylated, 3'-end amino-linked. Supplementary Table 3. List of the primers used for the analysis of inheritance manner of T-DNA integration loci by PCR. Target Region Primer Name Orientation Sequence (from 5' to 3') Left border genomic region primers LB1g LB1gex-S1 sense TAA TCA CGA TGT ACC CGT AGC LB2g LB2g-1072S sense CGT CGT TGT ATG ATG AAT CGC LB3g HaeLB3g-S1 sense CAA CAG TTC GCA GGC AAG TC LB4g HaeLB4g-S1 sense TGA CTA ATC CTG ACT CCA ACC Right border genomic region priers RB1g RB1g-460A anti-sense AGA ACC TTC GTA TGG CAG ATG RB2g RB2g-393A anti-sense CAA TCC TGC CTC CTA CAA TTC RB3g RB3g-588A anti-sense GGT CCA TTG ATA TGG CTA CTC RB4g RB4g-261A anti-sense TCG AAT CGA CGT AAA CTC TCC RB5g HaeRB5g-A1 anti-sense CCT GCA ACA ACT AAC AAC GAG RB6g HaeRB6g-A1 anti-sense GGG TGG TAT TGT AAC TTC ACT C T-DNA border primers T-DNA RB MAFF-226A anti-sense TTG TTG CAC GGC GAC GAT TGG T-DNA LB MAFF-14963S sense AGC CGA CAA CGT GCA ATT TGC

Supplementary Table 4. List of the primers used for the estimation of T-DNA copy number by real-time PCR. Target Region Primer Name Orientation Sequence (from 5' to 3') LB1-genome DNA LBm-S sense GCAGTAGTATCACTGACAAATCGCAC (LB1g) LBm-A anti-sense CCAGTAACACCCTGGGAATCC LB1-junction LBjm-S sense GGGGTAAACTCATCCAAACACAC (LB1j) LBjm-A anti-sense AAAACGTGCTCGAAAATCGC orf2m-S sense TCCGATGGAGCATTTCTATGG orf2 orf2m-A anti-sense ATGATCTACACGCGGAAGAAGC

Supplementary Table 5. List of the primers used for the RT-PCR analysis of selected morphine biosynthetic genes. Target Gene Accession No. Primer Name Orientation Sequence (from 5' to 3') PsCYP80B3-878S sense CAATAGAATGGGCGTTGTCTG CYP80B3 AF134590 PsCYP80B3-1377A anti-sense ATGATCAGTTGGCTAGGATCC Ps4'OMT-552S sense AGATTGTAGAGATACTTTTCAAGG 4'OMT1 AY217333 Ps4'OMT-1021A anti-sense TGATCTTATGAGACCGAAAGC PsSalAT-832S sense TCTCTAATATGGAAGTCCGTG SalAT AF339913 PsSalAT-1389A anti-sense GAACTTAGCCATATCATCCTC PsCor1-467S sense TTGGCTTCACTAGGGCAATCG Cor1-1 AF108432 PsCor1-958A anti-sense CTCATCCCAGAACTCTTCTTC PsCor2-463S sense ATGCTTGGATTAACCAAGTCG Cor2-1 AF108438 PsCor2-887A anti-sense AAGGATCACCGGTTGACACTC T6ODM-S2 sense CTCTACAAGTACAAGCAGCC T6ODM GQ500139 T6ODM-RTa anti-sense TCTGACATGCAATCACGTCG CODM-RTs sense GACTTATTTGAAGATGGGTTG CODM GQ500141 CODM-A2 anti-sense CTTCAAAATATCCTCATACCTACC PsACT1-145S sense CACACTGTGCCAATCTATGAG PsACT1 AB574417 PsACT1-488A anti-sense TGGATACCAGCAGCTTCCATC