Supplementary information

Suppl.Table 1 DNA primers used in the study

Primers / Sequences / Annealing Temperature (°C) / Amplicon Size
1Ac-1 forward / 5′GGATCCATGGACAACAACC3′ / 65 / 1770
1Ac-1 reverse / 5′ACACCCACGATGTTACCGAG3′
nptII forward / 5′TCTTCTCCAATACAGTTCCAGC3′ / 58 / 800
nptII reverse / 5′ACACCCACGATGTTACCGAG3′
1Ac-2 forward / 5′AGAGTTCGTGTGAGGTATGCT3′ / 63 / 160
1Ac-2 reverse / 5′ACTGTATTGGAGAAGATGGATGAAT3′
CAC forward / 5′CCTCCGTTGTGATGTAACTGG3′ / 63 / 170
CAC reverse / 5′ATTGGTGGAAAGTAACATCATCG3′
ad1 / 5′NTCGASTWTSGWGTT3′ / - / -
ad2 / 5′NGTCGASWGANAWGAA3′ / - / -
ad3 / 5′WGTGNAGWANCANAGA3′ / - / -
ad20 / 5′TCTTICGNACITNGGA3′ / - / -
w4 / 5′AGWGNAGWANCANAGA3′ / - / -
cry31 / 5′ACACCAGATCATGGCCTCTC3′ / - / -
cry32 / 5′TTCCGTGAGCATCATCAGAG3′ / - / -
cry33 / 5′TCCAGCGATTTCGGTTACTT3′ / - / -
cry51 / 5′TCTGATGATGCTCACGGAAC3′ / - / -
cry52 / 5′AGCGTGGTCGGTGTAGTTTC3′ / - / -
cry53 / 5′GGAGATGTCGATGGGAGTGT3′ / - / -

Suppl.Table 2 TAIL-PCR fragments that are matched to tomato genome

ID / 3' TAIL-PCR product 1 match to tomato chromosomes / 3' TAIL-PCR product 1 match to tomato MIPS repeat collection / 3' TAIL-PCR product 2 match to tomato chromosomes / 3' TAIL-PCR product 2 match to tomato MIPS repeat collection
T1-22 / >SL2.50ch05
(Length = 65875088, Score = 623 bits (311), Expect = e-176
Identities = 317/319 (99%))
acatgatattttgggaaaggggaaattagccctcatgatttccaacttagtctgctgaaactcatattgcaagtggcagatatagtcataaaattggtgattccacggactgacttccgtactgtacatctttatgagttcatctgcagcaccgtggaacaatgctcgaacttttccccagctgacatctggttgatctttgaagatatgcaattcgataatgatactcaggaagttggaatcccttttaaggagcctcagtctatcaaacaaagacatatgttcttctgaaaagaaatcgaaggaactccattcatct / - / >SL2.50ch05
(Length = 65875088, Score = 622 bits (311), Expect = e-176 Identities = 317/319 (99%)) acatgatattttgggaaaggggaaattagccctcatgatttccaactagtctgctgaaactcatattgcaagtggcagatatagtcataaaattggtgattccacggactgacttccgtactgtacatctttatgagttcatctgcagcaccgtggaacaatgctcgaacttttccccagctgacatctggttgatctttgaagatatgcaattcgataatgatactcaggaagttggaatcccttttaaggagcctcagtctatcaaacaaagacatatgttcttctgaaaagaaatcgaaggaactccattcatct / -
T1-20 / - / - / - / -
T1-25 / - / - / - / >k_29 |mips:kai|02.01.02.10 SINE|rptmsk SINE|tigr TERT04
(Length = 680, Score = 229 bits (114), Expect = 1e-59
Identities = 133/137 (97%), Gaps = 3/137 (2%))
cgtcgttttacaacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatccccctttcgccagctggtaattaacgaagaggcccgcaccgatcgcccttcccaacagttgcgcagc
T1-18 / - / >k_29 |mips:kai|02.01.02.10 SINE|rptmsk SINE|tigr TERT04
(Length = 680, Score = 228 bits (114), Expect = 1e-59 Identities = 133/137 (97%), Gaps = 3/137 (2%))
cgtcgttttacaacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatccccctttcgccagctggtaattaacgaagaggcccgcaccgatcgccctt cccaacagttgcgcagc / >k_29 |mips:kai|02.01.02.10 SINE|rptmsk SINE|tigr TERT04
(Length = 680, Score = 229 bits (114), Expect = 8e-60
Identities = 133/137 (97%), Gaps = 3/137 (2%))
cgtcgttttacaacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatccccctttcgccagctggtaattaacgaagaggcccgcaccgatcgcccttcccaacagttgcgcagc
ID / 5' TAIL-PCR product 1 match to tomato chromosomes / 5' TAIL-PCR product 1 match to tomato MIPS repeat collection / 5' TAIL-PCR product 2 match to tomato chromosomes / 5' TAIL-PCR product 2 match to tomato MIPS repeat collection
T1-22 / >SL2.50ch06
(Length = 49751636 , Score = 2096 bits (1049), Expect = 0.0 Identities = 1068/1073 (99%), Gaps = 1/1073 (0%))
agtagcacagatgcaacgattggctaacatcgtagggtgcaagattgagcgattcccaacaacttaattgggaatacctctgggaagcaatcataaagaatcactgatacgggatgggataatccagaggtcagagaagaagttcgccaaataaaaatctcaatacttgtcacttgggggcagacaaacactaataaatgcactgctggacaccctccccacatatgtcaggtctctatttcccttaccagctaaggtgccggaaaaattggacaaaattaaaagagactttctttggtatggaaataaagaaaagaaggggcactatcttgttaactgggtaacagtgcagctacctaagctccaaggtggtcttggagttaggaatcttcgaatctataatgagtgcctcttgatgaaatggttctggagatatgtggaagaagaacaggctctttggagagaagtcatacatcacaagtatgacccccaatggtgtatcaatgaggccagtataccatatggagtttcaacatggaaaacaataagatccttctggaccaaactagcaggaaacatcaaactcaaaataggaaatggagctaaagtactattccggaaagatgtttgagtaaagacgagatattaaaacaatctttccctgacttatttctttctgcagcaatataaatatactctagctgagagttgggcaaatggttgggatatatctttcaggagaaatttcaatgactggaaaatagatagggtggcacaattgttacatgcaatcgaagagtttattggtttagctggaaggccagacacagtctcgtggatacactctgaggatgtaaggtttacagttaacaaactctataaaaaggatctgaaaactcagcaaggcctcagattagctggatggaaatatgtatggacaagccaagaaccaaccaagatcaaatgttttgtatggttggtagctagagggcttgtctgactcaggaggtactgcaggtactgcagaggaaagatgcactactagtaccaaggtgttttctatgcaatgagac / >PRSiTERT00300001 |tigr: Solanaceae.v2|02.01.02.05 LINE|rptmsk LINE|tigr TERT03
(Length = 3585, Score = 1005 bits (503), Expect = 0.0 Identities = 945/1082 (87%), Gaps = 29/1082 (2%))
cacagatgcaaagattggctaacatactaaggtgcaagatcgagcaattcccgacaacttacttgggaatgcctctgggaagcaaccataacgaactactgatattgggatgggataatccagaggtcagagaagaagttagccatatggaaatctcaatacttgtcaattgggggccgacaaacataataaatgtagtgctggactccctccccacttatatcatgtctctatttacctgctaaggtgctggagaaattggacaaacttagaagagactttctttggtttgggaacaaagaaacgaaggggtactatctagttaactggaaacagtgcagctacctaagctctcaggtggtcttggagttaggaatcttcgaatccataatgagtgcctcttgatgaaatggctgtggagatatgtggaagaagggcatgctctttggagagaagttatacagcacaagtatggacaagactccctaacggtgtgccaatgaggtcacactataccatatggagtttcaatatggaaaacaataagatccttctggaccaaactagcaggaaacatcaaactcataataggaaatggagctaaaattctattttgtaaagatgtttgggtaagacatgaggcattaatgcaatctttccctgacttattttctttctgtagcaatccagatatcactctagctgagagttgggaaaatggttgggatatatcttttaggagacatttcaatgactgggaaatagatagggtggcacaattgttacatgtaatcaatgagtttaatggttttgctacaaggccagacacaatctcgtgggtacactctgaggatggaagattcacagttaacaagctctataagaaggaaatgggaactcaacaaggcctcagattggcttgatggaaatatgtatggacaagccaagcaccaaccaagatcaaatgttttgtatggttggtagctaagagggcttgtctgacacaggaggtactgcaaaggaaaggtgtacaactagtaccaaggtgttttctatgcaatgagaca / - / -
T1-20 / - / - / >SL2.50ch04
Length = 66470942 ( Score = 1951 bits (974), Expect = 0.0
Identities = 997/1002 (99%), Gaps = 2/1002 (0%))
cgtacgtgggagatcaatgtttgtcaccccgtataccctcctggtcattggctctgatgatgagcgtgagtgcgagtacgtgcccccaagctctgccactcttttacgatctacatgtgctaccagagctacacccaaaaaggtggcatccggcgtagtcactgcctcccattctgatgatgagcacacactaaccggcacattttctgggtcagctacttatgaagatggagcgtctagcttcttaggagtttcgtggtcggaggaagcctcctggtctgctgaagtcctgcacctggcacagctacacagtctgtctcgtctaataaggctgacagttctaatatcactcccgtctcatcgactcgtgctctcaccccggttgccaaccagcacaaccggtggtgtatcaacgggacaatatcaattttattcagacgccaagtttttgaatgataaagaagtcatgacacggacccttacataggagaggcggttctgtatgggaagtctccctacgatgcaagagatccataatctcttcaccagaaagcgactgaagtggacaacacgttcgttgtaccgttatagtaaagagttagtccgagagttctacgcctcttacgtggctactcttagatcacaaaattattggcgggatgctcccgccaaatagtccccacttgagcatgttcgagtatgtggcatttatgtcaatatttccgtgcctgccatccaccattatctatacggtgaagatattgatgccaaccggacccctctcatcgcttagttcgactatcggtggcaaattgtcaaagatggtcaattcttgagtgagccatcgctgagagagaccacaaagaggtggatggccctgcacttgtctgttgatggagagggtgccgactgggtaagagagccgaagggagacatcaagaaggaaaacttgaccttcacggctaagatctcatggttgattgtccgccactgcctttttcc
T1-25 / - / >k_29 |mips:kai|02.01.02.10 SINE|rptmsk SINE|tigr TERT04
Length = 680
( Score = 228 bits (114), Expect = 2e-59
Identities = 133/137 (97%), Gaps = 3/137 (2%))
cgtcgttttacaacgtcgtgactgggaaaaccctggcgttacccaacttaatcgccttgcagcacatccccctttcgccagctggtaattaacgaagaggcccgcaccgatcgcccttcccaacagttgcgcagc / - / >camv |Waksman|02.01 Retroelement|rptmsk -|tigr TERT
Length = 8031
( Score = 596 bits (298), Expect = e-170
Identities = 334/346 (96%))
attgagacttttcaacaaagggtaatatcgggaaacctcctcggattccattgcccagctatctgtcacttcatcaaaaggacagtagaaaaggaaggtggcacctacaaatgccatcattgcgataaaggaaaggctatcgttcaagatgcctctgccgacagtggtcccaaagatggacccccacccacgaggagcatcgtggaaaaagaagacgttccaaccacgtcttcaaagcaagtggattgatgtgatatctccactgacgtaagggatgacgcacaatcccactatccttcgcaagacccttcctctatataaggaagttcatttcatttggagagga
T1-18 / camv |Waksman|02.01 Retroelement|rptmsk -|tigr TERT
Length = 8031
(Score = 409 bits (203), Expect = e-114
Identities = 285/310 (91%), Gaps = 6/310 (1%))
tcttgcgaaggatagtgggattgtgcgtcatcccttacgtcagtggagatatcacatcaatccacttgctttgaagacgtggttggaacgtcttctttttccacgatgctcctcgtgggtgggggtccatctttgggaccactgtcggcagaggcatcttgaacgatagcctttcctttatcgcaatgatggcatttgtaggtgccaccttccttttctactgtccttttgatgaagtgacagatagctgggcaatggaatccgaggaggtttcccgatattaccctttgttgaaaagtctcaat / - / >camv |Waksman|02.01 Retroelement|rptmsk -|tigr TERT
Length = 8031
(Score = 472 bits (236), Expect = e-133
Identities = 312/332 (93%), Gaps = 5/332 (1%))
attgagacttttcaacaaagggtaatatcgggaaacctcctcggattccattgcccagctatctgtcacttcatcaaaaggacagtagaaaaggaaggtggcacctacaaatgccatcattgcgataaaggaaaggctatcgttcaagatgcctctgccgacagtggtcccaaagatggacccccacccacgaggagcatcgtggaaaaagaagacgttccaaccacgtcttcaaagcaagtggattgatgtgatatctccactgacgtaagggatgacgcacaatcccactatccttcgcaagacccttcctctatataaggaagttcatt

Suppl Figure Captions

Suppl. Fig. 1 T-DNA region containing cry1Ac gene within pRD400 plasmid.

Suppl. Fig. 2 PCR results for screening transformed T0 plants with 1Ac-1 primer. Non-transgenic Moneymaker tomato DNA was used as negative control (-). Plasmid DNA containing cry1Ac construct was used as positive control (+). Numbered samples (1-15) are T0 plants regenerated after genetic transformation. Transformed individuals contain the expected 1.8 kb amplification product.

Suppl. Fig. 3 Detection of Cry1Ac protein expression in transgenic tomato plants by Western Blot analysis. Cry1Acprotein (60 kDa) was detected using anti-Cry1Ac polyclonal antibodies. In left panel, the SDS-PAGE gel was stained with Commassie brilliant blue for control of protein loading. In the right panel, the blot is shown after immune detection.

Suppl. Fig. 1

Suppl. Fig. 2

Suppl. Fig. 3