Supplemental Table 1. Genomic localization and annotation of T-DNA insertions.

Linea / Genomic localizationb / Sequence annotationc / Predicted gene orthologue / Molecular function
NE-A1 / chr 6 (+) 23260453 / Exon 11 of gene GIDVvT00038119001
NE-A2 / chr 6 (-) 15965414 / 5’ flanking region at 459 bp from the gene GSVIVT00024002001 / AT2G31540.1 (Arabidopsis thaliana)
01_06_1206 (Oryza sativa)
jgi|Poptr1_1|774050|fgene (Populus trichocarpa) / GO:0006629 lipid metabolic process
NE-B / chr 18 (+) 6378102 / Intron 4 of gene GSVIVT00015055001
NE-C / chr 4 (+) 12285639 / Intron 5 of gene GSVIVT00025021001 / AT4G36860.2 (Arabidopsis thaliana) / GO:0008270 zinc ion binding
NE-E / chr 19 (+) 9259618 / 3’ flanking region at 1081 bp from the gene
GSVIVT00033444001
NE-F / chr 5 (-) 19924989 / 5’ flanking region at 558 bp from the gene GSVIVT00019823001 / AT1G54610.1 (Arabidopsis thaliana)
07_03_1614 (Oryza sativa)
jgi|Poptr1_1|420526|gw1.V(Populus trichocarpa) / GO:0004672 protein kinase activity
GO:0005524 ATP binding
GO:0004713 protein-tyrosine kinase activity
GO:0004674 protein serine/threonine kinase activity
NE-G / chr 7 (-) 11329380 / 3’ flanking region at 1519 bp from the gene GSVIVT00028055001 / AT2G47490.1 (Arabidopsis thaliana)
05_03_0668 (Oryza sativa)
jgi|Poptr1_1|755602|fgene (Populus trichocarpa) / GO:0005488 binding
GO:0005215 transporter activity
LU / chr 14 (+) 19219303 / Intron 1 of gene GIDVvT00035463001
BF-A / chr 8 (+) 9327423 / Intron 1 of gene GSVIVT00037473001 / jgi|Poptr1_1|577152|eugen (Populus trichocarpa) / GO:0004672 protein kinase activity
GO:0004713 protein-tyrosine kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0005524 ATP binding
110R / chr 5 (+) 20921511 / Intron 11 of gene GSVIVT00001977001
R3-11 / chr 10 (-) 2806782 / Intergenic
R3-12 / chr 13 (+) 2499733 / Intron 4 of gene GSVIVT00018550001 / AT3G55320.1 (Arabidopsis thaliana)
03_02_0569 (Oryza sativa)
jgi|Poptr1_1|833831|estEx (Populus trichocarpa) / GO:0005524 ATP binding
GO:0016887 ATase activity
GO:0000166 nucleotide binding
GO:0017111 nucleoside-triphosphatase activity
R3-2 / chr 6 (+) 8586666 / Exon of gene GSVIVT00023954001 / jgi|Poptr1_1|774064|fgene (Populus trichocarpa)
R3-6 / chr 13 (-) 4574336 / Intron 4 of gene GSVIVT00001691001
R3-7 / chr 17 (-) 5488467 / Exon 4 of gene GSVIVT00016271001 / 03_04_0133 (Oryza sativa) / GO:0003677 DNA binding
R3-11 / chr 12 (+) 3291205 / Exon 3 of gene GSVIVT00018694001
R3-12 / chr 7 (+) 6430795 / 5’ flanking region at 189 bp from the gene GSVIVT00007519001 / jgi|Poptr1_1|205794|gw1.V(Populus trichocarpa) / GO:0003700 transcription factor activity
R3-13 / chr 10 (-) 6935900 / Exon 1 of gene GSVIVT00028281001 / AT1G30040.1 (Arabidopsis thaliana)
01_06_0761 (Oryza sativa)
jgi|Poptr1_1|758699|fgene (Populus trichocarpa) / GO:0005506 iron ion binding
GO:0016216 isopenicillin-N synthase activity
R3-14 / chr 17 (+) 3721857 / Intergenic
R3-18 / chrUn_random (+) 128209966 / Intron 23 of gene GSVIVT00033781001 / AT5G58100.1 (Arabidopsis thaliana)
02_03_0171 (Oryza sativa)
jgi|Poptr1_1|560714|eugen(Populus trichocarpa)
R3-19 / chr 19 (-) 4221580 / Intron 1 of gene GSVIVT00014156001 / GO:0030693 caspase activity
R3-20 / chr 8 (+) 16138946 / Intron 9 of gene GSVIVT00021598001 / AT5G03910.1 (Arabidopsis thaliana)
04_03_0867 (Oryza sativa)
jgi|Poptr1_1|416282|gw1.V(Populus trichocarpa) / GO:0005524 ATP binding
GO:0016887 ATase activity
GO:0000166 nucleotide binding
GO:0017111 nucleoside-triphosphatase activity
R3-21 / chrUn_random (-) 82389966 / Intron 3 of gene GIDVvT00019525001
R3-25 / chr 19 (+) 2576906 / Intron 3 of gene GSVIVT00027709001 / AT5G53850.2 (Arabidopsis thaliana)
11_04_0330 (Oryza sativa)
jgi|Poptr1_1|827604|estEx (Populus trichocarpa) / GO:0046872 metal ion binding
GO:0003824 catalytic activity
GO:0008967 phosphoglycolate phosphatise activity
R3-34 / chr 4 (+) 11405600 / Intron 7 of gene GSVIVT00025101001 / AT3G02830.1 (Arabidopsis thaliana)
01_06_1805 (Oryza sativa)
jgi|Poptr1_1|424416|gw1.8(Populus trichocarpa) / GO:0003676 nucleic acid binding
GO:0008270 zinc ion binding
R3-35 / chrUn_random (-) 18642041 / 3’ flanking region at 413 bp from the gene GSVIVT00037301001 / GO:0006807 nitrogen compound metabolism
R3-37 / chr 7 (+) 3505401 / Intron 1 of gene GSVIVT00028001001 / AT1G02850.2 (Arabidopsis thaliana)
05_04_0043 (Oryza sativa) / GO:0015926 glucosidase activity
GO:0003824 catalytic activity
GO:0043169 cation binding
R3-38 / chrUn_random (-) 91012788 / 3’ flanking region at 932 bp from the gene GIDVvT00023319001

a In multicopy lines NE-A and R3-1 two different T-DNA integrations were isolated and are indicated respectively as NE A1, NE-A2, and R3-11, R3-12.

b Genomic localization refers to the genome sequence draft of the grapevine line PN40024 (Jaillon et al. 2007). In parentheses is indicated the strand polarity of the chromosome in which T-DNA was integrated.

c Sequence annotation refers to gene prediction from the genome sequence draft of the grapevine line PN40024 (Jaillon et al. 2007)

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Supplemental Fig. 1 Sequence microsimilarities between grapevine DNA and T-DNA RB (A) and T-DNA LB (B). T-DNA border repeats are shown in bold letters. The underlined sequences represent grapevine DNA , sequences in italics are duplicated grapevine DNA, while lowercase nucleotides are filler DNA. Nucleotide identities are shown as shaded letters: dark grey shading representing jointing points and light grey shading representing microsimilarities. For every transgenic grapevine the top sequence is the binary vector pGA643, the middle sequence is the point of junction between the T-DNA and grapevine DNA and the bottom sequence is the grapevine DNA before T-DNA integration


Supplemental Fig. 2 Molecular characterization of vector backbone sequences of some transgenic grapevine plants. Southern analysis of DNA digested with SacII (A) and EcoRI (B). The expected 2849 bp fragment of the right T-DNA vector junction is indicated (A). - : control DNA from an untrasformed grapevine plant. (C) Schematic representation of vector backbone sequences from the plasmid pGA643. The solid bar corresponds to the probe labelled with digoxigenin and the size of expected internal SacII fragment is shown above. RB: right border; LB: left border; Tet: tetracycline resistance gene


Supplemental Fig. 3 Agarose gel electrophoretic analysis of DNA fragments amplified from transgenic grapevines by nested PCR. A) Tandem repeat (TR) amplified in PCR by primers LBS-RBS and in nested PCR by LB1-RB1. B) Inverted repeat at the RB (IR-RB) amplified in PCR by primer RBS and in nested PCR RB1. C) Inverted repeat at the LB (IR-LB) amplified in PCR by primer LBS and in nested PCR LB1. M: 1 Kb DNA ladder

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