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Table 1 Soybean phenylpropanoid pathway genes responsive to infection by Pseudomonas syringae with (HR) or without (VIR) avrB

From: Transcriptome changes in the phenylpropanoid pathway of Glycine max in response to Pseudomonas syringaeinfection

     Ratio treatment vs MgCl2 controla
Gene Description 3'-Clone ID 5'-Clone ID 5' or 3' TIGR TC T2HR T8HR T24HR T2VIR T8VIR T24VIR
Phenylalanine ammonia-lyase (PAL) Gm-r1088-2170 Gm-c1027-2831 TC225162   2.46 1.93    
Phenylalanine ammonia-lyase (PAL) Gm-r1070-3081 Gm-c1015-4781 TC216854   6.23 3.81    2.07
Phenylalanine ammonia-lyase (PAL) Gm-r1021-3996 Gm-c1004-9203 TC225162   2.44 2.26 1.05 1.68  
Phenylalanine ammonia-lyase (PAL) Gm-b10BB-2 Gm-c1062-1285 TC225162   3.39 2.80 2.67 2.19  
Phenylalanine ammonia-lyase (PAL) Gm-r1083-3853 Gm-c1028-6208 TC225168   3.39 2.62    
Phenylalanine ammonia-lyase (PAL) Gm-r1070-4771 Gm-c1016-5168 NA   3.18 3.14    
Cinnamate 4 hydroxylase (C4H) Gm-r1021-162 Gm-c1004-446 TC204339   4.76 1.67   2.25  
Cinnamate 4 hydroxylase (C4H) Gm-r1021-1649 Gm-c1004-3560 TC204341   1.97     
Cinnamate 4 hydroxylase (C4H) Gm-r1021-3590 Gm-c1004-8721 TC204341   2.58 1.59 1.25 1.89  
Cinnamate 4 hydroxylase (C4H) Gm-r1083-1942 Gm-c1028-893 TC204341   3.43 1.93    
4-coumarate:CoA ligase (4CL) Gm-r1021-2611 Gm-c1004-5129 TC205641   2.13     
4-coumarate:CoA ligase (4CL) Gm-r1083-3061 Gm-c1028-3891 TC205641   3.20    1.84  
4-coumarate:CoA ligase (4CL) Gm-r1083-3414 Gm-c1028-4979 TC205641   2.01   1.97   
4-coumarate:CoA ligase (4CL) Gm-r1070-5094 Gm-c1016-6727 TC216082   1.67 2.50    2.17
4-coumarate:CoA ligase (4CL) Gm-r1021-2223 Gm-c1004-4431 TC216190   1.75 1.49    
4-coumarate:CoA ligase (4CL) Gm-r1021-3419 Gm-c1004-7053 TC216190   2.36 1.61   1.65  
4-coumarate:CoA ligase (4CL) Gm-r1070-3141 Gm-c1015-4689 TC216191   9.45   1.80  
4-coumarate:CoA ligase (4CL) Gm-r1070-7534 Gm-c1029-1150 TC220028   3.23 2.89   1.54 1.88
4-coumarate:CoA ligase (4CL) Gm-r1083-4331 Gm-c1028-7642 TC224198   2.93 1.57    
4-coumarate:CoA ligase (4CL) Gm-r1070-3331 Gm-c1015-4673 TC225974   6.32    2.53  
4-coumarate:CoA ligase (4CL) Gm-r1083-2896 Gm-c1028-3421 TC226636   2.60 2.20    
4-coumarate:CoA ligase (4CL) Gm-r1083-4078 Gm-c1028-6958 TC226636   5.28 2.13 1.28 2.16  
4-coumarate:CoA ligase (4CL) Gm-r1070-2770 Gm-c1015-4573 TC226637   7.06 4.96   1.56  
4-coumarate:CoA ligase (4CL) Gm-r1070-2942 Gm-c1015-3925 NA   1.77 2.36   1.53 1.85
4-coumarate:CoA ligase (4CL) Gm-r1083-1803 Gm-c1013-3118 TC229241   0.13 0.43    
4-coumarate:CoA ligase (4CL) Gm-r1083-779 Gm-c1009-3084 TC221808   0.34 0.36    
4-coumarate:CoA ligase (4CL) Gm-r1070-515 Gm-c1008-190 TC223132   0.37 0.29   0.61 0.54
Chalcone synthase (CHS) *Gm-b10BB-5 Genomic clone NA   36.35 13.22 1.83 12.47 7.15
Chalcone synthase (CHS) Gm-b10BB-6 Gm-c1004-1721 TC203259 1.07 48.80 63.70 3.31 20.48 16.68
Chalcone synthase (CHS) Gm-r1021-84 Gm-c1004-874 TC203259   30.70 37.53 1.49 9.06 7.21
Chalcone synthase (CHS) Gm-b10BB-7 Gm-c1004-2866 TC203319 4.92 34.39 50.20 2.07 14.32 15.41
Chalcone synthase (CHS) Gm-r1083-83 Gm-c1009-670 TC209602   48.84 33.82 1.61 10.48 11.39
Chalcone synthase (CHS) Gm-r1088-5931 Gm-c1065-3606 TC209886   20.25 15.56   3.25  
Chalcone synthase (CHS) Gm-b10BB-4 Gm-c1028-2741 TC214314   60.58 23.88 1.84 17.92 9.59
Chalcone synthase (CHS) Gm-r1070-3019 Gm-c1015-4593 TC214387 2.16 36.76 17.75 1.87 6.77 2.91
Chalcone synthase (CHS) Gm-b10BB-3 Gm-c1013-1524 TC214443   44.57 17.35 1.60 10.28 6.15
Chalcone synthase (CHS) Gm-r1083-556 Gm-c1009-2808 TC226663   23.10 20.97 1.45 7.36 8.40
Chalcone synthase (CHS) Gm-r1083-853 Gm-c1009-4010 NA   30.91 31.56   5.24 4.41
Chalcone reductase (CHR) Gm-r1021-1257 Gm-c1004-2376 TC225256   11.39 31.12   3.36 3.48
Chalcone reductase (CHR) Gm-r1021-720 Gm-c1004-1818 TC215169   7.01 18.77   3.94 2.20
Chalcone reductase (CHR) Gm-r1021-4150 Gm-c1004-8921 TC215169   12.17 23.51   3.93 4.24
Chalcone reductase (CHR) Gm-r1021-2517 Gm-c1004-5030 TC215169   8.94 18.25   4.82 3.20
Chalcone reductase (CHR) Gm-r1021-754 Gm-c1004-1771 TC225256   8.82 32.00   3.14 2.38
Chalcone reductase (CHR) Gm-r1088-2718 Gm-c1027-5959 TC203399   0.23 0.13    
Chalcone reductase (CHR) Gm-b10BB-36 Gm-c1062-753 TC203399   0.11 0.10   0.61 0.41
Chalcone isomerase (CHI) Gm-r1021-1566 Gm-c1004-3954 TC205496   21.11 10.70 1.71 5.82 2.03
Chalcone isomerase (CHI) Gm-r1021-154 Gm-c1004-613 TC205496   10.93 6.28 1.41 3.68  
Chalcone isomerase (CHI) Gm-r1083-3171 Gm-c1028-4494 TC205496   6.87 3.20   2.00  
Chalcone isomerase (CHI) Gm-r1021-1440 Gm-c1004-3529 TC205536   8.63 13.45   4.63 3.58
Chalcone isomerase (CHI) Gm-b10BB-9 Gm-c1026-2606 TC205536   11.42 12.79 9.96 6.30 7.47
Chalcone isomerase (CHI) Gm-r1083-43 Gm-c1009-620 TC206681   12.30 16.45   5.28 4.32
Chalcone isomerase (CHI) Gm-r1070-1290 Gm-c1010-653 TC216488   2.89 3.94    1.85
Chalcone isomerase (CHI) Gm-r1083-4382 Gm-c1028-7808 TC216488   20.68 7.21   2.51 3.23
Chalcone isomerase (CHI) Gm-r1088-8117 Gm-c1072-871 TC227583   5.17 4.23   2.06  
Chalcone isomerase (CHI) Gm-r1070-3127 Gm-c1015-4783 NA   2.14 2.39    
Isoflavone synthase (IFS1) *Gm-10BB-30 Gm-c1059-264 NA   11.09 8.35 1.39 5.40 3.79
Isoflavone synthase (IFS1) Gm-r1088-8309 Gm-c1072-1106 TC204648   4.72    2.14  
Isoflavone synthase (IFS1) Gm-r1021-1181 Gm-c1004-3075 TC215321   7.01 5.82 1.47 5.03 3.23
Isoflavone synthase (IFS1) Gm-r1088-1867 Gm-c1027-2050 TC218468   3.94 4.50   2.25  
Isoflavone synthase (IFS2) *Gm-b10BB-29 Gm-c1027-870 TC204612   17.30 13.84 1.61 8.12 7.06
Isoflavone synthase (IFS2) Gm-r1083-3218 Gm-c1028-4877 TC204612   15.24 20.97 1.37 6.41 6.82
isoflavone 7-o-methyltransferase (IOMT) Gm-r1021-2837 Gm-c1004-6344 TC206764   53.45 48.17   5.35 7.16
isoflavone 7-o-methyltransferase (IOMT) Gm-r1088-8483 Gm-c1074-35 TC206765   58.89 112.99   8.28 19.29
isoflavone 7-o-methyltransferase (IOMT) Gm-r1088-8769 Gm-c1074-599 TC210019   78.25 95.67   4.14  
isoflavone 7-o-methyltransferase (IOMT) Gm-r1021-435 Gm-c1004-1004 TC215839   5.28 4.89 1.40 4.23 4.06
isoflavone 7-o-methyltransferase (IOMT) Gm-r1021-2886 Gm-c1004-6334 TC215839   9.06 10.27 1.84 4.50 7.89
Isoflavone reductase (IFR1) Gm-r1021-2052 Gm-c1004-4918 TC206041   15.45 9.58 1.47 6.11 5.13
Isoflavone reductase (IFR1) Gm-r1070-7511 Gm-c1023-366 TC207832   16.00 4.00    
Isoflavone reductase (IFR1) Gm-b10BB-33 Gm-c1019-3319 TC207832   24.67 31.57 2.81 67.71 49.21
Isoflavone reductase (IFR1) Gm-r1088-4139 Gm-c1027-9301 TC215002   14.42 24.76    
Isoflavone reductase (IFR1) Gm-r1088-8260 Gm-c1072-1589 TC215002   15.35 7.52    
Isoflavone reductase (IFR1) Gm-r1070-6760 Gm-c1019-3354 TC215005   50.21 55.33   2.89 18.64
Isoflavone reductase (IFR1) Gm-r1021-3760 Gm-c1004-8266 TC226270   41.64 43.11   6.50 6.77
Isoflavone reductase (IFR1) Gm-r1083-4951 Gm-c1028-8510 TC226270   28.84 32.22   5.90 4.56
Flavonoid 3'-hydroxylase (F3'H) Gm-b10BB-22 Gm-c1053-348 TC216289   1.47 1.96 0.80  
Flavonoid 3'-hydroxylase (F3'H) *Gm-b10BB-23 Gm-c1019-10961 NA   0.45 1.70 0.76   
Flavanone 3-hydroxylase (F3H) *Gm-b10BB-12 Gm-c1012-683 TC226020   0.06 0.07    
Flavanone 3-hydroxylase (F3H) Gm-b10BB-13 Gm-c1019-2646 TC226020   0.24 0.18    0.67
Dihydroflavonol 4-reductase (DFR) Gm-r1070-8296 Gm-r1030-1389 TC225293   0.17 0.26    
Dihydroflavonol 4-reductase (DFR) Gm-r1021-3500 Gm-c1004-8647 TC225293   0.17 0.26    
Dihydroflavonol 4-reductase (DFR) Gm-r1083-1327 Gm-c1013-1350 TC225294   0.16 0.14    0.50
Dihydroflavonol 4-reductase (DFR) Gm-r1088-7258 Gm-c1067-1717 TC234668   0.12 0.20    
Dihydroflavonol 4-reductase (DFR) Gm-r1070-7401 Gm-c1019-4941 TC210161   4.63 9.99    5.50
Dihydroflavonol 4-reductase (DFR) Gm-r1083-2198 Gm-c1028-1633 TC218842   4.92     
Leucoanthocyanidin dioxygenase (LDOX) Gm-r1070-1246 Gm-c1010-216 TC217747       
Leucoanthocyanidin dioxygenase (LDOX) Gm-r1070-7484 Gm-c1029-932 TC214271   0.38 0.35    
Leucoanthocyanidin dioxygenase (LDOX) Gm-r1021-2183 Gm-c1004-4454 TC232276   1.39    1.48  
Flavonol synthase (FLS) Gm-b10BB-15 Gm-c1016-13124 NA   0.51 0.52    
Flavonol synthase (FLS) Gm-r1070-4167 Gm-c1016-3181 TC208467    0.51    
Flavonol synthase (FLS) Gm-r1083-823 Gm-c1009-3205 TC218780   0.21     
Cynnamoyl CoA reductase (CCR) Gm-r1021-2461 Gm-c1004-5052 TC226044   4.00 2.66   2.71 1.56
Cynnamoyl CoA reductase (CCR) Gm-r1021-523 Gm-c1004-1463 TC204998   3.63     
Cynnamoyl CoA reductase (CCR) Gm-r1021-2593 Gm-c1004-5056 TC226045   3.39 2.64   3.34 1.79
Cynnamoyl CoA reductase (CCR) Gm-r1070-3838 Gm-c1016-1700 TC226917   7.41    2.14  
Cynnamoyl CoA reductase (CCR) Gm-r1088-8005 Gm-c1072-6 TC233163   5.82 3.27    
Cynnamoyl CoA reductase (CCR) Gm-r1070-1367 Gm-c1008-2980 TC207664   0.10 0.10    0.61
Cynnamoyl CoA reductase (CCR) Gm-r1070-914 Gm-c1008-1235 TC225292   0.16 0.15    0.44
Cynnamoyl CoA reductase (CCR) Gm-r1070-2653 Gm-c1015-2660 TC225293   0.19 0.15    0.43
Cynnamyl alcohol dehydrogenase (CAD) Gm-r1083-4523 Gm-c1028-7532 TC225589   2.13 1.99   8.06  
Cynnamyl alcohol dehydrogenase (CAD) Gm-r1021-3795 Gm-c1004-7796 TC204437   1.51 1.93 1.27 1.34 1.32
Cynnamyl alcohol dehydrogenase (CAD) Gm-r1083-2221 Gm-c1028-695 TC206457   12.73 0.56   2.07 3.36
Cynnamyl alcohol dehydrogenase (CAD) Gm-r1021-1331 Gm-c1004-3272 TC225589    1.52    
Cynnamyl alcohol dehydrogenase (CAD) Gm-r1021-2196 Gm-c1004-5210 TC225589   2.25 2.55    
Cynnamyl alcohol dehydrogenase (CAD) Gm-r1070-5855 Gm-c1019-927 TC227395   0.73 0.72 0.73   0.56
Cynnamyl alcohol dehydrogenase (CAD) Gm-r1083-1322 Gm-c1013-1592 TC230620   0.82 0.56    0.60
Cynnamyl alcohol dehydrogenase (CAD) Gm-r1083-3802 Gm-c1028-6101 TC208568   0.39 0.32   0.56 0.59
Cynnamyl alcohol dehydrogenase (CAD) Gm-r1083-4013 Gm-c1028-6963 TC225589   0.24 0.30    
Caffeic acid O methyltransferase (COMT) Gm-r1083-548 Gm-c1009-2413 TC212974    2.25   0.76  
Caffeic acid O methyltransferase (COMT) Gm-r1083-3458 Gm-c1028-5510 TC219214   1.54 1.89   1.46 1.52
Caffeic acid O methyltransferase (COMT) Gm-r1021-973 Gm-c1004-2186 TC226262    2.01    
Caffeic acid O methyltransferase (COMT) Gm-r1083-2739 Gm-c1028-2911 TC226263    2.07   1.52 1.28
Caffeic acid O methyltransferase (COMT) Gm-r1083-3457 Gm-c1028-5374 TC226265   2.30 2.85   1.72 1.65
Caffeic acid O methyltransferase (COMT) Gm-r1083-2949 Gm-c1028-2922 TC226997   11.31 9.85    
Caffeic acid O methyltransferase (COMT) Gm-r1070-1306 Gm-c1008-2760 TC203610   0.19 0.09    
Caffeic acid O methyltransferase (COMT) Gm-r1070-1869 Gm-c1015-70 TC203610   0.18 0.10    
Caffeic acid O methyltransferase (COMT) Gm-r1070-3522 Gm-c1016-846 TC203610   0.14 0.10    
Caffeoyl Co-A transferase (CCoAMT) Gm-r1021-3573 Gm-c1004-7957 TC204613   1.85    1.88 1.54
Caffeoyl Co-A transferase (CCoAMT) Gm-r1070-3714 Gm-c1016-1000 TC204614   1.92    1.96  
Caffeoyl Co-A transferase (CCoAMT) Gm-r1070-6767 Gm-c1019-3293 TC213310   4.79     
Caffeoyl Co-A transferase (CCoAMT) Gm-r1083-141 Gm-c1009-796 TC215141   3.46 2.06 1.14 2.73 2.62
Caffeoyl Co-A transferase (CCoAMT) Gm-r1083-4593 Gm-c1028-8263 TC225342   1.93     
Caffeoyl Co-A transferase (CCoAMT) Gm-r1021-1921 Gm-c1004-4301 TC225343   1.67 2.41    
Caffeoyl Co-A transferase (CCoAMT) Gm-r1070-6093 Gm-c1019-1156 TC228561   2.69 6.87    3.48
Caffeoyl Co-A transferase (CCoAMT) Gm-r1070-5202 Gm-c1016-6589 TC228561   2.13 2.17    
Caffeoyl Co-A transferase (CCoAMT) Gm-r1088-8678 Gm-c1074-1097 TC228993   4.69 18.13    
Caffeoyl Co-A transferase (CCoAMT) Gm-r1083-956 Gm-c1009-4174 TC225339   0.62 0.50    
Caffeoyl Co-A transferase (CCoAMT) Gm-r1021-427 Gm-c1004-1316 TC225339   0.45 0.44    0.83