Supporting Information Tables S1–S5
Table S1 Genes down-regulated in young cin leaves
S.No.
Dragon No.
TAIR No.
Fold decrease
Description
Exp1
Exp2
1
AJ799275
AT3G25882
-5.634775292
-4.775980951
encodes a kinase that physically interacts with NPR1/NIM1 (NIMIN1)
2
AJ794515
AT5G45670
-5.123740139
-4.034680289
GDSL-motif lipase/hydrolase family protein
3
AJ802587
AT4G10490
-4.378295764
-4.138474611
4
AJ807867
AT1G52510
-4.275634157
-4.966159299
5
AJ795675
AT5G04290
-3.728558451
-2.842796166
6
AJ796113
AT5G44640
-3.700946323
-2.502866461
oxidoreductase, 2OG-Fe(II) oxygenase family protein, Flavonol synthase, Gibberellin 2O oxidase 2
(AT5G51810); hyoscyamine 6 beta-hydroxylase.
hydrolase, alpha/beta fold family protein, contains InterPro domain Epoxide hydrolase, chloroplastlocated
KOW domain-containing transcription factor, has domain of chromatin modification, transcription
elongation, RNP-fold
glycosyl hydrolase family 1 protein, carbohydrate metabolism process, endomembrane system
7
AJ792739
AT3G16660
-3.677707903
-2.337065069
Endomembrane system protein, function unknown
8
AJ793728/ AJ807895
AT3G07010
-3.552642537
-1.599691346
pectatelyase family protein; Identical to Probable pectatelyase 8 precursor; endomembrane system
9
AJ791543/AJ788654
AT2G33810
-3.487886247
-1.471591792
SPL3 (squamosa-promoter binding protein-like); homologous to SLP1,2,4,5,7,8, 12 as well
10
ZSchoIID6/AMA568238
AT5G36890
-3.330969953
-2.497318428
glycosyl hydrolase family 1 protein, similar to latex cyanogenic beta glucosidase
11
AJ789013
AT1G22370
-3.237797005
-2.063481774
UDP-glucoronosyl/UDP-glucosyltransferase family protein
12
AMA558661
AT4G2380/AT1G02820
-2.996462006
-2.258466156
AtLEA5/SAG21; AtLEA3; ATDI21 drought-induced 21); Has a role on oxidative stress tolerance.
13
AJ801139
NONE
-2.993496354
-1.133144707
None
14
AJ794821
AT1G10550
-2.916124659
-2.230653838
15
AJ790359
AT4G24010
-2.793374278
-3.106229571
Cell wall modification enzyme, hydrolase activity, XET, XTH33
(xyloglucal:xyloglucosyltransferase 33)
Cellulose synthase like-G1, transfers glycosyl groups
16
AMA56883/AJ808276
AT5G03980
-2.746879153
-1.144576109
GDSL-motif lipase/hydrolase; lipid metabolism, glycerol biosynthesis, endomembrane system
17
AJ800000
AT2G39170
-2.739325175
-2.363763079
similar to Os08g0152500 [Oryza sativa (japonica cultivar-group)]
18
AJ791727
AT1G28480
-2.65975733
-1.725054
glutaredoxin family protein; Identical to Glutaredoxin-C9 (AtGrxC9) (GRXC9)
19
AJ806946
AT5G58350
-2.516521714
-2.39699583
20
AJ805124/AJ803209
AT4G26530
-2.505742273
-2.823517901
A member of the WNK family (9 members in all) of protein kinases (regulated by circadian
rhythm)
fructose-bisphosphatealdolase (involved in glycolysis)
21
AJ796564
AT5G07420
-2.498961589
-2.180119114
pectinesterase family protein, Cell wall modification
22
AJ789299
NONE
-2.479041759
-1.405253194
NONE
23
AJ808276
AT5G03980
-2.390098393
-1.927940312
GDSL-motif lipase/hydrolase family protein, endomembrane system, lipid metabolism
24
AJ794227
AT5G18200
-2.38654997
-1.83192884
UDP-glucose:hexose-1-phosphate uridylyltransferase, galactose metabolic process
25
ZSL1_3E10
AT2G44480
-2.159758671
-1.375341624
glycosyl hydrolase family 1 protein, endomembrane system
26
AJ790994
AT1G12940
-2.136511931
-1.471635804
member of High affinity nitrate transporter family, Enoyl CoA hydratase/isomerase domain
27
AJ791405
AT3G14395,AT1G30260
-2.134705736
-1.451963538
unknown protein., AGL79 (AGAMOUS-LIKE 79); similar to galactosyltransferase family protein
28
AJ805296
AT1G77380
-2.120345231
-1.633069012
Amino acid permease which transports basic amino acids
29
AMA560094
AT4G16730
-2.093684012
-5.618190269
30
AJ789906
NONE
-2.018527246
-1.087776423
lyase/magnesium ion binding; similar to ATTPS03 (Arabidopsis thaliana terpene synthase 03),
Terpenoidcyclase domain/protein phenyltransferase ?- domain
NONE
31
AJ800487
AT1G80760
-1.919233364
-1.064354996
32
AJ802207
AT4G25810
-1.863748859
-1.797109309
33
AJ809153
AT5G36890
-1.8298288
-1.838001523
Similar to gb:D17443 major NIP6,NLM7,NOD26-like intrinsic protein from Oryza sativa, involved
in transport, located in membrane
xyloglucanendotransglycosylase-related protein (XTR6), cell wall protein, endomembrane system,
domain- glycosyl hydrolase
glycosyl hydrolase family 1 protein, carbohydrate metabolism
34
AJ802666
AT4G13440
-1.809197807
-1.913749559
calcium-binding EF hand family protein
35
AJ804987
AT4G37850
-1.787017167
-3.507310573
36
AJ807056
AT4G31500
-1.763451297
-1.748068486
37
AJ809024
NONE
-1.758476915
-5.286743957
basic helix-loop-helix (bHLH) family protein, similar to symbiotic ammonium transporter;
nodulin.(Has homology with transparent testa 8, enhancer of Glabra3, Jasmonate insensitive 1)
ATR4,Cytochrome P450 Monooxygenase 83B1,Encodes an oxime-metabolizing enzyme in the
biosynthetic pathway of glucosinolates. Is required for phytochrome signal transduction in red light.
Mutation confers auxin overproduction.
NONE
38
AMA568752
AT2G37170
-1.741906717
-2.010267698
39
AJ797470
AT4G24120
-1.736028147
-1.478853154
40
AMA568689
AT5G60660
-1.690593465
-2.116809007
41
AMA558368
AT1G23120
-1.6749256
-2.971862929
42
AJ790624
AT4G10040
-1.674395758
-1.495072421
major latex protein-related involved in defence response, similar to putative ripening-related
protein, contains InterPro domain Bet v I allergen
Cytochrome C2, electron carrier
43
AMA559968
AT1G65870
-1.667883803
-1.53595051
disease resistance-responsive family
44
AJ804859
AT2G33205
-1.667359656
-1.381482193
TMS membrane family protein
45
AJ793249
AT4G24000
-1.6607332
-1.800192115
46
AJ796956
AT3G26040
-1.658525541
-1.432074556
encodes a protein similar to cellulose synthase, homologous to CSLG1, CSLG2, CSLE1,
CESA6(CELLULAR SYNTHASE 6),CESA5,CESA2,CESA9,CESA7or IRX3 etc
transferase family protein
47
AJ808146
AT4G13440
-1.644063818
-1.075144652
calcium-binding EF hand family protein
48
AJ795075
AT2G22750
-1.629630531
-2.604336462
basic helix-loop-helix (bHLH) family
49
AJ801757
AT5G33370
-1.607744046
-1.03103383
GDSL-motif lipase/hydrolase
a member of the plasma membrane intrinsic protein subfamily PIP2. localizes to the plasma
membrane and exhibits water transport activity in Xenopus oocyte. expressed specifically in the
vascular bundles and protein level increases slightly during leaf dev
Member of a small family of oligopeptide transporters similar to the yellow stripe locus of maize
(ZmYS1).
PIP2F, plasma membrane, water channel
50
AJ797682
AT5G40370
-1.583018395
-1.627875433
glutaredoxin
51
AJ803945
AT4G32840
-1.540789996
-2.427842815
phosphofructokinase family protein
52
AJ796159
AT1G76470
-1.521700888
-2.144009665
cinnamoyl-CoA reductase
53
AMA568742
AT5G10760
-1.517014629
-1.330317982
aspartyl protease family protein; similar to chloroplast nucleoid DNA-binding protein
54
AJ790968
AT5G53486
-1.510815851
-1.11997327
unknown protein, Endomembrane system protein
55
AJ809133
AT1G22960
-1.464233996
-1.476050701
56
AJ805277
NONE
-1.449435892
-3.333653219
pentatricopeptide (PPR) repeat-containing protein; contains InterPro domain Protein
prenyltransferase.
NONE
57
AMA558720
NONE
-1.446520232
-1.124013179
NONE
58
AJ803222
AT2G36970
-1.442547991
-1.975523945
UDP-glucoronosyl/UDP-glucosyltransferase
59
AJ796467
AT5G47560
-1.440798919
-1.884246522
Encodes a tonoplast malate/fumarate transporter
60
AJ809141
AT1G42460
-1.413850861
-1.124691048
Ulp1 protease family protein, contains InterPro domain Peptidase C48
61
AMA568456
AT4G30210
-1.405376279
-4.258060314
62
AMA568943
AT2G30870
-1.399530909
-1.17710624
Encodes NADPH-cytochrome P450 reductase that catalyzes the first oxidative step of the
phenylpropanoid general pathway.
ERD13 (early dehydration-induced 13), ATGSTF10, glutathione transferasese
63
AJ796300
AT1G65445
-1.384430288
-1.558740272
transferase-related
64
AJ807059
AT4G24220
-1.376247734
-2.000399162
AWI31, VEP1 (vein patterning 1)
65
AMA560274
AT1G17420
-1.36912489
-1.365539661
Lipoxygenase,LOX3,Defence response, JA biosynthetic enz, response to wounding, groeth
66
AJ803085
AT1G43670
-1.355059865
-1.531501845
fructose-1,6-bisphosphatase, putative
67
AJ788079
AT1G67910
-1.33951
-1.77238
similar to unknown protein, serine rich protein related
68
AJ806443
AT3G61220
-1.339158836
-3.346235844
SDR (short chain dehydrogenase/reductase) family
69
AJ797289
AT2G45680
-1.34
-1.88
TCP family transcription factor, [TCP 9],contains InterPro domain TCP transcription factor
70
AJ797785
NONE
-1.333851986
-1.016238555
NONE
71
AJ804448
AT1G32780
-1.33149651
-1.326894455
alcohol dehydrogenase
72
AJ803635
AT3G49260
-1.329955541
-1.02668888
IQ-domain 21, calmodulin binding
73
AJ809139
AT1G49620
-1.318403572
-1.108608998
KRP7/ICN6/ICK5, (6e-15)
74
AJ803180
AT2G14750
-1.309206114
-2.142657705
AKN1/ATAKN1/APK (APS kinase) (5e-73)
75
AY534686
AT4G38460
-1.307755507
-4.449999937
76
AJ806669
NONE
-1.305881484
-1.784018895
GGR (GERANYLGERANYL REDUCTASE); farnesyltranstransferase; Identical to
Geranylgeranyl pyrophosphate synthase-related protein, chloroplast precursor (GGR), contains
InterPro domain Terpenoid synthase
NONE
77
AJ808569
NONE
-1.287074649
-1.580016342
NONE
78
AJ807170
AT2G33590
-1.280116874
-2.369665211
cinnamoyl-CoA reductase family
79
AJ795833
AT3G63250
-1.276042039
-1.115459499
ATHMT-2/HMT-2; homocysteine s-METHYLTRANSFERASE
80
AJ793435
NONE
-1.272926117
-1.56582676
NONE
81
AJ794513
AT2G47370
-1.272271052
-1.291800754
UNKNOWN (Alcohol Dehydrogease-like domain)
82
AJ788963
AT1G43670
-1.253175608
-1.409358318
fructose-1,6-bisphosphatase, putative
83
AMA558767
AT4G21990
-1.237563617
-2.013754807
PRH-26, ATAPR3, APS Reductase 3)
84
AJ792044
AT3G53420
-1.23175926
-1.945259415
PIP2A (PLASMA MEMBRANE INTRINSIC PROTEIN 2; WATER CHANNEL)
85
AJ791944
NONE
-1.211639093
-2.699957549
NONE
86
AJ804255
AT4G19840
-1.20272101
-1.569411552
ATPP2-A1 (Arabidopsis thaliana phloem protein 2-A1)
87
AJ794089
AT3G51895
-1.168308862
-1.545123359
AST12, ATST1, SULTR3;1, SULTR3 (SULFATE TRANSPORTER)
88
AJ803687
AT1G70810
-1.168217364
-1.389696048
C2-DOMAIN CONTAINING PROTEIN
89
AJ791963
AT5G04200
-1.166961873
-2.716303578
LATEX-ABUNDANT PROTEIN, AMC9: CASPASE FAMILY PROTEIN
90
AJ804255
AT4G19840
-1.159849635
-1.350141039
ATPP2-A1 (A. thaliana PHLOEM PROTEIN 2-A1)
91
AJ805825
AT2G23620
-1.152621661
-3.030836525
ESTERASE, PUTATIVE
92
AJ799455
AT2G14750
-1.152355475
-2.33915066
AKN1, APK (APS Kinase)
93
AJ797898
AT4G24120
-1.151625381
-1.796001155
YSL1 (YELLOW STRIPE LIKE 1); OLIGOPEPTIDE TRANSPORTER
94
AJ801395
AT5G62280
-1.138507007
-1.73828121
UNKNOWN
95
AJ794980
AT4G37990
-1.13576727
-4.491745151
ELI3-2 (ELICITOR-ACTIVATED GENE 3)
96
AJ790744
AT1G68570
-1.125202279
-1.285049375
PROTON-DEPENDENT OLIGOPEPTIDE TRANSPORT (POT) FAMILY PROTEIN
97
AJ789851
AT2G34070
-1.114105818
-1.263588981
UNKNOWN
98
AMA559497
NONE
-1.112828381
-1.812461582
NONE
99
AJ795752
NONE
-1.10523534
-1.403217634
NONE
100
AJ801897
AT5G15840
-1.100452241
-1.87204692
CONSTANS
101
AJ795364
AT5G50790
-1.059182798
-2.486413206
nodulin MtN3 family protein; senescence-associated protein (SAG29) [Arabidopsis thaliana]
102
AJ796089
AT3G61040
-1.028715191
-1.496453504
encodes a protein with cytochrome P450 domain
103
AJ799167
AT5G48810
-1.022718318
-2.475005434
Encodes a cytochrome b5 isoform
104
AMA568850
AT5G47700
-1.019373143
-2.910604143
60S acidic ribosomal protein P1 (RPP1C); InterPro domain Ribosomal protein 60S
105
AJ809130
NONE
-1.017248349
-1.440018414
NONE
106
AJ790214
AT3G15353
-1.010397079
-2.820971381
metallothionein, binds to and detoxifies excess copper and other metals, limiting oxidative damage
107
AJ792815
NONE
-1.010353428
-1.705618394
NONE
108
AJ807951
AT2G45550
-1.008282176
-1.762707323
member of CYP76C, CYP76C4, CYTOCHROME P450, FAMILY 76, SUBFAMILY C
109
AJ796269
AT2G45570
-1.000990519
-1.655626739
member of CYP76C
Table S2 Genes up-regulated in young cin leaves
S.No.
Dragon No.
TAIR No.
Fold Increase
Description
Exp1
Exp2
1
AMA559965
NONE
4.632589
4.875015
NONE (Up-1)
2
AJ796073
AT3G12580
3.158397
2.240245
HSP 70
3
AJ792486
AT4G37260
3.064101
1.968502
MYB 73, regulation of transcription; DNA dependent, response to- ABA, Auxin, Ethylene, GA, JA,SA, Cadmium ion
4
AJ792505
AT5G61600
3.002922
1.379206
Ethylene response factor (AP2 class)
5
AJ787178
AT1G70850
2.963041
1.956739
Bet v I allergen family protein; Identical to MLP-like protein 34 (MLP34)
6
AJ790801
AT2G38470
2.911741
1.263767
7
AJ790792
AT4G23140
2.721937
2.818696
WRKY DNA-BINDING PROTEIN 33,[ regulation of transcription, DNA-dependent, defense response to bacterium, defense
response to fungus]
Cysteine-rich receptor like kinase
8
AJ795483
AT5G35200
2.536321
1.685408
epsin N-terminal homology (ENTH) domain-containing protein; Identical to Putative clathrin assembly protein At5g35200
9
AJ800324
AT5G39670
2.504609
1.579522
calcium-binding EF hand family protein
10
AJ791652
AT1G62510
2.369444
3.619665
Protease inhibitor/seed storage/lipid transfer protein (LTP) family protein; similar to ELP (EXTENSIN-LIKE PROTEIN)
11
AJ798250
NONE
2.331414
2.084555
NONE
12
AJ805666
AT3G23980
2.196373
2.822087
13
AMA559197
AT5G03980
2.187913
2.393685
similar to CIP1, similar to heavy meromyosin-like protein; similar to Os01g0911800 [Oryza sativa (japonica cultivar-group)]
(GB:NP_001045163.1); contains InterPro domain Spectrin repeat; (InterPro:IPR002017)
GDSL-motif lipase/hydrolase family protein; similar to lipase
14
AJ806613
AT5G12960
2.183778
2.239038
similar to unknown protein
15
AMA558863
AT1G59560
2.166284
2.550161
ZCF61; protein binding / zinc ion binding; similar to zinc finger family protein
16
AJ803089
AT4G25470
2.13868
1.719742
17
AJ791638
AT2G44670
2.138231
1.242138
Encodes a member of the DREB subfamily A-1 of ERF/AP2 transcription factor family (CBF2). The protein contains one AP2
domain.
senescence-associated protein-related
18
AJ806624
AT1G20440
2.044922
2.260188
19
AJ796336
AT1G32640
1.980855
1.975367
20
AMA558864
AT1G69120
1.973258
2.406864
21
AJ803092
AT1G30040
1.711272
1.163428
Belongs to the dehydrin protein family, which contains highly conserved stretches of 7-17 residues that are repetitively
scattered in their sequences, the K-, S-, Y- and lysine rich segments.
Encodes a 68 kD MYC-related transcriptional activator with a typical DNA binding domain of a basic region helix-loop-helix
leucine zipper motif.
Floral homeotic gene encoding a MADS domain protein homologous to SRF transcription factors. Specifies floral meristem and
sepal identity. Required for the transcriptional activation of AGAMOUS. Interacts with LEAFY
Encodes a gibberellin 2-oxidase. AtGA2OX2 expression is responsive to cytokinin and KNOX activities
22
AJ794180
NONE
1.709118
2.429822
NONE
23
AJ790183
NONE
1.602345
1.492777
NONE
24
AMA558584
NONE
1.587897
1.477305
NONE
25
AJ790343
AT4G37990
1.536932
1.637402
26
AJ804131
AT4G29190
1.53086
1.034481
Encodes an aromatic alcohol:NADP+ oxidoreductase whose mRNA levels are increased in response to treatment with a variety
of phytopathogenic bacteria.
zinc finger (CCCH-type) family protein; similar to zinc finger (CCCH-type) family protein
27
AJ789493
AT4G37970
1.516412
1.654755
mannitol dehydrogenase, putative; similar to ELI3-2, similar to sinapyl alcohol dehydrogenase-like protein.
28
AJ793815
AT2G19810
1.467851
1.46861
zinc finger (CCCH-type) family protein; similar to zinc finger (CCCH-type) family protein
29
AMA559563
AT3G02000
1.453428
1.813553
30
AJ803437
AT1G50600
1.442989
1.089546
Roxy1 encodes a glutaredoxin belonging to a subgroup specific to higher plants. It is required for proper petal initiation and
organogenesis.
Encodes a scarecrow-like protein (SCL5). Member of GRAS gene family
31
AJ792444
NONE
1.440153
1.194919
NONE
32
AMA559761
AT4G39330
1.42418
1.110323
mannitol dehydrogenase, putative; Identical to Probable mannitol dehydrogenase
33
AJ789267
AT2G46490
1.381744
1.492912
Similar to unknown protein
34
AJ809148
NONE
1.379153
1.150418
NONE
35
AJ809113
AT4G29780
1.378719
2.257841
Similar to unknown protein
36
AJ800329
AT2G19810
1.352487
1.584558
zinc finger (CCCH-type) family protein
37
AJ805745
AT5G03980
1.343361
1.840284
GDSL-motif lipase/hydrolase family protein; similar to lipase
38
AJ806658
AT1G14820
1.331185
1.201106
SEC14 cytosolic factor family protein / phosphoglyceride transfer family protein; similar to SEC14 cytosolic factor
39
AJ798394
AT5G10100
1.295085
1.078101
Similar to trehalose-6-phosphate phosphatase
40
AJ808571
AT5G45390
1.291333
1.862421
One of several nuclear-encoded ClpPs (caseinolytic protease). Contains a highly conserved catalytic triad of Ser-type proteases
41
AJ800479
AT4G14270
1.267793
1.197725
Protein containing PAM2 motif which mediates interaction with the PABC domain of polyadenyl binding proteins.
42
AJ792118
AT3G55500
1.265621
1.095421
Expansin-like protein. Involved in the formation of nematode-induced syncytia in roots of Arabidopsis thaliana
43
AJ798626
AT5G05960
1.260809
1.541136
protease inhibitor/seed storage/lipid transfer protein (LTP) family protein
44
AMA560140
AT4G27280
1.251728
2.24731
calcium-binding EF hand family protein; similar to PBP1 (PINOID-BINDING PROTEIN 1)
45
AJ809029
AT1G19020
1.248985
1.100898
similar to unknown protein
46
AJ804190
AT4G25470
1.206219
2.099331
47
AJ790933
AT5G14070
1.181438
1.298345
Encodes a member of the DREB subfamily A-1 of ERF/AP2 transcription factor family (CBF2). The protein contains one AP2
domain
glutaredoxin family protein; Identical to Glutaredoxin-C8 (AtGrxC8) (GRXC8)
48
AJ796270
AT2G38185
1.174352
1.004719
zinc finger (C3HC4-type RING finger) family protein; similar to unknown protein
49
AJ809015
AT3G55840
1.165042
1.386389
similar to unknown protein, similar to putative Hs1pro-1-like receptor, contains InterPro domain Hs1pro-1
50
AJ802811
AT3G54720
1.156127
1.04152
Encodes glutamate carboxypeptidase
51
AJ798949
NONE
1.145477
1.184797
NONE
52
AJ808942
AT3G10410
1.134078
1.150721
SCPL49 (serine carboxypeptidase-like 49); serine carboxypeptidase; Identical to Serine carboxypeptidase precursor
53
AJ802728
AT5G10100
1.131951
1.133392
trehalose-6-phosphate phosphatase
54
AJ794642
AT3G23930
1.117225
1.117225
similar to unknown protein
55
AMA560140
AT4G27280
1.091185
2.423884
calcium-binding EF hand family protein; similar to PBP1 (PINOID-BINDING PROTEIN 1)
56
AJ789950
AT4G36500
1.067795
1.251367
similar to unknown protein
57
AJ798414
AT1G74660
1.052609
1.033828
58
AJ790546
AT5G67090
1.036161
1.070495
Constitutive overexpression of MIF1 caused dramatic developmental defects, seedlings were non-responsive to GA for cell
elongation [ZF-HD homeobox protein Cys/His-rich dimerisation ]
similar to subtilase family protein
59
AMA560239
AT4G25760
1.033272
1.540935
similar to unknown protein
Table S3 PCR primers and oligos used in the study
Primer
Number
Primer Sequence (5'-3')
Antirrhinum EST (Closest Arabidopsis Homolog)
P01597
Forward
(FP)/
Reverse
(RP)
Primer
FP
AGGTTGGGATTGCCTGGAGCTGA
AJ795150 (IAA1)
P01598
RP
TGTGCCTTTGGAGCTGGAGCA
AJ795150 (IAA1)
P01599
FP
GGAACACGACCTCCTCCGGC
AJ798118 (IAA7)
P01600
RP
GAGCCCCGTCAACTGCCACC
AJ798118 (IAA7)
P01601
FP
CCGTCGGATGTGAGGTCGTGC
AJ801045 (TGSAUR21)
P01602
RP
GCAACCGCACACGATCACCG
AJ801045 (TGSAUR21)
P01603
FP
GTCCGTACCCCGCGGACCAA
AJ803900 (ARG10)
P01604
RP
TCCCCAGTACAGCTTCACGCCA
AJ803900 (ARG10)
P01605
FP
AGCAGATGCCAGAGGATTGGGC
AJ790979 (IAA3)
P01606
RP
AGACTCTTCGAGAACCCAAGCTGT
AJ790979 (IAA3)
P01607
FP
AGGGCTACCGGGAACTGATAACGA
AJ799874 (IAA3)
P01608
RP
TCGAACCGGAGGCCATCCAACT
AJ799874 (IAA3)
P01609
FP
TGCTGCTGCTAAGAACAACAAGCG
AJ804892 (IAA3)
P01610
RP
CCGGTAAGACCTCACTGGTGGC
AJ804892 (IAA3)
P01611
FP
TCACCAGGTGTCCGTGGGTTGT
AJ807692 (HK4)
P01612
RP
ACTGCACGTCAGCCCCAAGC
AJ807692 (HK4)
P01613
FP
TGAGGTCCATGTTCTCGCGGTT
AJ804107 (ARR3)
P01614
RP
AGCCCTCCTCCCACTGTCCA
AJ804107 (ARR3)
P01615
FP
ACACCATCACCGTCGCCCCT
AJ787388 AND AJ801951 (ARR15)
P01616
RP
GGCAGCCCCATCAGTTTGGAGC
AJ787388 AND AJ801951 (ARR15)
P01617
FP
TGGAGGCGAGGATCTTGCATGG
AJ806940 (ARR6)
P01066
RP
GCTTCAGGTGGACCCTTGGCC
AJ806940 (ARR6)
P01067
FP
CCACTTCTCCCAGCTCGACCAAC
AJ799891 (APRR7)
P01618
RP
CGCTTCCCAATTACTCTGCGCCA
AJ799891 (APRR7)
P01619
FP
GGACGGCGGTTTGGGACTGT
AJ792505 (Ethylene response factor-AP2 class)
P01620
RP
CCCCAGACTATTACCGTCAGGTGC
AJ792505 (Ethylene response factor-AP2 class)
P01621
FP
AGTCCGGGTTCTCCCCTGGA
AJ806643 (LOX2)
P01622
RP
CCGCCACAGCCACTCCCCTA
AJ806643 (LOX2)
P01072
FP
GTACTTCGGCGTCGCCATGCC
AMA560274 (LOX3)
P01073
RP
GCTTAGCCGCACCAACGAGTGTC
AMA560274 (LOX3)
P01623
FP
TCGACGGGAACTGACGTTCCAA
AJ798778 (putative auxin-inducible SAUR gene)
P01624
RP
CACCCATTGGATGGTTGAACCCAAA
AJ798778 (putative auxin-inducible SAUR gene)
P01625
FP
GGCGGATAAGCTAGGCGGGGA
AMA560140 (similar to PBP1 - PINOID-BINDING PROTEIN 1)
P01626
RP
CCCCTCCTGTTGAAGTGCCTCT
AMA560140 (similar to PBP1 - PINOID-BINDING PROTEIN 1)
PO1660
FP
AGCTGAGGTTGGGATTGCCTGGA
AJ795082 (IAA1)
PO1661
RP
TGCCCTTGGAGCTGGAGCAGA
AJ795082 (IAA1)
PO1662
FP
GCCTTCTTCACCTCCTGGCCG
AJ795336 (IAA12/11)
PO1663
RP
GGCTGGCGATTTTGTATGGTTTGCC
AJ795336 (IAA12/11)
PO1664
FP
TCACGCCATGTGCAACTCCGT
AJ791402 (IAA4/5)
PO1665
RP
GCGCAACAGATCGTCGAGACCAC
AJ791402 (IAA4/5)
PO1666
FP
AGCTGAGATTGGGTTTGCCTGGT
AY062215 (IAA4 AUX/IAA1)
PO1667
RP
TGTGCCTTTGGAGCTGGTGCT
AY062215 (IAA4 AUX/IAA1)
PO1668
FP
AGCTTTGCCCGGCGATGAGG
AJ568789 (IAA16)
PO1669
RP
GGCATTGGGGGCCATCCCAC
AJ568789 (IAA16)
PO1670
FP
TGAGCTTAGATTGGGTTTGCCTGGT
AJ802114 (IAA4)
PO1671
RP
TGGAGCTGGTGCTATTGATTCCTCT
AJ802114 (IAA4)
PO1672
FP
GTGGTGGGATGGCCTCCGGT
AJ793214 (IAA16)
PO1673
RP
GCGCTCCGTCCATGCTCACC
AJ793214 (IAA16)
PO1674
FP
TGCAAGCGCCTTCGCATCAT
AJ559808 (IAA16)
PO1675
RP
TGCTCCATCAAACCAAGTTGCACA
AJ559808 (IAA16)
PO1676
FP
GTGACTGGATGCTCGTGGGGG
AJ791366 (IAA16)
PO1677
RP
TGCACTTCTCCACTGCTCTTGGT
AJ791366 (IAA16)
PO1678
FP
TCCCCTGCCAAGGCCCAAGT
AJ806977 (IAA16)
PO1679
RP
CGGTGCCCCATCAACGCTCA
AJ806977 (IAA16)
PO1680
FP
TCTGTCGGAAAGTGGAACTATGGC
AJ789312 (ARR15)
PO1681
RP
CAAATCCAACAGAACCCCTTTCTCC
AJ789312 (ARR15)
PO1682
FP
ACCAGGAACCCCCAATGCAGC
AJ558353 (APRR7)
PO1683
RP
GGGGCATCAGCCGCCAACTT
AJ558353 (APRR7)
PO1684
FP
GGCACGAGTGAATGCACACAGTTT
AJ808985 (AHP4)
PO1685
RP
TCGAGCTTCCTTTTCAGGACTGC
AJ808985 (AHP4)
P00330
FP
AGGCCGATTGTGCTGTTCTG
Antirrhinum EF1
P00331
RP
GAAAGCAAGCAATGCATGCTC
Antirrhinum EF1
P00332
FP
CCACATTCGCAGTCCCATC
CINCINNATA
P00333
RP
GAAACGACTGAGCTCCGCAG
CINCINNATA
RT-PCR and cloning the fragments into pGEM T - Easy for in-vitro transcription
P00939
FP
TGACGATACAATCTTGTCCAAGGG
AJ807692 (HK4)
P00940
RP
TTGGTATGTGCCACTCGGTAC
AJ807692 (HK4)
P00265
FP
TGGCAAGTGTTATGGCTCATGGAAC
AJ790979 (IAA3)
P00266
RP
TCAAACAGAACAGCCCAATCCTCTG
AJ790979 (IAA3)
Primers used for ChIP
Primer
Number
Primer Sequence (5'-3')
Gene/Binding Site
PO1783
FP
GAGTACGCATATTTAAAGGTCAACTCGC
AmHK4 BS1
PO1784
RP
GTACTGATTCAGTAAACTGCTTGGGG
AmHK4 BS1
PO1785
FP
CAGTTTATTCTTATGCGCTAATGTTGATG
AmHK4 BS2
PO1786
RP
CCATCCATTGACCCTTAGTTAACTATC
AmHK4 BS2
PO1787
FP
ACGGGAGGGCAGAGCCTGAT
AmHK4 BS3
PO1788
RP
AAGTGAGGGAGGGAGGGCGA
AmHK4 BS3
PO1789
FP
CCATTTCTGTTTCTCTCTCACAAGTCC
AmHK4 BS4
PO1790
RP
CCTGCATTTGGGTCCTCAGAATAAG
AmHK4 BS4
PO1791
FP
CAGGATACGTTTGCTGAATACACCGC
AmHK4 BS5
PO1792
RP
TGACAGGAGCATACTCATCCCTTGC
AmHK4 BS5
PO1793
FP
CATGGCTTTCCTAGTCTCTTCTCTCC
AmHK4 BS6
PO1794
RP
GAGAGTGATCGTGTGTATCTTTCTTCAGC
AmHK4 BS6
PO1795
FP
CATCACCGGTCGGGTAACATAACTTTC
AmHK4 BS7
PO1796
RP
CGGGAAGAACTACATTAGGTGGGC
AmHK4 BS7
PO1797
FP
GCCGATGTGGCTAAATCTCAGGTTC
AmHK4 BS8
PO1798
RP
GCAGTGCCAACATCCCTAAAAGCAC
AmHK4 BS8
PO1799
FP
GAGAGGAAAGTGTCGGAAATGATTTATG
AmHK4 BS9
PO1800
RP
GAGAGCAATTTGTGAACACCTGCAATA
AmHK4 BS9
PO1261B
FP
GGAAACCAAGACTCTGATTCATAACC
AmIAA3 BS1
PO1262
FP
GGTGCCTCCCATGTGGAGGAG
AmIAA3 BS1
PO1263
RP
GGAATCAGGTGTGTCCGATTTGG
AmIAA3 BS1
PO1264
FP
GTTCAAGCTCACCATAGGTAGG
AmIAA3 BS2
PO1265
RP
GTAGCCTTCTCTCTCTGAGTATTC
AmIAA3 BS2
PO1266
FP
GAGAAGAAGATGCTGTATCTGAGG
AmIAA3 BS3
PO1267
RP
ACAGGATTACAAAACCGCCAAGGC
AmIAA3 BS3
Primers used for EMSA
PO1801
FP
TTTTTATTGGCCCTGCAACT
AmHK4 BS1
PO1802
RP
AGTTGCAGGGCCAATAAAAA
AmHK4 BS1
PO1803
FP
ATATTAATGGACCAATATGA
AmHK4 BS2
PO1804
RP
TCATATTGGTCCATTAATAT
AmHK4 BS2
PO1805
FP
GTGGAAGGTGGACCTTTTGGT
AmHK4 BS3
PO1806
RP
ACCAAAAGGTCCACCTTCCAC
AmHK4 BS3
PO1807
FP
TGCAACAGGACCATGCTTTA
AmHK4 BS4
PO1808
RP
TAAAGCATGGTCCTGTTGCA
AmHK4 BS4
PO1809
FP
AGCATGGGTGGACCATTCGGA
AmHK4 BS5
PO1810
RP
TCCGAATGGTCCACCCATGCT
AmHK4 BS5
PO1811
FP
CTTGGTTTGGACCTGCTGAA
AmHK4 BS6
PO1812
RP
TTCAGCAGGTCCAAACCAAG
AmHK4 BS6
PO1813
FP
CAAGTAAGGGCCAATTCCAT
AmHK4 BS7
PO1814
RP
ATGGAATTGGCCCTTACTTG
AmHK4 BS7
PO1815
FP
TGTGTAAGGACCATTTTTTT
AmHK4 BS8
PO1816
RP
AAAAAAATGGTCCTTACACA
AmHK4 BS8
PO1817
FP
CATGCTGGTGGGCCTCTTAGC
AmHK4 BS9
PO1818
RP
GCTAAGAGGCCCACCAGCATG
AmHK4 BS9
PO1256
FP
ACTACTAGGCCCACATGGTCA
AmIAA3 BS1
PO1257
RP
TGACCATGTGGGCCTAGTAGT
AmIAA3 BS1
PO1258
FP
TGTTGAATGGTCCTTGGATA
AmIAA3 BS2
PO1259
RP
TATCCAAGGACCATTCAACA
AmIAA3 BS2
PO1260
FP
TTTTATCTGGACCTCATCTG
AmIAA3 BS3
PO1261A
RP
CAGATGAGGTCCAGATAAAA
AmIAA3 BS3
Primers used for SELEX
G704
FP
GGAAACAGCTATGACCA TG(N)18ACTGGCCGTCGTTTTAC
RP
GTAAAACGACGGCCAGT
Primers used for cloning in protoplast assays
5742
FP
CCGCTCGAGCATGGGAGGAGCAGGAGGA
CIN ORF
5743
RP
CCGCTCGAGTCAATGGCGAGATTCGGAG
CIN ORF
P02118
FP
TAGGATCCCGTCCGAAGGCTGAAACCACGC
AmIAA3 promoter
P02119
RP
TACCATGGGGTTGGAGTCTTTGGTGTTTTGGG
AmIAA3 promoter
P02225
FP
ATTCTGCAGCTCTGATTCATAACCCCAACCCCTC
AmIAA3 promoter
P02226
FP
AAACTGCAGCACCAACCACCCATGTAGACCCTC
AmIAA3 promoter
P02227
RP
AAACCATGGCGTATCCTGTATTACCCACGGAAGC
AmIAA3 promoter
P02183
FP
TTCTGCAGCTAAGGGTCAATGGATGGAAGGG
AmHK4 promoter
P02184
FP
TTCTGCAGCCTCCCTTCCATCCATTGACCC
AmHK4 promoter
P02184
RP
AAACCATGGAAAATATGACAGGAGCATACTCATCC
AmHK4 promoter
P02123
RP
TACCATGGGCAAGCTTTGTGAGTGACTGAACAC
AmHK4 promoter
Table S4 Genes involved in auxin and cytokinin signaling differentially expressed in cin leaf
Auxin signaling pathway
Sl.
No.
Dragon ID
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
AJ799874
AJ804892
A_84_P21812
AJ790979
AJ798118
AJ795082
AJ795336
AJ806069
AJ791402
AY062215
AJ568789
AJ802114
AJ793214
AJ559808
AJ791366
AJ806977
AJ801045
AJ559301
AJ793092
AJ798778
AJ789007
AJ803535
AJ792146
-----
TAIR ID
Closest Homologue in Arabidopsis
Young
leaf
AT1G04240.1
AT1G04240.1
AT1G04240.1
AT4G14550.1
AT1G04240.1
AT4G28640.2
AT1G04550.2
AT5G43700.1
AT5G43700.1
AT3G04730.1
AT5G43700.1
AT3G04730.1
AT3G04730.1
AT3G04730.1
AT3G04730.1
AT5G20820.1
AT3G12830.1
AT4G38840.1
AT4G38840.1
AT4G38840.1
AT3G60690.1
AT4G38840.1
At4g34770
At4g34810
IAA3/SHY2
IAA3/SHY2
IAA11 homolog
IAA3/SHY2
IAA14/ SLR
IAA3/SHY2
IAA11
IAA12/BDL
IAA4/ATAUX2-11
IAA4/ATAUX2-11
IAA16
IAA4/ATAUX2-11
IAA16
IAA16
IAA16
IAA16
SAUR-like auxin-responsive protein
SAUR-like auxin-responsive protein
SAUR-like auxin-responsive protein
SAUR-like auxin-responsive protein
SAUR-like auxin-responsive protein
SAUR-like auxin-responsive protein
SAUR-like auxin-responsive protein
SAUR-like auxin-responsive protein
SAUR-like auxin-responsive protein
Fold change
Mature
Base/Tip
leaf
+13.5
-2.5
+28.3
-1.7
-2.2
-5.6
+3.3
+2.1
+2.2
+3.9
+8.4
+4.9
4.4
+3.7
+2.3
-3
+3.4
+2.3
-2.5
-2.2
-2.1
+4.1
-23
-4.6
2.9
+60.9
-2.7
-4.1
-2.4
2.6
Cytokinin signaling pathway
Sl. No.
Dragon ID
TAIR ID
Closest Homologue in Arabidopsis
Young
leaf
1.
2.
3.
4.
5.
6.
7.
8.
9.
AJ807692
AJ787388
AJ789312
AJ804107
AJ799891
AJ558353
AJ808985
AJ808120
AJ559786
AT1G27320
AT1G74890
AT1G74890
AT1G59940
AT5G02810
AT5G02810
AT3G16360
AT5G53290
AT4G23750
AHK4 homologue
ARR15
ARR15
ARR3
APRR7
APRR7
AHP4
CRF3
CRF2
Fold change
Mature Base/Tip
leaf
-38.4
-2.6
-3.3
-3.6
-4.3
-3.5
+4.7
+28.3
-2.3
-2.1
-2.4
-9.3
+9.3
+7.6
Table S5 Accession number of genes used for sequence analysis and phylogeny
Gene
Species
Accession
Sas SHK300
Striga asiatica
ABG35782
Sas SHK279
Striga asiatica
ABG35783
Ptr CR1A
Populus trichocarpa
ACE63264
Vvi HK4-like
Vitis vinifera
XP_002285117
Rco HK-like
Ricinus communis
XP_002527541
Ptr CR1B
Populus trichocarpa
ERP57582
Bpe CR1-like
Betula pendula
ACE63259
Gma HK4-like
Glycine max
XP_003530935
Zma HK3-like
Zea mays
BAE80688
Osa HK1-like
Oryza sativa
ABF98563
Bpe HK2-like
Betula pendula
ACE63260
Cro CKR1
Catharanthus roseus
AAM14700
Vvi HK2-like
Vitis vinifera
XP_002269977
Sly HK2-like
Solanum lycopersicum
XP_004243558
Csa HK2-like
Cucumis sativus
XP_004140009
Gma HK2-like
Glycine max
XP_003545073
TAIR ID
Gma HK4-like
Glycine max
XP_003531201
Msa HK1
Medicago sativa
ABJ74169
Lja HK2
Lotus japonicus
ABI48270
Lal HK1
Lupinus albus
ABJ74170
Zma HK3
Zea mays
BAD01586
Mtr HK
Medicago truncatula
XP_003617960
Cma HK
Cucurbita maxima
CAF31355
Sbi HK-like
Sorghum bicolor
XP_002466563
Hvu HK-like
BAJ89805
Osa HK2-like
Hordeum vulgare subsp.
vulgare
Oryza sativa
Smo CR1
Selaginella moellendorffii
XP_002967800
Phy HK-like
Petunia x hybrida
BAL43559
Ppt CRE1
Physcomitrella patens
ABD49494
Ppt CRE2
Physcomitrella patens
ABD49495
Ppt HK4-like
Physcomitrella patens
XP_001779177
At HK1
Arabidopsis thaliana
816291
AT2G17820
At HK2
Arabidopsis thaliana
833552
AT5G35750
At HK3
Arabidopsis thaliana
839621
AT1G27320
BAD88305
At HK4, CRE1
Arabidopsis thaliana
814714
AT2G01830
IAA3, SHY2
Arabidopsis thaliana
839570
AT1G04240
IAA6
Arabidopsis thaliana
841717
AT1G52830
IAA8
Arabidopsis thaliana
816798
AT2G22670
IAA9
Arabidopsis thaliana
836693
AT5G65670
IAA10
Arabidopsis thaliana
839290
AT1G04100
IAA13
Arabidopsis thaliana
817894
AT2G33310
IAA16
Arabidopsis thaliana
819633
AT3G04730
ARF11, ARF19, IAA22
Arabidopsis thaliana
838505
AT1G19220
IAA26, PAP1
Arabidopsis thaliana
820898
AT3G16500
IAA27, PAP2
Arabidopsis thaliana
829029
AT4G29080
IAA29
Arabidopsis thaliana
829361
AT4G32280
IAA31
Arabidopsis thaliana
821026
AT3G17600
IAA33
Arabidopsis thaliana
835848
AT5G57420
AXR5, IAA1
Arabidopsis thaliana
827103
AT4G14560
IAA2
Arabidopsis thaliana
821877
AT3G23030
IAA5, AUX2-27
Arabidopsis thaliana
838128
AT1G15580
IAA6, SHY1
Arabidopsis thaliana
841717
AT1G52830
IAA7
Arabidopsis thaliana
821879
AT3G23050
IAA11
Arabidopsis thaliana
828982
AT4G28640
IAA12, BDL
Arabidopsis thaliana
839495
AT1G04550
IAA14
Arabidopsis thaliana
827102
AT4G14550
IAA15
Arabidopsis thaliana
844379
AT1G80390
IAA18
Arabidopsis thaliana
841623
AT1G51950
IAA20
Arabidopsis thaliana
819313
AT2G46990
IAA21, IAA23, IAA25,
ARF7
IAA30
Arabidopsis thaliana
832196
AT5G20730
Arabidopsis thaliana
825383
AT3G62100
IAA32
Arabidopsis thaliana
814648
AT2G01200
IAA34
Arabidopsis thaliana
838070
AT1G15050