Heat
C
Salt
Sus-C
Sus-T
Tol-C
Tol-T
Sus-C
Sus-T
Tol-C
Tol-T
Drought
Les.3702.1.A1_at
Les.5442.1.S1_at
Les.4087.1.S1_at
Les.4095.1.S1_at
LesAffx.67531.1.S1_at
Les.3703.1.A1_at
Les.3706.1.A1_at
LesAffx.58084.1.S1_at
LesAffx.3360.2.A1_at
Supplementary Fig. S1: Hierarchical clustering of AUX/IAA genes, showing significant
differential expression under at least one abiotic stress condition. The fold change values in
treated sample as compared to its corresponding mock-treated control sample were used for
clustering. The gene probe-set IDs are on the left of the heat map while the gene names are
presented on the right. The color bar present below represents the range of log2 signal for heat map.
C, control; Salt, salt stress; Sus-C, susceptible-control; Sus-T, susceptible-treated; Tol-C; tolerantcontrol; Tol-T; tolerant-treated.
RR
MG
Healthy
Wounded
B. cinerea
Healthy
Wounded
B. cinerea
Control
C. coccodes
MG
Les.1298.1.S1_at
Les.4087.1.S1_at
Les.4095.1.S1_at
Les.5442.1.S1_at
Les.3702.1.A1_at
LesAffx.58084.1.S1_at
Supplementary Fig. S2: Hierarchical clustering of AUX/IAA genes showing significant
differential expression under at least biotic stress condition is shown. The fold change values in
treated sample as compared to its corresponding mock-treated control sample were used for
clustering. The gene probe-set IDs are on the left of the heat map while the gene names are
presented on the right. The color bar present below represents the range of log2 signal for heat map.
B. cinerea, Botrytis cinerea inoculated; C. coccodes; Colletotrichum coccodes inoculated.
Pusa Ruby
R
HYP
COT
3rd L
L-3W
L-5W
MG
B
B+3
B+5
B+20
MicroTom
Les.1298.1.S1_at
Les.256.1.A1_at
Les.4097.1.S1_at
Les.3701.1.A1_at
Les.3707.1.A1_at
Les.3705.1.A1_at
LesAffx.3360.2.A1_at
Les.3703.1.A1_at
Les.3706.1.A1_at
Les.3702.1.A1_at
LesAffx.58084.1.S1_at
Les.4095.1.S1_at
Les.4087.1.S1_at
Les.5442.1.S1_at
LesAffx.67531.1.S1_at
Supplementary Fig. S3: Expression profiles of SlIAAs in tomato development in various tissues
and developmental stages in MicroTom and Pusa Ruby. The expression profiles of SlIAA genes
in different tissues and stages of tomato development was analyzed by using normalized GC-RMA
signal intensities generated in microarray experiments. The gene probe-set IDs are on the left of the
heat map while the gene names are presented on the right. The color bar present below represents
the range of log2 signal for heat map. R, root; HYP, hypocotyl; COT, cotyledon; 3rd L, third leaf; L3W, 3-week old leaf; L-5W, 5-week old leaf; MG, mature green; B, breaker; B+3 days old fruit,
breaker+3 days old fruit; B+5; breaker+5 days old fruit; Breaker+20 days old fruit, breaker+ 20 days
old fruit.
3000
Relative transcript abundance
12
SlIAA1
2500
120
SlIAA2
10
2000
8
80
1500
6
60
1000
4
40
500
2
20
0
0
10000
MG
B
B+3
B+5
B+20
SlIAA4
8000
6000
4000
2000
0
MG
7000
B
B+3
B+5
B
B+3
SlIAA5
B+5
B+20
200
1000
100
0
B
B+3
B+5
B+20
SlIAA24
SlIAA26
160
160
140
140
120
120
100
100
80
80
60
60
40
40
20
20
00
B+5
B+20
0
B
B+3
B+5
B+20
SlIAA9
0
MG
B+3
SlIAA6
100
300
2000
B
200
400
3000
MG
300
500
4000
500
400
600
5000
10
160
140
8
120
6
100
80
4
60
40
2
20
00
0
MG
MG
B+20
SlIAA8
6000
8
7
6
5
4
3
2
1
0
SlIAA3
100
MG
B
B+3
B+5
B+20
SlIAA26
800
160
700
140
600
120
500
100
400
80
300
60
40
200
20
100
00
MG
MG
MG
B
B+3
B+5
B+20
BB
B+3
B+3
B+5
B+5
B+20
B+20
SlIAA21
SlIAA26
M
Microarray
M
RReal time
R
200
200
150
150
100
Supplementary Fig. S4: Validation
of microarray expression profiles for tomato Aux/IAA genes
at different developmental stages by
QPCR. Three biological replicates for each stage were used
100
to generate microarray and QPCR expression profiles. Y-axis represents the normalized raw
50
expression values obtained from the microarray
analysis in the form of relative transcript abundance
while X-axis shows five fruit developmental
50 stages in tomato. Standard error bars are shown for data
obtained using both techniques. MG; mature green, B; breaker. B+3, B+5 and B+20 represent 3, 5
0
and 20 days post breaker stages of fruit ripening.
0
MG
B
B+3
B+5
MG
B
B+3
B+5
MG
B
B+3
B+3
B+5
B+5
B+20
B+20
MG
MG
B
B
B+3
B+3
B+5
B+5
B+20
B+20
Supplementary Fig. S5: Expression profiles of ARF and Aux/IAA genes from tomato and pepper.
Heatmaps showing expression of members of these two gene families in various tissues/organs and
developmental stages (labeled on top) of tomato (A), pepper (B) and potato (C). Color scale represents
log2(RPKM) values in case of RNA-seq data publically available for tomato (TGC 2012) and pepper
(Kim et al., 2014). MG, mature green; B, breaker; DPA, days post anthesis; cm, fruit diameter in
centimeter.
Control
Bright field
Merged
IAA1
IAA3
IAA5
IAA7
IAA10
IAA11
IAA13
IAA15
IAA17
IAA21
IAA22
IAA23
IAA24
Supplementary Fig. S6: Sub-cellular
localization tomato Aux/IAA proteins
in onion peel epidermal cells.