Les.3702.1.A1_at

Les.5442.1.S1_atLes.4087.1.S1_at

Les.4095.1.S1_at

LesAffx.67531.1.S1_atLes.3703.1.A1_atLes.3706.1.A1_at

LesAffx.58084.1.S1_atLesAffx.3360.2.A1_at

C Sal

tS

us-C

Sus

-TT

ol-C

Tol

-TS

us-C

Sus

-TT

ol-C

Tol

-T

Drought Heat

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; tolerant-control; Tol-T; tolerant-treated.

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.

Les.1298.1.S1_atLes.4087.1.S1_at

Les.4095.1.S1_atLes.5442.1.S1_atLes.3702.1.A1_at

LesAffx.58084.1.S1_at

Hea

lthy

Wou

nded

B. c

iner

ea

C. c

occo

des

Hea

lthy

Wou

nded

MG RR MG

B. c

iner

eaC

ontr

ol

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; 3 rd L, third leaf; L-3W, 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.

Les.3702.1.A1_at

Les.5442.1.S1_atLes.4087.1.S1_at

LesAffx.67531.1.S1_at

Les.3703.1.A1_atLes.3706.1.A1_at

LesAffx.3360.2.A1_at

Les.1298.1.S1_at

Les.4097.1.S1_at

Les.4095.1.S1_at

Les.3707.1.A1_at

LesAffx.58084.1.S1_at

Les.256.1.A1_at

Les.3701.1.A1_at

Les.3705.1.A1_at

R HY

PC

OT

3rdL

L-3

WL

-5W

MG

B B+

3B

+5

B+

20

MicroTom Pusa Ruby

0

100

200

300

400

500

600

MG B B+3 B+5 B+20

SlIAA9

0

1000

2000

3000

4000

5000

6000

7000

MG B B+3 B+5 B+20

SlIAA8

0

100

200

300

400

500

MG B B+3 B+5 B+20

SlIAA6

0

500

1000

1500

2000

2500

3000

MG B B+3 B+5 B+20

SlIAA1

0

2

4

6

8

10

12

MG B B+3 B+5 B+20

SlIAA2

0

20

40

60

80

100

120

MG B B+3 B+5 B+20

SlIAA3

0

2000

4000

6000

8000

10000

MG B B+3 B+5 B+20

SlIAA4

0100200300400500600700800

MG B B+3 B+5 B+20

SlIAA21

012345678

MG B B+3 B+5 B+20

SlIAA5

0

2

4

6

8

10

MG B B+3 B+5 B+20

SlIAA24

020406080

100120140160

MG B B+3 B+5 B+20

SlIAA26

020406080

100120140160

MG B B+3 B+5 B+20

SlIAA26

020406080

100120140160

MG B B+3 B+5 B+20

SlIAA26

020406080

100120140160

MG B B+3 B+5 B+20

SlIAA26

0

50

100

150

200

MG B B+3 B+5 B+20

M

R

Microarray

0

50

100

150

200

MG B B+3 B+5 B+20

M

R

Real time

Rel

ativ

e tr

ansc

ript

abu

ndan

ce

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 to generate microarray and QPCR expression profiles. Y-axis represents the normalized raw expression values obtained from the microarray analysis in the form of relative transcript abundance while X-axis shows five fruit developmental 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 and 20 days post breaker stages of fruit ripening.

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.

IAA3

IAA5

IAA7

IAA11

IAA15

IAA17

IAA21

IAA13

IAA22

IAA1

IAA23

IAA24

IAA10

Control Bright field Merged

Supplementary Fig. S6: Sub-cellular localization tomato Aux/IAA proteins in onion peel epidermal cells.