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 log 2 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 log 2 signal for heat map. B. cinerea, Botrytis cinerea inoculated; C. coccodes; Colletotrichum coccodes inoculated.

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.

Relative transcript abundance 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.

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