File S1 - Characterization of the Tomato ARF Gene Family Uncovers a Multi-Levels Post-Transcriptional Regulation Including Alternative Splicing

Supporting tables and figures. Table S1. uORF prediction in the 5′UTR leader sequences of Sl-ARFs. Table S2. In silico analysis of Sl-ARF gene promoters. Table S3. Quantitative RT-PCR primers of Sl-ARF genes. Table S4. PCR primers for identifying the alternative splicing expressed forms in Sl-ARF genes. Figure S1. Sl-ARF genes genomic distribution on the tomato chromosomes. The arrows next to gene names show the direction of transcription. The number near to each Sl-ARF designates the position megabases (Mb) of the first ATG in the tomato chromosome pseudomolecules (tomato genome version SL2.40). The chromosome numbers and their corresponding size are indicated at the top and bottom of each bar. Figure S2. Phylogenetic relationship between tomato Sl-ARF genes. The unrooted tree was generated using MEGA4 program by neighbor-joining method. Bootstrap values (above 50%) from 1000 replicates are indicated at each branch. Sl-ARFs with a star (*) are deprived of domain III and IV necessary for interaction with Aux/IAAs. Figure S3.1-6. Predicted alternative splicing in six Sl-ARFs (Figure S3.1 to Figure S3.6). RNA-seq reads generated during the fruit-set and mapped on the corresponding Sl-ARF gene sequence (Sl-ARF2B, 3, 4, 8A, 8B, and 24) showing predicted alternative splicing events. RNA-seq reads are represented by red and blue rod arrows. (PDF)