Supplementary Table 1 Primers used in this study

Primer name / Primer sequence （5'→3'）
STTM858/858-88ntlink-PF / gccATTTAAATatggtctaaagaagaagaatatggtctaaagaagaagaatAAGGTCGAACActaGACAACGAAAgaattcggtacgctgaaatcaccag
STTM858/858-88ntlink-PR / gccATTTAAATtagaccataacaacaacaactagaccataacaacaacaacTTTCGTTGTCTagtGTTCGACCTTaagcttgggctgtcctctccaaatg
Origin-del-PacI-PF / TCCCTTAATTAAGTTTGCAAGCAGCAGATTACGCG
Origin-del-PacI-PR / TCCCTTAATTAAGAAAGGCGGACAGGTATCCGGTAAG
miR858-stem-loop RT primer / GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACAAGGTC
MiR858-real-PF / cgagTTTCGTTGTCTGTTC
MiR858-real-PR / CGAGCAGTGCAGGGTCCGAGGT
U6-real-PF / TGGACCATTTCTCGATTT
U6-real-PR / TTCCCGACCTGCACCAAGCGA
STTM-common-real-PF: / CATTTGGAGAGGACAGCCCAAG
STTM-common-real-PR: / CTGGTGATTTCAGCGTACCGAA
SGN-U320618-SlMYB7-like -real-PF / TTCACTTCTGGGTAATCGTTGG
SGN-U320618-SlMYB7-like -real-PR / GAGCTTCTTGGTCAAATGCGT
SGN-U322556-SlMYB12-real-PF / GCAACTTTGGGTAACAGATGGT
SGN-U322556-SlMYB12-real-PR / ACTTCTCATCGCTTGGTATCCT
SGN-U328066-SlMYB48-like-real-PF / ACTTCACTCCAAATATGGAAAT
SGN-U328066-SlMYB48-like-real-PR / GGACTATTGGCAGAGGAAGAGG
SlCAC-real-PF / CCTCCGTTGTGATGTAACTG
SlCAC-real-PR / ATTGGTGGAAAGTAACATCATC
M83314PAL-real-PF / ATTGGGAAATGGCTGCTGATT
M83314PAL-real-PR / TCAACATTTGCAATGGATGCA
X55194-SlCHS-real-PF / TGGTCACCGTGGAGGAGTATC
X55194-SlCHS-real-PR / GATCGTAGCTGGACCCTCTGC
Z18277-SlDFR-real-PF / CAAGGCAGAGGGAAGATTCATTTG
Z18277-SlDFR-real-PR / GCACCATCTTAGCCACATCGTA
AJ785263-SlANS-real-PF / GCTTCCATAGCCTTGGACAT
AJ785263-SlANS-real-PR / TCGGATGAGCTAATTGAACG
BP893263-Sl3GT-real-PF / GCACATAAGAGTGTTGGCGTTT
BP893263-Sl3GT-real-PR / TTTCCAAACACTTTCCACCA
SGN-U320618-SlMYB7-like-GeneRacer 5’ primer / CACCAAAGCCCATAAGGATTTCTTGTGG
SGN-U320618-SlMYB7-like-nested primer / AAAGGAGAAATCAAGAAAAGAAGTGG
SGN-U322556-SlMYB12-GeneRacer 5’ primer / ATATGCCAGCTTGTGATATGCCATGGAAT
SGN-U322556-SlMYB12-5’nested primer / TACCTAAAGCCGTAGTTGATTTGGC
SGN-U328066-SlMYB48-like-GeneRacer 5’ primer / AGGACTTCCGTACTGAAAGAAATGAGTTG
SGN-U328066-SlMYB48-like-RACE nested primer / CCTCTTCCTCTGCCAATAGTCCTGTTGAG

Supplementary Table 2 Predicted targets for miR858 in tomato by psRNATarget

Target gene accession / Target position / Score / Target gene annotation
SGN-U322556 / 319-338 / 2.0 / myb family transcription factor MYB12-like
SGN-U321318 / 296-315 / 2.0 / myb family transcription factor MYB15-like
SGN-U320618 / 385-404 / 2.0 / myb family transcription factor
SGN-U328746 / 191-210 / 2.5 / myb family transcription factor
SGN-U318565 / 628-648 / 2.5 / synaptosomal-associated protein SNAP25-like
SGN-U319386 / 403-422 / 2.5 / myb family transcription factor MYB15-like
SGN-U330402 / 1274-1293 / 2.5 / similar totranscription factor jumonji (jmjC) domain-containing protein
SGN-U317694 / 411-430 / 3.0 / myb family transcription factor MYB4-like
SGN-U328066 / 394-413 / 3.0 / myb family transcription factor MYB48-like
SGN-U335382 / 437-456 / 3.0 / zinc finger (C3HC4-type RING finger) family protein
SGN-U315887 / 1195-1214 / 3.0 / zinc finger (C3HC4-type RING finger) family protein
SGN-U336560 / 461-481 / 3.0 / SNAP25 homologous protein SNAP33 (SNAP33)
SGN-U322749 / 829-849 / 3.0 / MATE efflux family protein, similar to ripening regulated protein DDTFR18

Supplementary Figure Legend

Supplementary Figure S1. Multiple alignment and phylogenetic analysis of selected R2R3 MYB proteins. aAlignment of deduced amino acid sequences of SlMYB7-like with orthologs from Arabidopsis thaliana (AtMYB7) and Antirrhinum majus (AmMYB330). The conserved protein-protein interaction motif (([D/E]LX2[R/K]X3LX6L X3R) and the putative repressor motif (LNLE/DL)are indicated by a red and blue line, respectively. bThe phylogenetic tree of SlMYB7-like along with selected R2R3 MYBs was constructed using neighbor-joining method using MEGA5 software. The R2R3 MYB proteins, their respective plant species, andGenBank accession numbers are as follows: PhAn2, Petunia hybrida (AAF66727); NtAn2, Nicotiana tabacum (ACO52470);SlANT1, Solanum lycopersicum (AAQ55181); PAP1 (AAG42001), Arabidopsis thaliana; PAP2, A. thaliana (AAG42002); AmRosea, Antirrhinum majus (ABB83826); ZmC1, Zea mays (AAA33482); AtMYB123, A. thaliana (NP_179263); SlMYB7-like, S. lycopersicum (XP_004246088); AtMYB7, A. thaliana (NP_179263); AmMYB330, A. majus (MYB30_ANTMA).

Supplementary Figure S2.Map pOT2-STTM858 cloningvector and pC2300-pOT2-STTM858 binary vector over-expressing STTMmiR858.

Supplementary Figure S3.PCR analysis of STTM858 transgenic tomato lines. The numbers refer to the independent transgenic lines.

Supplementary Figure S4. Analysis of the expression levels of SlMYB12in STTM858 transgenic tomatoes.Relative expression of SlMYB12 in transgenic tomato lines was measured using qRT-PCR. SlCAC was used as an endogenous control for normalization. The expression level of each gene in the control is set to 1. Values represent mean ± SD of triplicate experiments from three independent biological samples.