*4.5. Chromosomal Locations and Identification of Interaction Network*

To determine the chromosomal locations of tomato MADS-box genes, we obtained the physical genome annotation files from the SGN and NCBI database. The physical map of the tomato MADS-box genes was drawn by the Tomato-EXPEN 2000 (Available online: https://solgenomics.net/cview/map.pl).

The interaction network was conducted by STRING (functional protein association networks, Available online: https://string-db.org/) software using the search of multiple proteins sequences [94].

## *4.6. Digital Gene Expression Analysis of Tomato MADS-Box Genes*

To obtain the expression profile of tomato MADS-box genes, the RNA-seq data based on the locus/gene names of SGN were analyzed. We downloaded the RNA-seq data from TFGD (the Tomato Functional Genomics Database), and the sequence data were obtained from various tissues in wild species LA1589 (*S. pimpinellifolium*). In addition, the data of the tomato lab and Tomato eFP Browser were also used to analyze the gene expression of tomato MADS-box genes. A heatmap was generated by Heml 1.0 (Heatmap illustrator, Available online: http://hemi.biocuckoo.org/) using the relative expression values or ratios of each tomato MADS-box gene [95].
