**5. Conclusions**

In this study, a comprehensive and systematic analysis of the tomato *MADS-box* transcription factor family was first conducted. A total of 131 genes encoding MADS-box transcription factors, including 81 type I and 50 type II genes, were extensively identified in the tomato genome. Then, we classified the genes according to their phylogenetic relationships between tomato and Arabidopsis. The phylogenetic relationships, gene structures, conserved motifs, chromosomal distribution, and expression patterns of the genes were characterized. The 131 tomato MADS-box genes showed differential expression levels in different organs. Since the MADS-box genes are the most powerful TFs that regulate floral organ identity and fruit development and ripening in plants, we showed that 15 tomato MADS-box genes were involved in floral organ development, and we studied the expression of five tomato MADS-box genes in different stages of fruit development and ripening. These results provide evidence of the relationship between MADS-box genes and floral organ and fruit development. Our study provides comprehensive information on the tomato MADS-box gene family, enables a better understanding of the structure–function relationships among the tomato MADS-box gene family members, and lays a solid foundation of comprehensive functional characteristics in the tomato MADS-box gene family. Furthermore, our bioinformatics and evolutionary analysis will be helpful for better understanding the underlying evolutionary relationship of the MADS-box family in higher plants.

## **Supplementary Materials:** Supplementary materials can be found at http://www.mdpi.com/1422-0067/20/12/ 2961/s1.

**Author Contributions:** G.C. and Z.H. designed and managed the research work and improved the manuscript; Y.W. and X.G. performed the bioinformatics analysis; J.Z. performed the experiments; Y.W. wrote the manuscript; Y.W. and J.Z. prepared all figures. All the authors reviewed the manuscript.

**Funding:** This work was supported by National Natural Science Foundation of China (31572129), the National Natural Science Foundation of Chongqing of China (cstc2018jcyjAX0458) and Training Program of Chongqing University Bioengineering College (0221001105301).

**Conflicts of Interest:** The authors declare no conflict of interest.
