Two major duplication events shaped the transcription factor repertoires in Solanaceae species

Solanaceae is a significant plant family widely dispersed in the world, and most of them are important vegetable resources. Transcription factors (TFs) play critical roles in regulating plant growth and various stresses. However, there was no comprehensive and systematic analysis of TFs in all released Solanaceae genomes. In this study, 51,169 TFs were identified and systematically analyzed from 18 Solanaceae and 10 non-Solanaceae species. In some Solanaceae species, whole-genome duplication/triplication (WGD/T) and tandem duplication (TD) were the main duplicated types leading to the TF expansion. We further divided all TF families into 1,209 orthogroups (OGs), of which 298 were unique to Solanaceae. Despite all Solanaceae species shared the recent WGT event, 10 species had more gene family contractions than expansions among the 18 Solanaceae species. Functional enrichment analysis showed that 6 gene families (AP2, ARF, ARR-B, BBB-BPC, NF-YB, and NF-YC) showed different contraction and expansion trends in Solanaceae species, indicating that these Solanaceae species have different selection requirements for these gene families during evolution. In conclusion, our study provides an understanding between the evolution of the TFs family and the gene duplications of other plants. Meanwhile, this study also provides rich genetic resources for gene function research and molecular breeding of Solanaceae in the future.