Assessing Evolutionary Divergence in Genome-Wide MADS-Box Genes and Expression Profiles Between Toona ciliata and Toona sinensis

Toona ciliata and Toona sinensis, two economically important timber species in China, exhibit interspecific variation in floral traits that are related to mating systems. The MADS-box genes play a crucial role in floral patterning of angiosperms. Here we identified 97 and 75 MADS-box genes at the genome scale in T. ciliata and T. sinensis, respectively, which were classified into Type I and Type II groups. Genes within the same subfamily exhibited high homology and conserved motifs. Promoter analysis revealed cis-acting elements related to growth, light response, hormone signaling, and stress response. Gene duplication was prevalent, with several genes undergoing multiple duplications. Most MADS-box genes were under purifying selection between T. ciliata and T. sinensis, while eight orthologous genes in the AGL32, Mβ, MIKC*, AG/STK, and AP1/FUL subfamilies were under weakly positive selection. Transcriptomic analysis showed high gene expression in SEP, AP1/FUL, AG/STK, PI, and AP3 subfamilies, highlighting their roles in floral development. A significantly negative correlation occurred between the evolutionary rate ($K_a/K_s$) and gene expression level of MADS-box genes, suggesting evolutionary constraints on highly expressed genes. TWAS (transcription-wide association study) indicated that some MADS-box genes were significantly associated with floral traits in T. sinensis. The overall findings provide insights into the roles of MADS-box gene family in evolving interspecific divergence in floral development between T. ciliata and T. sinensis.