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Expression divergence is thought to be a hallmark of functional diversification between homologs post duplication. Modification in regulatory elements has been invoked to explain expression divergence after duplication for several MADS-box genes, however, verification of reciprocal loss of  cis -regulatory elements is lacking in plants. Here, we report that the evolution of  MPF2-like  genes has entailed degenerative mutations in a core promoter CArG-box and an auxin response factor (ARF) binding element in the large 1 st  intron in the coding region. Previously,  MPF2-like  genes were duplicated into  MPF2-like-A  and  -B  through genome duplication in  Withania  and  Tubocapsicum  (Withaninae). The calyx of  Withania  grows exorbitantly after pollination unlike  Tubocapsicum , where it degenerates. Besides inflated calyx syndrome formation, MPF2-like transcription factors are implicated in functions both during the vegetative and reproductive development as well as in phase transition.  MPF2-like-A  of  Withania  ( WSA206 ) is strongly expressed in sepals, while  MPF2-like-B  ( WSB206 ) is not. Interestingly, their combined expression patterns seem to replicate the pattern of their closely related hypothetical progenitors from  Vassobia  and  Physalis . Using phylogenetic shadowing, site-directed mutagenesis and motif swapping, we could show that the loss of a conserved CArG-box in  MPF2-like-B  of  Withania  is responsible for impeding its expression in sepals. Conversely, loss of an ARE in  MPF2-like-A  relaxed the constraint on expression in sepals. Thus, the ARE is an active suppressor of  MPF2-like  gene expression in sepals, which in contrast is activated via the CArG-box. The observed expression divergence in  MPF2-like  genes due to reciprocal loss of  cis -regulatory elements has added to genetic and phenotypic variations in the Withaninae and enhanced the potential of natural selection for the adaptive evolution of ICS. Moreover, these results provide insight into the interplay of floral developmental and hormonal pathways during ICS development and add to the understanding of the importance of polyploidy in plants.

Reciprocal Loss of CArG-Boxes and Auxin Response Elements Drives Expression Divergence of MPF2-Like MADS-Box Genes Controlling Calyx Inflation