Ancient tandem duplication of CYCLOIDEA is associated with the evolution of capitulum development in Asteraceae

Asteraceae is one of the largest and most diverse families of flowering plants. Much of their evolutionary success is attributed to their unique inflorescence structure-the capitulum. Despite their profound adaptive and taxonomic significance, the evolutionary genetic mechanisms underlying Asteraceae capitulum diversification remains poorly understood. We integrated comparative genomic analyses of 35 Asteraceae genomes with developmental transcriptome profiling of ray and disc florets. Our results uncovered a deeply conserved CYC2e-CYC2c-CYC2d-CYC2g-CYC2b tandem gene cluster that is prevalent across the Asteraceae family. We demonstrated that this tandem cluster arose during the early evolutionary diversification of Asteraceae. Subsequent lineage-specific gene retention and loss events have reshaped the composition of this cluster across different Asteraceae lineages. Notably, key members of this cluster, particularly CYC2c, CYC2d, and CYC2g, are preferentially retained in lineages with ray florets, which is consistent with their roles in regulating the ray floret development. Collectively, our findings establish a mechanistic link between the evolutionary divergence, spatiotemporal expression differentiation of the CYC2 tandem cluster as a key genetic driver underlying the morphological diversification and evolutionary success of Asteraceae.