Tracing TCP evolution in plants and the divergence of the CYC and CIN subfamilies: evidence from phylogenetic and synteny network analyses

The TCP (TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTORS) family, a plant-specific group of transcription factors, plays crucial roles in plant growth, development, and environmental adaptation. To trace its evolutionary history, we investigated 78 species spanning algae to angiosperms, featuring a significantly expanded sampling of algal lineages, and systematically identified 684 TCP genes across 52 of these species. Through integrated phylogenetic and synteny network analyses, we demonstrate that TCP genes first emerged in charophyte algae, where the divergence between Class I and Class II had already occurred. Throughout plant evolution, the TCP gene family expanded gradually, driven by lineage-specific duplication events that are particularly pronounced in angiosperms. Notably, our synteny analysis revealed conserved relationships between angiosperm CYC genes and CIN genes from multiple plant lineages, strongly suggesting a shared homology between these two subfamilies. Furthermore, analysis of protein structural evolution showed that the CYC subfamily stably retains the ancestral R domain, whereas the CIN subfamily has largely lost it during subsequent evolution. This provides structural-level evidence supporting the evolutionary divergence between the CYC and CIN subfamilies. Ultimately, this study offers comprehensive new insights into the origin, expansion, and structural evolution of the TCP gene family.