Ancestral polyploidy and non-linear dosage shifts define the photosynthetic transition in the Heliantheae alliance
Whole-genome duplications (WGDs) have played a central role in plant evolutionary innovation, yet their genome-wide influence on complex physiological traits such as carbon-concentrating mechanisms (CCMs) remains poorly resolved. Here, we present high-quality genome assemblies and annotations for 35 species within the Heliantheae alliance (Asteraceae), spanning the complex photosynthetic spectrum from C3 to C4. Ks-based analyses combined with gene tree-species tree reconciliation identified a shared paleopolyploid event (WGD-2) ~30 million years ago. Using phylogenetically informed association mapping with these species, we detected 451 functional MapMan BINs with copy number variation significantly associated with interspecific variation in the CO2 compensation point. Notably, 303 of these BINs contain greater than 10% WGD-2-derived genes, indicating a strong enrichment of duplicated loci within photosynthetically relevant functional modules. Effect-size analysis revealed that the C3-to-C4 transition is governed by threshold-dependent genomic architecture rather than gradual additive change. Substantial expansions in key transcription factor modules, including HD-ZIP, HSF, LOB, and TCP, were associated with strong non-linear physiological shifts, consistent with genomic tipping points. By integrating comparative genomics, physiological trait variation, and evolutionary analysis, this study establishes a mechanistic link between ancient polyploidy and contemporary photosynthetic diversification. These findings provide a framework for understanding the genetic basis of carbon concentrating mechanism evolution and inform future optimization of photosynthetic efficiency in Asteraceae crops such as sunflower.