A dominant role of transcriptional regulation during the evolution of C photosynthesis in Flaveria species.

C photosynthesis exemplifies convergent evolution of complex traits. Herein, we construct chromosome-scale genome assemblies and perform multi-omics analysis for five Flaveria species, which represent evolutionary stages from C to C photosynthesis. Chromosome-scale genome sequence analyses reveal a gradual increase in genome size during the evolution of C photosynthesis attributed to the expansion of transposable elements. Systematic annotation of genes encoding C enzymes and transporters identify additional copies of three C enzyme genes through retrotranspositions in C species. C genes exhibit elevated mRNA and protein abundances, reduced protein-to-RNA ratios, and comparable translation efficiencies in C species, highlighting a critical role of transcriptional regulation in C evolution. Furthermore, we observe an increased abundance of ethylene response factor (ERF) transcription factors and cognate cis-regulatory elements associated with C genes regulation. Altogether, our study provides valuable genomic resources for the Flaveria genus and sheds lights on evolutionary and regulatory mechanisms underlying C photosynthesis.