Summary In multicellular systems changes to the patterning of gene expression drive modifications in cell function and trait evolution. One striking example is found in more than sixty plant lineages where compartmentation of photosynthesis between cell types allowed the evolution of the efficient C 4 pathway from the ancestral C 3 state. The molecular events enabling this transition are unclear. We used single nuclei sequencing to generate atlases for C 3 rice and C 4 sorghum during photomorphogenesis. Our analysis revealed that initiation of photosynthesis gene expression is conditioned by cell identity. In both species a conserved cistrome defines each cell type, and photosynthesis genes switching expression from mesophyll in rice to bundle sheath in sorghum acquire hallmarks of bundle sheath identity. The sorghum bundle sheath has also acquired gene networks associated with C 3 guard cells. We conclude C 4 photosynthesis is based on rewiring in cis that exapts cell identity networks of C 3 plants.

Single nuclei sequencing reveals C4photosynthesis is based on rewiring of ancestral cell identity networks