Genomic and Cis-Regulatory Basis of a Plastic C₃-C₄ Photosynthesis in Eleocharis Baldwinii

C₄ photosynthesis is a crucial trait for efficient carbon fixation; however, the genomic basis and environmental influences on its formation remain under explored. Here, we examined Eleocharis baldwinii, a sedge that exhibits photosynthetic plasticity with C₃-like traits underwater and C₄-like traits on land, to expand knowledge of C₄ photosynthesis. A gap-free allopolyploid genome was assembled and a cellular expression atlas is reconstructed by applying single-nucleus RNA-seq.Subgenome dominance influencing expression of C₄ enzyme genes was detected across cell types. cis-regulatory patterns linked to the C₄ pathway, Kranz anatomy specialization, and environmental responses are evaluated using single-nucleus transposase-accessible chromatin sequencing and found that the formation of the C₄ pathway involves a few environmentally triggered, cell-specialized cis-regulatory elements. Comparative analyses between E. baldwinii and maize further implied that cis-regulator families for Kranz anatomy specialization are conserved across species, whereas those for C₄ metabolism differ, underscoring the genetic diversity underlying convergent traits. This study provides genomic and regulatory insights into how plants evolve C₄ photosynthesis, especially regarding the effects of environmental factors.