Genomic and Cis-Regulatory Basis of a Plastic C(3)-C(4) Photosynthesis in Eleocharis Baldwinii.

C(4) 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 C(3)-like traits underwater and C(4)-like traits on land, to expand knowledge of C(4) 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 C(4) enzyme genes was detected across cell types. cis-regulatory patterns linked to the C(4) pathway, Kranz anatomy specialization, and environmental responses are evaluated using single-nucleus transposase-accessible chromatin sequencing and found that the formation of the C(4) 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 C(4) metabolism differ, underscoring the genetic diversity underlying convergent traits. This study provides genomic and regulatory insights into how plants evolve C(4) photosynthesis, especially regarding the effects of environmental factors.