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.

Full Paper：https://advanced.onlinelibrary.wiley.com/doi/full/10.1002/advs.202415681