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Danforth Plant Science Centerhttps://www.ebi.ac.uk/ena/browser/view/PRJNA190188Zea mays subsp. maysMaize and rice are the two most economically important grass crops and utilize distinct photosynthetic mechanisms to fix carbon. Rice, like most plant species, directly fixes carbon into C3 acid via the Calvin-Benson cycle. Maize, a semi-tropical plant, uses a two-step process with a C4 acid intermediate that reduces photorespiration and affords higher water and nitrogen use efficiencies under hot arid conditions. To define key innovations in C4 photosynthesis, we profiled metabolites and gene expression along a developing leaf gradient. A novel statistical method was implemented to compare transcriptomes from these two species along a unified leaf developmental gradient and define candidate cis-regulatory elements and transcription factors driving photosynthetic gene expression. We also present comparative primary and secondary metabolic profiles along the gradients that provide new insight into nitrogen and carbon metabolism in C3 and C4 grasses. The power of this comparative approach is illustrated by defining an aerial suberin biosynthetic pathway for maize and identifying transcriptional regulators of suberin biosynthesis, a novel innovation associated with C4 photosynthesis. These resources, including community viewers to access and mine these datasets, will enable the elucidation and engineering of C4 photosynthetic networks to improve the photosynthetic capacity of C3 and C4 grasses.ENAfalseZea mays subsp. maysZea mays subsp. mays Transcriptome or Gene expression2025-09-242014-03-05PRJNA190188381124