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bioRxiv · 10.1101/2025.09.21.677582

Genome-wide Identification, Structural Features and Single-Cell Expression Atlas of the Carbonic Anhydrase Gene Family in Maize (Zea mays L.)

Gao, Y.·Zhao, C.
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Abstract

Maize is a cornerstone C{square} crop underpinning food, feed and bioenergy. Carbonic anhydrases (CAs) are zinc metalloenzymes that catalyze the interconversion of CO{square} and HCO{square}{square}, underpinning photosynthesis, pH homeostasis and stress acclimation. Despite extensive work on plant CA families, a maize-focused synthesis integrating genome-wide cataloging, structural divergence, regulatory logic, and cell-type specificity is still lacking.Here we present a genome-wide census and a single-cell-resolved expression atlas of the maize CA family. We identified 18 CA genes partitioning into (8), {beta} (5) and {gamma} (5) subfamilies. Proteins span 206-452 aa, pI 6.09-10.58 and 22.67-49.36 kDa, with predominantly hydrophilic profiles. Phylogeny resolved three robust clades (UFboot >90%) and indicated closer affinity to rice than to Arabidopsis; synteny recovered 15 maize-rice and 3 maize-Arabidopsis orthologs. Promoters are enriched for ABRE, TCA-element and ARE, suggesting ABA, SA and redox regulation. Bulk RNA-seq across 21 tissues revealed strong tissue specificity ({tau} >0.7 for 12 genes), with {beta}-CAs elevated in leaves and -CAs in roots. Single-cell analyses further showed Zm{beta}CA3 enriched in mesophyll cells and ZmCA2 enriched in vascular/root-cap cells. Together, these data position {beta}-CAs as chloroplast-centered hubs for C4 photosynthesis, while /{gamma}-Cas support ion/pH buffering and mitochondrial metabolism. We nominate cell-type-specific CA members as candidates for genetic improvement toward stress resilience in maize.

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Gao, Y., Zhao, C.. 2025-09-21. Genome-wide Identification, Structural Features and Single-Cell Expression Atlas of the Carbonic Anhydrase Gene Family in Maize (Zea mays L.). https://doi.org/10.1101/2025.09.21.677582

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