A Bryophyte Transcription Factor Landscape Reveals Lineage-Specific Zinc-Finger Protein Evolution and Differential Stress Mobilization Between Mosses and Liverworts

Bryophytes possess a gene family repertoire substantially larger than vascular plants, yet the functional evolution of their transcription factors remains poorly understood. We conducted a nested analysis across 144 bryophyte genomes, cataloging 58 transcription factor families and deeply characterizing the C2H2 zinc-finger protein family. We identified 8246 C2H2 zinc-finger genes classified into four structural types based on zinc-finger architecture. Domain-level scanning of 11,565 zinc fingers revised Z-type frequency from ~20% to 4.2%. The plant-specific Q-type was most prevalent in mosses and least prevalent in liverworts, with the major Q-type radiation occurring in seed plants. C2H2 zinc-finger gene expansion in mosses was driven by whole-genome duplication, and gene count correlated with genome size. Through re-analysis of publicly available RNA-seq datasets, cross-species expression profiling showed that mosses mobilized 23–28% of their C2H2 zinc-finger repertoires under dehydration, whereas the liverwort Marchantia polymorpha showed no significant response to osmotic stress and only a weak, transient response to salt. Notably, the aluminum-tolerance regulator STOP1 was downregulated under dehydration. Together, these results suggest a marked divergence in stress-responsive C2H2-ZFP deployment between mosses and liverworts, although the underlying mechanisms remain to be validated functionally.