Pan-genomic and pan-transcriptomic integration unveils evolutionary dynamics and regulatory diversification of the...

The WRKY transcription factor family, characterized by its conserved WRKYGQK motif and zinc finger structure, serves as a central regulatory module in plants, mediating developmental, stress-responsive, and metabolic processes through W-box binding. In Camellia sinensis, WRKY genes act as molecular integrators that link environmental cues to the biosynthesis of quality-related compounds, underscoring the importance of understanding their evolutionary patterns for genetic improvement. However, previous research has been limited by single-reference genome approaches, which fail to capture the full spectrum of WRKY gene presence-absence variation across diverse tea plant cultivars.

This study presents the first pan-genome-wide analysis of the WRKY family in any plant species, integrating data from 22 tea plant genomes. We identified a comprehensive set of WRKY genes and classified them into core and dispensable categories, revealing extensive presence-absence variants (PAVs) that were overlooked in single-reference studies. Phylogenetic reconstruction resolved 11 subfamilies, with notable lineage-specific expansions. Mechanistically, core gene evolution was predominantly driven by whole-genome or segmental duplication under strong purifying selection, whereas dispensable genes, particularly in certain subfamilies, showed signals of adaptive evolution and were enriched through dispersed duplication. Transcriptomic analysis uncovered co-expression networks among highly expressed WRKY clusters, indicating functional redundancy and sub-functionalization in stress adaptation.

The findings from the present study provide insights into the evolutionary dynamics of presence-absence and copy-number variation within the WRKY family in tea plants, establishing a valuable genetic resource for enhancing stress resilience and metabolic traits in tea breeding programs.