The origin and evolutionary dynamics of long non-coding RNAs (lncRNAs) represent a pivotal frontier in plant functional genomics. Here, we investigated pseudo-GhFAD2-1 ( pGhFAD2-1 ), a functionally validated lncRNA regulating cottonseed fatty acid metabolism in Gossypium hirsutum , delineating its evolutionary origin and structural dynamics through a comprehensive cross-genomic comparative strategy. Homologous sequence identification, phylogenetic reconstruction, and molecular evolutionary analy