A comprehensive landscape of the Gossypium arboreum circRNAome under multiple abiotic stresses

Circular RNAs (circRNAs) serve as key post-transcriptional regulators in plant stress adaptation. Here, we comprehensively characterize the circRNA landscape of cotton ( Gossypium arboreum ) under multiple abiotic stresses condition using RNase R-enhanced sequencing. Through a stringent KNIFE-based algorithm pipeline, we identified 4,365 high-confidence circRNAs. Mechanistically, circRNA biogenesis was associated with long flanking introns and exhibited complex patterns of alternative splicing, revealing conserved production propensities but dynamic splice sites across species. Nuclear circRNAs frequently exhibited expression patterns decoupled from their host genes, typically in a stress-specific manner. By integrating miRNA-seq data, we constructed a circRNA-miRNA-mRNA regulatory network and found it centered mainly on cotton-specific miRNAs. Notably, we discovered an extraordinary dominance of chloroplast-derived circRNAs, accounting for over 80% of the total circRNAs repertoire. These chloroplast circRNAs clustered dominantly at clustering at the 3’ terminus of the photosynthetic gene psbA gene, suggesting a specialized post-transcriptional regulatory mechanism within the chloroplast. This study provides a high-resolution cotton circRNA atlas and highlights psbA -derived circRNAs as potential molecular targets for improving environmental resilience in crop.