Irregular phototherapeutic keratectomy caused corneal opacity and significantly disrupted stromal ultrastructure, characterized by increased haze density (P < 0.0001), change in central corneal thickness (P = 0.0005), and interfibrillar spacing (P < 0.0001), along with decreased fibril diameter (P < 0.0001), matrix order (P < 0.0001), CS/DS (P < 0.0001) and KS (P < 0.0001) PGs, lumican, and decorin. The gene discussed is DCN; the disease is Corneal opacity.