Fig 7.

TEs response to cold stress in cotton. A Number of differentially expressed transposable elements (TEs) identified by comparing the cold stress samples to the control (0 h sample). B Venn diagram showing the overlap among differentially expressed TEs across five cold stress time points. C Clustering analysis of differentially expressed TEs. The heatmap displays normalized read counts for each TE locus across all samples, following z-score transformation. Clusters were identified using k-means clustering. D TE family-specific enrichment analysis per expression clusters. Only significantly enriched TE families are shown (p-value < 0.01, Fisher’s exact test). The odds ratio represents the degree of enrichment, with larger values indicating stronger enrichment and smaller values suggesting under-representation. Both p-values and odds ratios were calculated using the fisher.test function in R. Class I elements (retrotransposons): LINE, LTR/Copia, LTR/Gypsy, LTR/unknown. Class II elements (DNA transposons): hAT (DTA), CACTA (DTC), PIF–Harbinger (DTH), Mutator (DTM), Tc1–Mariner (DTT), Helitron