Fig S1: The summary of PCGs and lncRNAs in this study
A: The number of PCGs and lncRNAs (lincRNA, intronRNA and NAT) under different expression threshold
B: The percentage of PCGs and lncRNAs (lincRNA, intronRNA and NAT) under different expression threshold
Fig S2: Repeatability detection of RNA sequencing samples
A: The heatmaps represent the samples’ correlative expression levels from the RNA-seq profiling for the drought, NaCl, and heat abiotic stress treatments in the cotton seedlings.
B: The heatmaps represent the samples’ correlative expression levels from the RNA-seq profiling for the cold abiotic stress treatment in the cotton seedlings.
Fig S3: The association examination of the PCG and lncRNA
A: Density distributions of the Pearson correlation coefficients between a pair of PCG and its adjacent lncRNA (FPKM < 0.5 lncRNA were included, n = 5,314). That of the two PCGs flanking to a lncRNA (FPKM < 0.5 lncRNA were included, n = 4,053) are used as control, respectively.
B: Density distributions of the Pearson correlation coefficients among lincRNA (FPKM > 0.5, n = 3,522), intronic RNA(FPKM > 0.5, n = 169) and NAT(FPKM > 0.5, n = 347).
C: Density distributions of the Pearson correlation coefficients between a pair of PCG and its adjacent lncRNA (FPKM > 0.5, lincRNA, n = 3,522). That of the two PCGs flanking to a lncRNA (FPKM > 0.5, lincRNA, n = 3,149) are used as control.
D: Density distributions of the Pearson correlation coefficients between a C-lncRNA (FPKM > 0.5, lincRNA, n = 569) and its adjacent PCG, and an NC-lncRNA (FPKM > 0.5, lincRNA, n = 2,953) and its adjacent. The p-value was calculated by the two-sided Wilcoxon signed-rank test.
Table S1: The number of differential expressed PCGs and lncRNAs under four stress treatments
Table S2: The expression of lncRNA and its 1:1 orthologous adjacent PCG within 50kb and 1:1 orthologous PCG with lncRNA’s adjacent PCG within 50kb
Table S3: The expression of C_lncRNA and NC_ lncRNA with adjacent PCG within 50kb
Table S4: The expression of all lncRNA and its 1:1 orthologous adjacent PCG within 50kb and 1:1 orthologous PCG with all lncRNA’s adjacent PCG within 100kb
Table S5: The expression of lincRNA, intronicRNA and NAT with adjacent PCG within 50kb
Table S6:The expression of lncRNA(lincRNA) and its 1:1 orthologous adjacent PCG within 50kb and 1:1 orthologous PCG with lncRNA’s adjacent PCG within 50kb
Table S7: The expression of C_lncRNA(lincRNA) and NC_ lncRNA(lincRNA) with adjacent PCG within 50kb
Table S8: The expression, conservation of VIGS lncRNA and the phenotype after VIGS
Table S9: Gene annotation co-expressed with Gh_A08G1105
Table S10: Gene annotation co-expressed with Gh_A05G0714
Table S11: The recombination primer of lncRNA
Table S12: qPCR primer used in this study
Table S13: Statistics of RNAseq libraries in this study.