Extended Data Fig. 1: Transcriptome analysis to identify the (−)-gossypol biosynthetic gene in upland cotton.
From: Dirigent gene editing of gossypol enantiomers for toxicity-depleted cotton seeds
a, Scatter plot, constructed from 35 RNA-seq samples, illustrates the correlation values of the downregulated genes in glandless cotton (edgeR, log2[FC] < = −8, log2[FC]: log2-transformed fold change) with CYP71BE79. Differential RNA expression of genes was analyzed in R software using edgeR68. Point sizes indicate the FDR-adjusted P-value of differential expression. FDR-adjusted P values were calculated using Benjamini-Hochberg correction of the obtained P values. Different colors distinguish between protein families. Correlation analysis was measured by Pearson’s correlation coefficient with ‘Cor’ function from R software. b, Sequence alignment of Gh_A04G0066 (GhDIR5) and Gh_A05G2499 (GhDIR6) conducted by BioEdit software 7.2.5. c, Global heatmap showing the abundance of gossypol in different organs or in ovules at different stages. d, Global heatmap showing the expressions of CYP71BE79, Gh_A04G0066 (GhDIR5) and Gh_A05G2499 (GhDIR6) in different organs or in ovules at different stages. For c and d: DPA, days post anthesis. ROT: root; STE, stem; LEA, leaf; PET, petal; PIS, pistil; CAL, calycle. e, Relative expressions of Gh_A04G0066 (GhDIR5) and Gh_A05G2499 (GhDIR6) in leaf and ovule (35 DPA) of the wild-type (gland, G) and gossypol-deficient (glandless, GL) cultivars, in cotyledons two days post-elicitor treatment, and in GoPGF-silencing leaves. GoPGF is the regulator of pigment gland formation. FPKM (fragments per kilobase million) values obtained from the gland cotton leaves or ovules and the elicitor-treated cotyledons were set to 1 and used to estimate relative values of the paired samples. Data shown are means ± s. d. (n = 3 biological replicates).
