Fig. 5
Identification and expression analysis of miRNA clusters. A Location distribution of all expressed miRNAs and DEMs contained in Pre-miRNA Clusters (PmCs) on different chromosomes of upland cotton. Different colors indicate different categories of miRNAs, namely black, red, purple, green, olive, and cyan belong to the miRNAs of ‘gp1a’, ‘gp1b’ ‘gp2a’, ‘gp2b’, ‘gp3’ and ‘gp4’ categories, respectively. Among them, miRNAs with bold italics and enlarged fonts and underlined are identified DEMs. The blue columns on the left side of each chromosome or scaffold represent the specific genomic position of all 39 PmCs (Inter-distance < = 50,000 nts), and in particular, the blue column on the left side of Chir_D05 chromosome signifies the mapped interval of the fertility restorer gene Rf1 in our previous study [6]. B Statistics of the number of PmCs and their distribution of miRNAs and DEMs on different chromosomes. The X-axis represents chromosome name; the Y-axis and the numbers above each bar represent the PmC and miRNA numbers on each chromosome. C Venn diagram showing the number of DEMs in PmCs. D Hierarchical cluster analysis of the identified 39 DEMs in PmCs using a heat map drawn by TBtools software. The relative expression levels in the figure are the normalized expression data displayed with log10 (norm + 1) value. AP_NH, NH under mild HT stress; AP_SH, SH under mild HT stress; JP_NH, NH under extreme HT stress; JP_SH, SH under extreme HT stress