Fig. 3

Impact of extra chromosomes on changes in gene expression. a Proportions of DEGs with different expression levels in T11 (T11-P, T11-F and T11-FN) and T12 (T12-P, T12-F, T12-FN). Based on the expression levels of Zhongxian 3037, genes were divided into three clusters: (i) high-expression genes (FPKM > 100), (ii) medium-expression genes (10 < FPKM ≤ 100) and (iii) low-expression genes (0 < FPKM ≤ 10). Y-axis represents the proportion of DEGs in different expression level genes. b, c and d The Log₂(fold change) frequency distribution of genes with different expression levels in T11-P, T11-F and T11-FN, respectively. X-axis represents the Log₂(fold change) in gene expression levels between diploid and trisomy and Y-axis represents frequency distributions of Log₂(fold change). The red, blue and green lines indicate low (0 < FPKM ≤ 10), medium (10 < FPKM ≤ 100) and high (FPKM > 100) -expression genes, respectively; ns, not significant Boxplot on the right is a statistical analysis of the expression levels of the different types of genes (Wilcoxon test, ** p-value < 0.01)