Fig. 4

Diploid and autotetraploid C. paliurus gene family evolution. a Proportions of genes with 1–4 alleles in the autotetraploid genome. b Relationship between the number of alleles per gene and expression (TPM, transcripts per million). (Wilcox test, p value ≤ 0.001: ***; p value ≥ 0.05: ns). c Comparison of the associations with structural variations (SVs), transposable elements (TEs), and protein‒protein interactions (PPIs) between the genes with allele loss and no allele loss. d Phylogenetic tree for diploid C. paliurus and four outgroup species. The estimated divergence time (million years ago, Mya) is specified at each node, and green bars indicate the 95% CI (each center is defined as the mean value). Gene family expansion and contraction are indicated in orange and blue, respectively, in the pie charts, and the corresponding numbers are shown using the same colors. Genes of diploid C. paliurus and other reference genomes were classified into five classes. The absolute numbers of genes are shown in the bars. e The expression of six genes encoding sulfotransferase and 1,3-beta-D-glucan synthase was significantly upregulated in autotetraploids compared to diploids. (Fisher’s exact test, p value ≤ 0.0001: ****)