Comparative transcriptome and methylome of polar bears, giant and red pandas reveal diet-driven adaptive evolution

Abstract

Epigenetic regulation plays an important role in the evolution of species adaptations, yet little information is available on the epigenetic mechanisms underlying the adaptive evolution of bamboo-eating in both giant pandas (Ailuropoda melanoleuca) and red pandas (Ailurus fulgens). To investigate the potential contribution of epigenetic to the adaptive evolution of bamboo-eating in giant and red pandas, we performed hepatic comparative transcriptome and methylome analyses between bamboo-eating pandas and carnivorous polar bears (Ursus maritimus). We found that genes involved in carbohydrate, lipid, amino acid, and protein metabolism showed significant differences in methylation and expression levels between the two panda species and polar bears. Clustering analysis of gene expression revealed that giant pandas did not form a sister group with the more closely related polar bears, suggesting that the expression pattern of genes in livers of giant pandas and red pandas have evolved convergently driven by their similar diets. Compared to polar bears, some key genes involved in carbohydrate metabolism and biological oxidation and cholesterol synthesis showed hypomethylation and higher expression in giant and red pandas, while genes involved in fat digestion and absorption, fatty acid metabolism, lysine degradation, resistance to lipid peroxidation and detoxification showed hypermethylation and low expression. Our study elucidates the special nutrient utilization mechanism of giant pandas and red pandas and provides some insights into the molecular mechanism of their adaptive evolution of bamboo feeding. This has important implications for the breeding and conservation of giant pandas and red pandas.

Keywords: adaptive evolution; giant panda; methylome; polar bear; red panda; transcriptome.

FIGURE 1

PCA and clustering analyses of the mRNA expressions for all samples. (a) PCA of the log‐transformed normalized expression levels of all orthologue genes across liver samples from different species. Species are represented by point shapes and colours. (b) Clustering analyses of the log‐transformed normalized expression levels of all orthologue genes across liver samples from different species. Distance between samples is measured by Spearman's rank correlation coefficient. Aml, giant panda; Afu, red panda; Umr, polar bear.

FIGURE 2

Scatter bar chart of upregulated DEGs that are convergently expressed in Aml versus Umr group and Afu versus Umr group. (a) Glucose catabolism‐related genes. (b) Other saccharide metabolism‐related genes. (c) Cholesterol synthesis‐related genes. (d) Unsaturated fatty acid synthesis‐related genes. (e) Phospholipid synthesis related genes. (f) Sphingolipid metabolism‐related genes. X‐axis indicates different species and Y‐axis indicates count‐per‐million (CPM) normalized expression. Aml, giant panda; Afu, red panda; Umr, polar bear.

FIGURE 3

Scatter bar chart of downregulated DEGs that are convergently expressed in Aml versus Umr group and Afu versus Umr group. (a) Lysine degradation‐related genes. (b) Glutathione metabolism‐related genes. (c) Lipid catabolism‐related genes. (d) Fat digestion and absorption‐related genes. (e) Cholesterol clearance‐related genes. (f) Fatty acid synthesis‐related genes. X‐axis indicates different species and Y‐axis indicates CPM normalized expression. Aml, giant panda; Afu, red panda; Umr, polar bear.

FIGURE 4

The DNA methylation levels and patterns. (a) Distribution of CG methylation levels across the genome for liver samples in giant pandas, red pandas, and polar bears. X‐axis indicates different sample among three species, Y‐axis indicates methylation levels. Every 10 kb is taken as a bin. The width of each violin indicates how many bins are below this methylation level. (b) The mean CG methylation level of different gene elements in liver samples among giant pandas, red pandas, and polar bears. X‐axis indicates different functional regions of genes, Y‐axis indicates methylation levels, different colours represent different species. (c) The dynamic changes of methylation levels in the upstream and downstream regions of genes in liver samples in giant pandas, red pandas and polar bears. X‐axis indicates different regions, Y‐axis indicates methylation level, Colours represent different samples. Aml, giant panda; Afu, red panda; Umr, polar bear.

FIGURE 5

PCA and clustering analyses of the CG methylation levels for all samples. (a) PCA analyses of the CG methylation levels for liver samples from different species. Species are represented by point shapes and colours. (b) Clustering of liver samples based on CG methylation levels. Distance between samples is measured by Spearman's rank correlation coefficient. Aml, giant panda; Afu, red panda; Umr, polar bear.

FIGURE 6

Significantly enriched GO categories and KEGG categories of genes with promoter region methylation levels negatively correlated with expression. (a) Significantly enriched GO categories for genes with higher expression and hypomethylated promoter in Aml versus Umr group. (b) Significantly enriched KEGG categories for genes with higher expression and hypomethylated promoter in Aml versus Umr group. (c) Significantly enriched GO categories for genes with lower expression and hypermethylated promoter in Aml versus Umr group. (d) Significantly enriched KEGG categories for genes with lower expression and hypermethylated promoter in Aml versus Umr group. (e) Significantly enriched GO categories for genes with higher expression and hypomethylated promoter in Afu versus Umr group. (f) Significantly enriched KEGG categories for genes with higher expression and hypomethylated promoter in Afu versus Umr group. (g) Significantly enriched GO categories for genes with lower expression and hypermethylated promoter in Afu versus Umr group. (h) Significantly enriched KEGG categories for genes with lower expression and hypermethylated promoter in Afu versus Umr group. The top 15 most significantly enriched items/pathways are shown. X‐axis indicates the GeneRatio of the GO enriched items or the −log₁₀ (p value) of KEGG enriched pathways, Y‐axis indicates the name of the item/pathway. The number of genes in the KEGG enriched pathway is indicated by the size of the circle. Aml, giant panda; Afu, red panda; Umr, polar bear.

FIGURE 7

Scatter bar chart and box plot of genes negatively associated with convergent expression and convergent methylation in Aml versus Umr group and Afu versus Umr group. X‐axis indicates different species, Y‐axis in the scatter bar chart indicates CPM normalized expression, and Y‐axis in the box plot indicates gene promoter region methylation levels. Aml, giant panda; Afu, red panda; Umr, polar bear.