Gene expressions between obligate bamboo-eating pandas and non-herbivorous mammals reveal converged specialized bamboo diet adaptation

Abstract

Background: It is inevitable to change the function or expression of genes during the environmental adaption of species. Both the giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to Carnivora and have developed similar adaptations to the same dietary switch to bamboos at the morphological and genomic levels. However, the genetic adaptation at the gene expression level is unclear. Therefore, we aimed to examine the gene expression patterns of giant and red panda convergent specialized bamboo-diets. We examined differences in liver and pancreas transcriptomes between the two panda species and other non-herbivorous species.

Results: The clustering and PCA plots suggested that the specialized bamboo diet may drive similar expression shifts in these two species of pandas. Therefore, we focused on shared liver and pancreas DEGs (differentially expressed genes) in the giant and red panda relative to other non-herbivorous species. Genetic convergence occurred at multiple levels spanning carbohydrate metabolism, lipid metabolism, and lysine degradation. The shared adaptive convergence DEGs in both organs probably be an evolutionary response to the high carbohydrate, low lipid and lysine bamboo diet. Convergent expression of those nutrient metabolism-related genes in both pandas was an intricate process and subjected to multi-level regulation, including DNA methylation and transcription factor. A large number of lysine degradation and lipid metabolism related genes were hypermethylated in promoter regions in the red panda. Most genes related to carbohydrate metabolism had reduced DNA methylation with increased mRNA expression in giant pandas. Unlike the red panda, the core gene of the lysine degradation pathway (AASS) doesn't exhibit hypermethylation modification in the giant panda, and dual-luciferase reporter assay showed that transcription factor, NR3C1, functions as a transcriptional activator in AASS transcription through the binding to AASS promoter region.

Conclusions: Our results revealed the adaptive expressions and regulations of the metabolism-related genes responding to the unique nutrients in bamboo food and provided data accumulation and research hints for the future revelation of complex mechanism of two pandas underlying convergent adaptation to a specialized bamboo diet.

Keywords: Convergence; Dietary shift; Gene expression pattern; Giant panda; Red panda.

Fig. 1

Maximum likelihood phylogeny of the eight species in this study based on 1:1 single-copy orthologues coding sequences. The numbers in the nodes represent the bootstrap values. The scale bar indicates the number of substitutions per site

Fig. 2

PCA and clustering analyses of the expression for each tissue based on different gene sets. A PCA of the log-transformed normalized expression levels of all orthologs across liver samples. Species are represented by point shape. B PCA of the log-transformed normalized expression levels of all orthologs across pancreas samples. Species are represented by point shape. C Clustering of liver samples based on log-transformed normalized expression values. Distance between samples was measured by Spearman's rank correlation coefficient. D Clustering of pancreas samples based on log-transformed normalized expression values. Distance between samples was measured by Spearman's rank correlation coefficient

Fig. 3

Transcriptional patterns in liver. A Bar plots in blue and red circles indicate numbers of shared DEGs in giant panda and red panda relative to other non-herbivorous species in liver, respectively. Numbers in red and blue indicate shared up- and down-regulated DEGs in both panda species. B Heat map plot of shared DEGs in both panda species using log-transformed normalized expression value of genes across liver samples by adopting hierarchical clustering method

Fig. 4

The expression tendency of DEGs associated with lipid metabolism in liver samples. Y-axis represents log-transformed normalized expression levels. Boxplot edges indicate the 25th and 75th percentiles, and whiskers indicate non-outlier extremes

Fig. 5

The expression tendency of DEGs associated with lysine degradation in liver samples. Y-axis represents log-transformed normalized expression levels. Boxplot edges indicate the 25th and 75th percentiles, and whiskers indicate non-outlier extremes

Fig. 6

Transcriptional patterns in pancreas. A Bar plots in blue and red circles indicate numbers of shared DEGs in giant panda and red panda relative to other non-herbivorous species in pancreas, respectively. Numbers in red and blue indicate shared up- and down-regulated DEGs in both panda species. B Heat map plot of shared DEGs in both panda species using log-transformed normalized expression value of genes across pancreas samples by adopting hierarchical clustering method

Fig. 7

The expression tendency of DEGs associated with carbohydrate metabolism and respiratory electron transport in pancreas samples. Y-axis represents log-transformed normalized expression levels. Boxplot edges indicate the 25th and 75th percentiles, and whiskers indicate non-outlier extremes

Fig. 8

NR3C1 acts as an activator of AASS promoter activity. *** P<0.001