Gene expression variations in high-altitude adaptation: a case study of the Asiatic toad (Bufo gargarizans)

Abstract

Background: Genome-wide investigation of molecular mechanisms for high-altitude adaptation has attracted great attention in the last few years. In order to understand the contribution of gene expression level variations to high-altitude adaptation in Asiatic toads (Bufo gargarizans), we implemented a reciprocal transplant experiment between low- and high-altitude sites and sequenced 12 transcriptomes from brain, heart, and liver tissues.

Results: A large number of genes with expression differences (DEGs) between high- and low-altitude individuals (193 fixed and 844 plastic) were identified, and the majority of them were tissue specific. Heart displayed the largest number of DEGs, both plastic and fixed. Fixed DEGs were particularly concentrated in functions associated with muscle contraction, and the majority of them were down-regulated in high-altitude individuals. Plastic DEGs were highly concentrated in several energy metabolism related functional categories, and the majority of them were also down-regulated at high-altitude environments. In liver samples, genes associated with nutrient metabolism experienced a broad-scale expression down-regulation in high-altitude toads.

Conclusions: These broadly suppressed expression patterns at high altitudes are in strong contrast to those of endothermic homeotherms, suggesting poikilothermic vertebrates may have adopted different strategies at high altitudes. Our results strongly support that both genotypic specialization and phenotypic plasticity play crucial role in adaptation to high altitude for Asiatic toads. Poikilothermic vertebrates are among the most hypoxia-tolerant animals known, and many molecular mechanisms remain elusive. We hope that our results will provide useful directions for future research.

Keywords: Cardiac functions; Down-regulation; Gene expression; High-altitude; Nutrient metabolism; Toads.

Fig. 1

Design of the reciprocal transplant experiment

Fig. 2

Differentially expressed genes (DGEs) of Asiatic toads at high altitudes. a. Heatmaps of gene expression profiles for the four treatment groups. There are more plastic DEGs than fixed ones in any tissue, and the heart has more DEGs than other tissues, both fixed and plastic. b. Venn-diagram of fixed and plastic DEGs among three tissues. Most DEGs are tissue-specific. c. Spearman rank correlations between O_LOW and O_HIGH treatment groups (fixed DEGs) and between F_LOW and F_HIGH treatment groups (plastic DEGs). Correlation coefficients are smaller among plastic DEGs than among fixed DEGs. The heart had the weakest correlation in both comparisons

Fig. 3

Related functions of differentially expressed genes (DEGs). a. Expression patterns of DEGs by main functional clusters and tissue type for O_HIGH-F_HIGH treatment group. DEGs in stimulus response related clusters show a clear up-regulation trend; DGEs related to nutrient metabolism in the liver and DGEs related to muscle contraction and cellular respiration in the heart exhibit a clear broad-scale down-regulation. The numbers in each bar are numbers of genes. b. The positions of two core genes, ACTC1 and TNNC1, within the cardiac contraction pathway, and their expression levels in the four treatment groups