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

BMC Genomics

Research

Yan Huang¹  Honglin Wu¹  Jinnan Ma²  Zhenxin Fan³  Bisong Yue³  Xiuyue Zhang³  Zhaobin Song³  Yang Geng⁴  Fujun Shen⁵  Liang Zhang⁵  Rong Hou⁵ 

[1] China Conservation and Research Center for the Giant Panda, 623006, Wolong, Sichuan, China;Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, 610065, Chengdu, China;College of Continuing Education, Yunnan Normal University, 650092, Kunming, China;Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, 610065, Chengdu, China;Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, 610065, Chengdu, China;Sichuan Key Laboratory of Conservation Biology On Endangered Wildlife, College of Life Sciences, Sichuan University, No.24 South Section 1, Yihuan Road, 610065, Chengdu, China;The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, 610081, Chengdu, China;

关键词: Giant panda;    Red panda;    Gene expression pattern;    Dietary shift;    Convergence;   

DOI  :  10.1186/s12864-023-09111-z

 received in 2022-07-28, accepted in 2023-01-03,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundIt 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.ResultsThe 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.ConclusionsOur 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.

【 授权许可】

CC BY   
© The Author(s) 2023

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