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Chen L, Ma J, Xu W, Shen F, Yang Z, Sonne C, Dietz R, Li L, Jie X, Li L, Yan G, Zhang X. Comparative transcriptome and methylome of polar bears, giant and red pandas reveal diet-driven adaptive evolution. Evol Appl 2024; 17:e13731. [PMID: 38894980 PMCID: PMC11183199 DOI: 10.1111/eva.13731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 05/18/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024] Open
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.
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Affiliation(s)
- Lei Chen
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Jinnan Ma
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
- College of Continuing EducationYunnan Normal UniversityKunmingChina
| | - Wencai Xu
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Fujun Shen
- Sichuan Key Laboratory for Conservation Biology of Endangered WildlifeChengdu Research Base of Giant Panda BreedingChengduChina
| | | | - Christian Sonne
- Arctic Research Centre, Faculty of Science and Technology, Department of EcoscienceAarhus UniversityRoskildeDenmark
| | - Rune Dietz
- Arctic Research Centre, Faculty of Science and Technology, Department of EcoscienceAarhus UniversityRoskildeDenmark
| | - Linzhu Li
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Xiaodie Jie
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Lu Li
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Guoqiang Yan
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
| | - Xiuyue Zhang
- Key Laboratory of bio‐Resources and eco‐Environment, Ministry of Education, College of Life ScienceSichuan UniversityChengduChina
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life SciencesSichuan UniversityChengduChina
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Jie X, Wu H, Yang M, He M, Zhao G, Ling S, Huang Y, Yue B, Yang N, Zhang X. Whole genome bisulfite sequencing reveals DNA methylation roles in the adaptive response of wildness training giant pandas to wild environment. Front Genet 2022; 13:995700. [PMID: 36303550 PMCID: PMC9592921 DOI: 10.3389/fgene.2022.995700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
DNA methylation modification can regulate gene expression without changing the genome sequence, which helps organisms to rapidly adapt to new environments. However, few studies have been reported in non-model mammals. Giant panda (Ailuropoda melanoleuca) is a flagship species for global biodiversity conservation. Wildness and reintroduction of giant pandas are the important content of giant pandas’ protection. However, it is unclear how wildness training affects the epigenetics of giant pandas, and we lack the means to assess the adaptive capacity of wildness training giant pandas. We comparatively analyzed genome-level methylation differences in captive giant pandas with and without wildness training to determine whether methylation modification played a role in the adaptive response of wildness training pandas. The whole genome DNA methylation sequencing results showed that genomic cytosine methylation ratio of all samples was 5.35%–5.49%, and the methylation ratio of the CpG site was the highest. Differential methylation analysis identified 544 differentially methylated genes (DMGs). The results of KEGG pathway enrichment of DMGs showed that VAV3, PLCG2, TEC and PTPRC participated in multiple immune-related pathways, and may participate in the immune response of wildness training giant pandas by regulating adaptive immune cells. A large number of DMGs enriched in GO terms may also be related to the regulation of immune activation during wildness training of giant pandas. Promoter differentially methylation analysis identified 1,199 genes with differential methylation at promoter regions. Genes with low methylation level at promoter regions and high expression such as, CCL5, P2Y13, GZMA, ANP32A, VWF, MYOZ1, NME7, MRPS31 and TPM1 were important in environmental adaptation for wildness training giant pandas. The methylation and expression patterns of these genes indicated that wildness training giant pandas have strong immunity, blood coagulation, athletic abilities and disease resistance. The adaptive response of giant pandas undergoing wildness training may be regulated by their negatively related promoter methylation. We are the first to describe the DNA methylation profile of giant panda blood tissue and our results indicated methylation modification is involved in the adaptation of captive giant pandas when undergoing wildness training. Our study also provided potential monitoring indicators for the successful reintroduction of valuable and threatened animals to the wild.
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Affiliation(s)
- Xiaodie Jie
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Honglin Wu
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, China
| | - Miao Yang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Ming He
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, China
| | - Guangqing Zhao
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Shanshan Ling
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Nan Yang
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, China
- *Correspondence: Nan Yang, ; Xiuyue Zhang,
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, China
- *Correspondence: Nan Yang, ; Xiuyue Zhang,
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Huang X, Ouyang Q, Ran M, Zeng B, Deng L, Hu S, Yang M, Li G, Deng T, He M, Li T, Yang H, Zhang G, Zhang H, Zeng C, Wang J. The immune and metabolic changes with age in giant panda blood by combined transcriptome and DNA methylation analysis. Aging (Albany NY) 2020; 12:21777-21797. [PMID: 33188156 DOI: 10.18632/aging.103990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 08/14/2020] [Indexed: 11/25/2022]
Abstract
Giant panda (Ailuropoda melanoleuca) is an endangered mammalian species. Exploring immune and metabolic changes that occur in giant pandas with age is important for their protection. In this study, we systematically investigated the physiological and biochemical indicators in blood, as well as the transcriptome, and methylation profiles of young, adult, and old giant pandas. The white blood cell (WBC), neutrophil (NEU) counts and hemoglobin (HGB) concentrations increased significantly with age (young to adult), and some indicators related to blood glucose and lipids also changed significantly with age. In the transcriptome analysis, differentially expressed genes (DEGs) were found in comparisons of the young and adult (257), adult and old (20), young and old (744) groups. Separation of the DEGs into eight profiles according to the expression trend using short time-series expression miner (STEM) software revealed that most DEGs were downregulated with age. Functional analysis showed that most DEGs were associated with disease and that these DEGs were also associated with the immune system and metabolism. Furthermore, gene methylation in giant pandas decreased globally with age, and the expression of CCNE1, CD79A, IL1R1, and TCF7 showed a highly negative correlation with their degree of methylation. These results indicate that the giant panda's immune function improves gradually with age (young to adult), and that changes in the methylation profile are involved in the effects of age on immune and metabolic functions. These results have important implications for the understanding and conservation of giant pandas.
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Affiliation(s)
- Xiaoyu Huang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.,China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Qingyuan Ouyang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Mingxia Ran
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Bo Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Linhua Deng
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Mingyao Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Guo Li
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Tao Deng
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Ming He
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Ti Li
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Haidi Yang
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Guiquan Zhang
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Heming Zhang
- China Conservation and Research Center for the Giant Panda, Dujiangyan 611830, Sichuan, China.,Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, Dujiangyan 611830, Sichuan, China
| | - Changjun Zeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
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