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  • Jie, Xiaodie  (3)
  • Shen, Fujun  (3)
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  • 1
    Online Resource
    Online Resource
    Comparative Transcriptomics and Methylomics Reveal Adaptive Responses of Digestive and Metabolic Genes to Dietary Shift in Giant and Red Pandas
    MDPI AG ; 2022
    In:  Genes Vol. 13, No. 8 ( 2022-08-14), p. 1446-
    Details
    In: Genes, MDPI AG, Vol. 13, No. 8 ( 2022-08-14), p. 1446-
    Abstract: Both the giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to the order Carnivora, but have changed their dietary habits to eating bamboo exclusively. The convergent evolution characteristics of their morphology, genome and gut flora have been found in the two pandas. However, the research on the convergent adaptation of their digestion and metabolism to the bamboo diet, mediated by the dietary shift of the two pandas at the gene-expression and epigenetic regulation levels, is still lacking. We therefore used RNA sequencing among five species (two pandas and three non-herbivore mammals) and bisulfite sequencing among three species (two pandas and a carnivore ferret) to sequence key digestion and metabolism tissues (stomach and small intestine). Our results provide evidence that the convergent differentially expressed genes (related to carbohydrate utilization, bile secretion, Lys and Arg metabolism, vitamin B12 utilization and cyanide detoxification) of the two pandas are adaptive responses to the bamboo diet containing low lipids, low Lys and Arg, low vitamin B12 and high cyanide. We also profiled the genome-wide methylome maps of giant panda, red panda and ferret, and the results indicated that the promoter methylation of the two pandas may regulate digestive and metabolic genes to adapt to sudden environmental changes, and then, transmit genetic information to future generations to evolve into bamboo eaters. Taken together, our study provides new insights into the molecular mechanisms of the dietary shift and the adaptation to a strict bamboo diet in both pandas using comparative transcriptomics and methylomics.
    Type of Medium: Online Resource
    ISSN: 2073-4425
    URL: Article
    DOI: 10.3390/genes13081446
    Language: English
    Publisher: MDPI AG
    Publication Date: 2022
    detail.hit.zdb_id: 2527218-4
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  • 2
    Online Resource
    Online Resource
    Table1.XLSX
    Frontiers Media SA ; 2023
    In:  Frontiers in Genetics Vol. 14 ( 2023-7-4)
    Details
    In: Frontiers in Genetics, Frontiers Media SA, Vol. 14 ( 2023-7-4)
    Abstract: The changes in the expression of genes related to digestion and metabolism may be various in different dietary mammals from juvenile to adult, especially, the giant panda ( Ailuropoda melanoleuca ) and red panda ( Ailurus fulgens ), which were once carnivores but have shifted to being specialized bamboo eaters, are unique features of their changes are more unclear. To elucidate the changing patterns of gene expression related to digestion and metabolism from juvenile to adult in different dietary mammals, we performed transcriptome analysis of the liver or pancreas in giant and red pandas, herbivorous rabbits ( Oryctolagus cuniculus ) and macaques ( Macaca mulatta ), carnivorous ferrets ( Mustela putorius furo ), and omnivorous mice ( Mus musculus ) from juvenile to adult. During the transition from juvenile to adulthood, giant and red pandas, as well as rabbits and macaques, show significant upregulation of key genes for carbohydrate metabolism, such as starch hydrolysis and sucrose metabolism, and unsaturated fatty acid metabolism, such as linoleic acid, while there is no significant difference in the expression of key genes for fatty acid β-oxidation. A large number of amino acid metabolism related genes were upregulated in adult rabbits and macaques compared to juveniles. While adult giant and red pandas mainly showed upregulation of key genes for arginine synthesis and downregulation of key genes for arginine and lysine degradation. In adult stages, mouse had significantly higher expression patterns in key genes for starch hydrolysis and sucrose metabolism, as well as lipid and protein metabolism. In contrast to general expectations, genes related to lipid, amino acid and protein metabolism were significantly higher expressed in adult group of ferrets, which may be related to their high metabolic levels. Our study elucidates the pattern of changes in the expression of genes related to digestion and metabolism from juvenile to adult in different dietary mammals, with giant and red pandas showing adaptations associated with specific nutritional limitations of bamboo.
    Type of Medium: Online Resource
    ISSN: 1664-8021
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fgene.2023.1198977
    DOI: 10.3389/fgene.2023.1198977.s001
    DOI: 10.3389/fgene.2023.1198977.s002
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2606823-0
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  • 3
    Online Resource
    Online Resource
    Comparative transcriptome and methylome of polar bears, giant and red pandas reveal diet‐driven adaptive evolution
    Wiley ; 2024
    In:  Evolutionary Applications Vol. 17, No. 6 ( 2024-06)
    Details
    In: Evolutionary Applications, Wiley, Vol. 17, No. 6 ( 2024-06)
    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.
    Type of Medium: Online Resource
    ISSN: 1752-4571 , 1752-4571
    URL: Issue
    URL: Article
    DOI: 10.1111/eva.v17.6
    DOI: 10.1111/eva.13731
    Language: English
    Publisher: Wiley
    Publication Date: 2024
    detail.hit.zdb_id: 2405496-3
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