Comparative Transcriptomics and Methylomics Reveal Adaptive Responses of Digestive and Metabolic Genes to Dietary Shift in Giant and Red Pandas
Both the giant panda (<i>Ailuropoda melanoleuca</i>) and red panda (<i>Ailurus fulgens</i>) 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 ha...
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MDPI AG
2022-08-01
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| author | Lu Li Fujun Shen Xiaodie Jie Liang Zhang Guoqiang Yan Honglin Wu Yan Huang Rong Hou Bisong Yue Xiuyue Zhang |
| author_facet | Lu Li Fujun Shen Xiaodie Jie Liang Zhang Guoqiang Yan Honglin Wu Yan Huang Rong Hou Bisong Yue Xiuyue Zhang |
| author_sort | Lu Li |
| collection | DOAJ |
| description | Both the giant panda (<i>Ailuropoda melanoleuca</i>) and red panda (<i>Ailurus fulgens</i>) 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. |
| first_indexed | 2024-03-09T04:23:49Z |
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| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-09T04:23:49Z |
| publishDate | 2022-08-01 |
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| series | Genes |
| spelling | doaj.art-493dd27558074a728d1894f1521be90c2023-12-03T13:43:14ZengMDPI AGGenes2073-44252022-08-01138144610.3390/genes13081446Comparative Transcriptomics and Methylomics Reveal Adaptive Responses of Digestive and Metabolic Genes to Dietary Shift in Giant and Red PandasLu Li0Fujun Shen1Xiaodie Jie2Liang Zhang3Guoqiang Yan4Honglin Wu5Yan Huang6Rong Hou7Bisong Yue8Xiuyue Zhang9Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, ChinaThe Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, ChinaKey Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, ChinaThe Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, ChinaSichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, ChinaChina Conservation and Research Center for the Giant Panda, Dujiangyan 611800, ChinaChina Conservation and Research Center for the Giant Panda, Dujiangyan 611800, ChinaThe Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, ChinaKey Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, ChinaKey Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, ChinaBoth the giant panda (<i>Ailuropoda melanoleuca</i>) and red panda (<i>Ailurus fulgens</i>) 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.https://www.mdpi.com/2073-4425/13/8/1446giant pandared pandaadaptive evolutiondietary shiftstomachsmall intestine |
| spellingShingle | Lu Li Fujun Shen Xiaodie Jie Liang Zhang Guoqiang Yan Honglin Wu Yan Huang Rong Hou Bisong Yue Xiuyue Zhang Comparative Transcriptomics and Methylomics Reveal Adaptive Responses of Digestive and Metabolic Genes to Dietary Shift in Giant and Red Pandas Genes giant panda red panda adaptive evolution dietary shift stomach small intestine |
| title | Comparative Transcriptomics and Methylomics Reveal Adaptive Responses of Digestive and Metabolic Genes to Dietary Shift in Giant and Red Pandas |
| title_full | Comparative Transcriptomics and Methylomics Reveal Adaptive Responses of Digestive and Metabolic Genes to Dietary Shift in Giant and Red Pandas |
| title_fullStr | Comparative Transcriptomics and Methylomics Reveal Adaptive Responses of Digestive and Metabolic Genes to Dietary Shift in Giant and Red Pandas |
| title_full_unstemmed | Comparative Transcriptomics and Methylomics Reveal Adaptive Responses of Digestive and Metabolic Genes to Dietary Shift in Giant and Red Pandas |
| title_short | Comparative Transcriptomics and Methylomics Reveal Adaptive Responses of Digestive and Metabolic Genes to Dietary Shift in Giant and Red Pandas |
| title_sort | comparative transcriptomics and methylomics reveal adaptive responses of digestive and metabolic genes to dietary shift in giant and red pandas |
| topic | giant panda red panda adaptive evolution dietary shift stomach small intestine |
| url | https://www.mdpi.com/2073-4425/13/8/1446 |
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