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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.<\/jats:p>","DOI":"10.3390\/genes13081446","type":"journal-article","created":{"date-parts":[[2022,8,15]],"date-time":"2022-08-15T01:47:21Z","timestamp":1660528041000},"page":"1446","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Comparative Transcriptomics and Methylomics Reveal Adaptive Responses of Digestive and Metabolic Genes to Dietary Shift in Giant and Red Pandas"],"prefix":"10.3390","volume":"13","author":[{"given":"Lu","family":"Li","sequence":"first","affiliation":[{"name":"Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fujun","family":"Shen","sequence":"additional","affiliation":[{"name":"The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaodie","family":"Jie","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2792-0240","authenticated-orcid":false,"given":"Liang","family":"Zhang","sequence":"additional","affiliation":[{"name":"The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guoqiang","family":"Yan","sequence":"additional","affiliation":[{"name":"Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Honglin","family":"Wu","sequence":"additional","affiliation":[{"name":"China Conservation and Research Center for the Giant Panda, Dujiangyan 611800, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan","family":"Huang","sequence":"additional","affiliation":[{"name":"China Conservation and Research Center for the Giant Panda, Dujiangyan 611800, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rong","family":"Hou","sequence":"additional","affiliation":[{"name":"The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bisong","family":"Yue","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China"},{"name":"Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiuyue","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China"},{"name":"Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610065, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,8,14]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"6548","DOI":"10.1126\/science.aay1513","article-title":"Echolocation in soft-furred tree mice","volume":"372","author":"He","year":"2021","journal-title":"Science"},{"key":"ref_2","first-page":"20182185","article-title":"Convergent evolution of bird-mammal shared characteristics for adapting to nocturnality","volume":"286","author":"Wu","year":"2019","journal-title":"Proc. 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