KMS Of Academy of mathematics and systems sciences, CAS
| Modes of genetic adaptations underlying functional innovations in the rumen | |
Pan, Xiangyu1; Cai, Yudong1; Li, Zongjun1; Chen, Xianqing2; Heller, Rasmus3; Wang, Nini1; Wang, Yu1; Zhao, Chen1; Wang, Yong4,5,6 ; Xu, Han1; Li, Songhai7; Li, Ming1; Li, Cunyuan8; Hu, Shengwei8; Li, Hui1,9; Wang, Kun2; Chen, Lei2; Wei, Bin1; Zheng, Zhuqing1; Fu, Weiwei1; Yang, Yue2; Zhang, Tingting1; Hou, Zhuoting2; Yan, Yueyang1; Lv, Xiaoyang10; Sun, Wei10,11; Li, Xinyu12; Huang, Shisheng13; Liu, Lixiang14; Mao, Shengyong14; Liu, Wenqing15; Hua, Jinlian15; Li, Zhipeng16; Zhang, Guojie5,17,18,19; Chen, Yulin1; Wang, Xihong1; Qiu, Qiang2,20; Dalrymple, Brian P.21,22; Wang, Wen2,5,19; Jiang, Yu1
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| 2020-11-05 | |
| Source Publication | SCIENCE CHINA-LIFE SCIENCES
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| ISSN | 1674-7305 |
| Pages | 21 |
| Abstract | The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers. We analyzed 897 transcriptomes from three Cetartiodactyla lineages: ruminants, camels and cetaceans, as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen functional innovations. We identified genes with relatively high expression in the rumen, of which many appeared to be recruited from other tissues. These genes show functional enrichment in ketone body metabolism, regulation of microbial community, and epithelium absorption, which are the most prominent biological processes involved in rumen innovations. Several modes of genetic change underlying rumen functional innovations were uncovered, including coding mutations, genes newly evolved, and changes of regulatory elements. We validated that the key ketogenesis rate-limiting gene (HMGCS2) with five ruminant-specific mutations was under positive selection and exhibits higher synthesis activity than those of other mammals. Two newly evolved genes (LYZ1 and DEFB1) are resistant to Gram-positive bacteria and thereby may regulate microbial community equilibrium. Furthermore, we confirmed that the changes of regulatory elements accounted for the majority of rumen gene recruitment. These results greatly improve our understanding of rumen evolution and organ evo-devo in general. |
| Keyword | rumen innovations comparative transcriptomics comparative genomics evo-devo evolution of organs |
| DOI | 10.1007/s11427-020-1828-8 |
| Indexed By | SCI |
| Language | 英语 |
| Funding Project | National Natural Science Foundation of China[31822052] ; National Natural Science Foundation of China[31572381] ; National Natural Science Foundation of China[31660644] ; National Natural Science Foundation of China[41422604] ; National Thousand Youth Talents Plan ; Villum Foundation[VKR 023447] ; Independent Research Fund Denmark[8049-00098B] |
| WOS Research Area | Life Sciences & Biomedicine - Other Topics |
| WOS Subject | Biology |
| WOS ID | WOS:000587977700002 |
| Publisher | SCIENCE PRESS |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/52422 |
| Collection | 应用数学研究所 |
| Corresponding Author | Wang, Wen; Jiang, Yu |
| Affiliation | 1.Northwest A&F Univ, Coll Anim Sci & Technol, Key Lab Anim Genet Breeding & Reprod Shaanxi Prov, Yangling 712100, Shaanxi, Peoples R China 2.Northwestern Polytech Univ, Sch Ecol & Environm, Xian 710072, Peoples R China 3.Univ Copenhagen, Dept Biol, Sect Computat & RNA Biol, DK-2100 Copenhagen, Denmark 4.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 5.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China 6.Chinese Acad Sci, Acad Math & Syst Sci, CEMS, NCMIS,MDIS, Beijing 100080, Peoples R China 7.Chinese Acad Sci, Inst Deep Sea Sci & Engn, Marine Mammal & Marine Bioacoust Lab, Sanya 572000, Peoples R China 8.Shihezi Univ, Coll Life Sci, Shihezi 832003, Peoples R China 9.Guangxi Univ, Coll Anim Sci & Technol, State Key Lab Conservat & Utilizat Subtrop Agrobi, Nanning 530005, Peoples R China 10.Yangzhou Univ, Coll Anim Sci & Technol, Yangzhou 225009, Jiangsu, Peoples R China 11.Yangzhou Univ, Joint Int Res Lab Agr & Agriprod Safety, Minist Educ China, Yangzhou 225009, Jiangsu, Peoples R China 12.Guangzhou Med Univ, Key Lab Major Obstet Dis Guangdong Prov, Affiliated Hosp 3, Guangzhou 510150, Peoples R China 13.Shanghai Tech Univ, Sch Life Sci & Technol, Shanghai 201210, Peoples R China 14.Nanjing Agr Univ, Coll Anim Sci & Technol, Nanjing 210095, Peoples R China 15.Northwest A&F Univ, Shaanxi Ctr Stem Cells Engn & Technol, Coll Vet Med, Yangling 712100, Shaanxi, Peoples R China 16.Chinese Acad Agr Sci, Inst Special Anim & Plant Sci, Dept Special Econ Anim Nutr & Feed Sci, Changchun 130112, Peoples R China 17.Univ Copenhagen, Dept Biol, Sect Ecol & Evolut, DK-2100 Copenhagen, Denmark 18.BGI Shenzhen, China Natl GeneBank, Shenzhen 518083, Peoples R China 19.Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming 650223, Yunnan, Peoples R China 20.Lanzhou Univ, Coll Life Sci, State Key Lab Grassland Agroecosyst, Lanzhou 730000, Peoples R China 21.Univ Western Australia, Sch Anim Biol, Crawley, WA 6009, Australia 22.Univ Western Australia, Inst Agr, Crawley, WA 6009, Australia |
| Recommended Citation GB/T 7714 | Pan, Xiangyu,Cai, Yudong,Li, Zongjun,et al. Modes of genetic adaptations underlying functional innovations in the rumen[J]. SCIENCE CHINA-LIFE SCIENCES,2020:21. |
| APA | Pan, Xiangyu.,Cai, Yudong.,Li, Zongjun.,Chen, Xianqing.,Heller, Rasmus.,...&Jiang, Yu.(2020).Modes of genetic adaptations underlying functional innovations in the rumen.SCIENCE CHINA-LIFE SCIENCES,21. |
| MLA | Pan, Xiangyu,et al."Modes of genetic adaptations underlying functional innovations in the rumen".SCIENCE CHINA-LIFE SCIENCES (2020):21. |
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