Modes of genetic adaptations underlying functional innovations in the rumen  

作　　者：Xiangyu Pan Yudong Cai Zongjun Li Xianqing Chen Rasmus Heller Nini Wang Yu Wang Chen Zhao Yong Wang Han Xu Songhai Li Ming Li Cunyuan Li Shengwei Hu Hui Li Kun Wang Lei Chen Bin Wei Zhuqing Zheng Weiwei Fu Yue Yang Tingting Zhang Zhuoting Hou Yueyang Yan Xiaoyang Lv Wei Sun Xinyu Li Shisheng Huang Lixiang Liu Shengyong Mao Wenqing Liu Jinlian Hua Zhipeng Li Guojie Zhang Yulin Chen Xihong Wang Qiang Qiu Brian PDalrymple Wen Wang Yu Jiang 

机构地区：[1]Key Laboratory of Animal Genetics,Breeding and Reproduction of Shaanxi Province,College of Animal Science and Technology,Northwest A&F University,Yangling,712100,China [2]School of Ecology and Environment,Northwestern Polytechnical University,Xi’an,710072,China [3]Section for Computational and RNA Biology,Department of Biology,University of Copenhagen,Copenhagen,DK-2100,Denmark [4]University of Chinese Academy of Sciences,Beijing,100049,China [5]Center for Excellence in Animal Evolution and Genetics,Chinese Academy of Sciences,Kunming,650223,China [6]CEMS,NCMIS,MDIS,Academy of Mathematics and Systems Science,Chinese Academy of Sciences,Beijing,100080,China [7]Marine Mammal and Marine Bioacoustics Laboratory,Institute of Deep-sea Science and Engineering,Chinese Academy of Sciences,Sanya,572000,China [8]College of Life Sciences,Shihezi University,Shihezi,832003,China [9]State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources,College of Animal Science and Technology,Guangxi University,Nanning,530005,China [10]College of Animal Science and Technology,Yangzhou University,Yangzhou,225009,China [11]Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China,Yangzhou University,Yangzhou,225009,China [12]Key Laboratory for Major Obstetric Diseases of Guangdong Province,The Third Affiliated Hospital of Guangzhou Medical University,Guangzhou,510150,China [13]School of Life Science and Technology,Shanghai Tech University,Shanghai,201210,China [14]College of Animal Science and Technology,Nanjing Agricultural University,Nanjing,210095,China [15]College of Veterinary Medicine,Shaanxi Centre of Stem Cells Engineering&Technology,Northwest A&F University,Yangling,712100,China [16]Department of Special Economic Animal Nutrition and Feed Science,Institute of Special Animal and Plant Sciences,Chinese Academy of Agricultural Sciences,Changchun,130112,China [17]Section for Ecology and Evolution,Department of Biology,University of Copenhagen,Copenha

出　　处：《Science China(Life Sciences)》2021年第1期1-21,共21页中国科学（生命科学英文版）

基　　金：supported by the National Natural Science Foundation of China(31822052,31572381);the National Thousand Youth Talents Plan to Y.J.;National Natural Science Foundation of China(31660644)to S.H.;National Natural Science Foundation of China(41422604)to S.L.;The Villum Foundation(VKR 023447);the Independent Research Fund Denmark(8049-00098B)。

摘　　要：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.

关 键 词：rumen innovations comparative transcriptomics comparative genomics EVO-DEVO evolution of organs 

分 类 号：Q953[生物学—动物学]