Modes of genetic adaptations underlying functional innovations in the rumen

查看全文 作　　者：Xiangyu [1]Pan;Yudong [1]Cai;Zongjun [1]Li;Xianqing [2]Chen;Rasmus [3]Heller;Nini [1]Wang;Yu [1]Wang;Chen [1]Zhao;Yong [4,5,6]Wang;Han [1]Xu;Songhai [7]Li;Ming [1]Li;Cunyuan [8]Li;Shengwei [8]Hu;Hui [9]Li;Kun [2]Wang;Lei [1]Chen;Bin [1]Wei;Zhuqing [1]Zheng;Weiwei [1]Fu;Yue [2]Yang;Tingting [1]Zhang;Zhuoting [2]Hou;Yueyang [1]Yan;Xiaoyang [10]Lv;Wei [10,11]Sun;Xinyu [12]Li;Shisheng [13]Huang;Lixiang [14]Liu;Shengyong [14]Mao;Wenqing [15]Liu;Jinlian [15]Hua;Zhipeng [16]Li;Guojie [5,17,18,19]Zhang;Yulin [1]Chen;Xihong [1]Wang;Qiang [2,20]Qiu;Brian [21]PDalrymple;Wen [2,5,19]Wang;Yu [1]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,Copenhagen,DK-2100,Denmark;[18]China National GeneBank,BGI-Shenzhen,Shenzhen,518083,China;[19]State Key Laboratory of Genetic Resources and Evolution,Kunming Institute of Zoology,Chinese Academy of Sciences,Kunming,650223,China;[20]State Key Laboratory of Grassland Agro-Ecosystem,College of Life Sciences,Lanzhou University,Lanzhou,730000,China;[21]School of Animal Biology and Institute of Agriculture,The University of Western Australia,Crawley,WA,6009,Australia

出　　处：《Science China(Life Sciences)》索引2021年第64卷第1期,共21页

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

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Modes of genetic adaptations underlying functional innovations in the rumen

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