Modes of genetic adaptations underlying functional innovations in the rumen
Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
Standard
Modes of genetic adaptations underlying functional innovations in the rumen. / Pan, Xiangyu; Cai, Yudong; Li, Zongjun; Chen, Xianqing; Heller, Rasmus; Wang, Nini; Wang, Yu; Zhao, Chen; Wang, Yong; Xu, Han; Li, Songhai; Li, Ming; Li, Cunyuan; Hu, Shengwei; Li, Hui; Wang, Kun; Chen, Lei; Wei, Bin; Zheng, Zhuqing; Fu, Weiwei; Yang, Yue; Zhang, Tingting; Hou, Zhuoting; Yan, Yueyang; Lv, Xiaoyang; Sun, Wei; Li, Xinyu; Huang, Shisheng; Liu, Lixiang; Mao, Shengyong; Liu, Wenqing; Hua, Jinlian; Li, Zhipeng; Zhang, Guojie; Chen, Yulin; Wang, Xihong; Qiu, Qiang; Dalrymple, Brian P.; Wang, Wen; Jiang, Yu.
I: Science China Life Sciences, Bind 64, Nr. 1, 2021, s. 1-21.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
Harvard
APA
Vancouver
Author
Bibtex
}
RIS
TY - JOUR
T1 - Modes of genetic adaptations underlying functional innovations in the rumen
AU - Pan, Xiangyu
AU - Cai, Yudong
AU - Li, Zongjun
AU - Chen, Xianqing
AU - Heller, Rasmus
AU - Wang, Nini
AU - Wang, Yu
AU - Zhao, Chen
AU - Wang, Yong
AU - Xu, Han
AU - Li, Songhai
AU - Li, Ming
AU - Li, Cunyuan
AU - Hu, Shengwei
AU - Li, Hui
AU - Wang, Kun
AU - Chen, Lei
AU - Wei, Bin
AU - Zheng, Zhuqing
AU - Fu, Weiwei
AU - Yang, Yue
AU - Zhang, Tingting
AU - Hou, Zhuoting
AU - Yan, Yueyang
AU - Lv, Xiaoyang
AU - Sun, Wei
AU - Li, Xinyu
AU - Huang, Shisheng
AU - Liu, Lixiang
AU - Mao, Shengyong
AU - Liu, Wenqing
AU - Hua, Jinlian
AU - Li, Zhipeng
AU - Zhang, Guojie
AU - Chen, Yulin
AU - Wang, Xihong
AU - Qiu, Qiang
AU - Dalrymple, Brian P.
AU - Wang, Wen
AU - Jiang, Yu
PY - 2021
Y1 - 2021
N2 - 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.
AB - 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.
KW - rumen innovations
KW - comparative transcriptomics
KW - comparative genomics
KW - evo-devo
KW - evolution of organs
KW - EPIDERMAL DIFFERENTIATION
KW - PHYLOGENETIC ANALYSIS
KW - EXPRESSION ANALYSIS
KW - EVOLUTION
KW - STOMACH
KW - PACKAGE
KW - DOMAIN
KW - ANNOTATION
KW - PHYSIOLOGY
KW - STRATEGY
U2 - 10.1007/s11427-020-1828-8
DO - 10.1007/s11427-020-1828-8
M3 - Journal article
C2 - 33165812
VL - 64
SP - 1
EP - 21
JO - Science China Life Sciences
JF - Science China Life Sciences
SN - 1674-7305
IS - 1
ER -
ID: 252471367