Modes of genetic adaptations underlying functional innovations in the rumen

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 FuYue 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 P. Dalrymple, Wen Wang, Yu Jiang

Research output: Contribution to journalArticlepeer-review

15 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)1-21
Number of pages21
JournalScience China Life Sciences
Issue number1
Early online date5 Nov 2020
Publication statusPublished - Jan 2021


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