PT  - JOURNAL ARTICLE
AU  - Xiangyu Pan
AU  - Yu Wang
AU  - Zongjun Li
AU  - Xianqing Chen
AU  - Rasmus Heller
AU  - Nini Wang
AU  - Chen Zhao
AU  - Yudong Cai
AU  - Han Xu
AU  - Songhai Li
AU  - Ming Li
AU  - Cunyuan Li
AU  - Shengwei Hu
AU  - Hui Li
AU  - Kun Wang
AU  - Lei Chen
AU  - Bin Wei
AU  - Zhuqing Zheng
AU  - Weiwei Fu
AU  - Yue Yang
AU  - Tingting Zhang
AU  - Zhuoting Hou
AU  - Yueyang Yan
AU  - Xiaoyang Lv
AU  - Wei Sun
AU  - Xinyu Li
AU  - Shisheng Huang
AU  - Lixiang Liu
AU  - Shengyong Mao
AU  - Wenqing Liu
AU  - Jinlian Hua
AU  - Zhipeng Li
AU  - Guojie Zhang
AU  - Yulin Chen
AU  - Xihong Wang
AU  - Qiang Qiu
AU  - Brian P. Dalrymple
AU  - Wen Wang
AU  - Yu Jiang
TI  - Tracing the origin of a new organ by inferring the genetic basis of rumen evolution
AID  - 10.1101/2020.02.19.955872
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.02.19.955872
4099  - http://biorxiv.org/content/early/2020/02/20/2020.02.19.955872.short
4100  - http://biorxiv.org/content/early/2020/02/20/2020.02.19.955872.full
AB  - The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers. We used 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 origin and evolution. Comparative analyses reveal that the rumen and the first-chamber stomachs of camels and cetaceans shared a common tissue origin from the esophagus. The rumen recruited genes from other tissues/organs and up-regulated many esophagus genes to aquire functional innovations involving epithelium absorption, improvement of the ketone body metabolism and regulation of microbial community. These innovations involve such genetic changes as ruminant-specific conserved elements, newly evolved genes and positively selected genes. Our in vitro experiements validate the functions of one enhancer, one positively selected gene and two newly evolved antibacterial genes. Our study provides novel insights into the origin and evolution of a complex organ.