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| 1 | Modes of genetic adaptations underlying functional innovations in the rumen显示文摘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. | 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 | 2021 | Science China(Life Sciences)2021，64，1： | 3 |
| 2 | Single-cell transcriptomic landscape of the sheep rumen provides insights into physiological programming development and adaptation of digestive strategies显示文摘As an important evolutionary innovation and unique organ,the rumen has played a crucial role in ruminant adaptation to complex ecological environments.However,the cellular basis of its complex morphology and function remains largely unknown.In this study,we identified eight major cell types from seven representative prenatal and postnatal rumen samples using~56600 single-cell transcriptomes.We captured the dynamic changes and high heterogeneity in cellular and molecular profiles before,during,and after the appearance of keratinized stratified squamous epithelium with neatly arranged papillae and functional maturity.Basal cells,keratinocytes,differentiating keratinocytes,terminally differentiated keratinocytes,and special spinous cells provided the cellular basis for rumen epithelium formation.Notably,we obtained clear evidence of two keratinization processes involved in early papillogenesis and papillae keratinization and identified TBX3 as a potential marker gene.Importantly,enriched stratum spinosum cells played crucial roles in volatile fatty acid(VFA)metabolism and immune response.Our results provide a comprehensive transcriptional landscape of rumen development at single-cell resolution,as well as valuable insight into the interactions between dietary metabolism and the rumen. | Yuan Yuan Da-Ming Sun Tao Qin Sheng-Yong Mao Wei-Yun Zhu Yu-Yang Yin Jie Huang Rasmus Heller Zhi-Peng Li Jun-Hua Liu Qiang Qiu | 2022 | Zoological Research2022，43，4： | 1 |
| 3 | CNEReg Interprets Ruminant-specific Conserved Non-coding Elements by Developmental Gene Regulatory Network显示文摘The genetic information coded in DNA leads to trait innovation via a gene regulatory network(GRN)in development.Here,we developed a conserved non-coding element interpretation method to integrate multi-omics data into gene regulatory network(CNEReg)to investigate the ruminant multi-chambered stomach innovation.We generated paired expression and chromatin accessibility data during rumen and esophagus development in sheep,and revealed 1601 active ruminantspecific conserved non-coding elements(active-RSCNEs).To interpret the function of these activeRSCNEs,we defined toolkit transcription factors(TTFs)and modeled their regulation on rumenspecific genes via batteries of active-RSCNEs during development.Our developmental GRN revealed 18 TTFs and 313 active-RSCNEs regulating 7 rumen functional modules.Notably,6 TTFs(OTX1,SOX21,HOXC8,SOX2,TP63,and PPARG),as well as 16 active-RSCNEs,functionally distinguished the rumen from the esophagus.Our study provides a systematic approach to understanding how gene regulation evolves and shapes complex traits by putting evo-devo concepts into practice with developmental multi-omics data. | Xiangyu Pan Zhaoxia Ma Xinqi Sun Hui Li Tingting Zhang Chen Zhao Nini Wang Rasmus Heller Wing Hung Wong Wen Wang Yu Jiang Yong Wang | 2023 | Genomics, Proteomics & Bioinformatics2023，21，3： | 0 |
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