Ruminants comprise a highly successful group of mammals with striking morphological innovations,including the presence of a rumen.Many studies have shown that species-specific or lineage-specific genes(referred to as new genes)play important roles in phenotypic evolution.In this study,we identified 1064 ruminant-specific genes based on the newly assembled high-quality genomes of representative members of two ruminant families and other publically available high-quality genomes.Ruminant-specific genes shared similar evolutionary and expression patterns with new genes found in other mam-mals,such as primates and rodents.Most new genes were derived from gene duplication and tended to be expressed in the testes or immune-related tissues,but were depleted in the adult brain.We also found that most genes expressed in the rumen were genes predating sheep-sperm whale split(referred to as old genes),but some new genes were also involved in the evolution of the rumen,and contributed more during rumen development than in the adult rumen.Notably,expression levels of members of the ruminant-specific PRD-SPRRII gene family,which are subject to positive selection,varied throughout rumen development and may thus play important roles in the development of the keratin-rich surface of the rumen.Overall,this study generated two novel ruminant genomes and also provided novel insights into the evolution of new mammalian organs.

Chunyan Chen;Yuan Yin;Haorong Li;Botong Zhou;Jiong Zhou;Xiaofang Zhou;Zhipeng Li;Guichun Liu;Xiangyu Pan;Ru Zhang;Zeshan Lin;Lei Chen;Qiang Qiu;Yong E.Zhang;Wen Wang

School of Ecology and Environment,Northwestern Poly technical University,Xi'an 710072,China;College of Animal Science and Technology,Jilin Agricultural University,Changchun 130118,China;State Key Laboratory of Genetic Resources and Evolution,Kunming Institute of Zoology,Chinese Academy of Sciences,Kunming 650223,China;Department of Gastroenterology,Guangdong Provincial People's Hospital,Guangdong Academy of Medical Sciences,Guangzhou 510080,China;Guangdong Cardiovascular Institute,Guangzhou 510080,China;Key Laboratory of Zoological Systematics and Evolution,Institute of Zoology,Chinese Academy of Sciences,Beijing 100101,China;University of Chinese Academy of Sciences,Beijing 100049,China;Center for Excellence in Animal Evolution and Genetics,Chinese Academy of Sciences,Kunming 650223,China

科学通报（英文版）

[1]Chunyan Chen;Yuan Yin;Haorong Li;Botong Zhou;Jiong Zhou;Xiaofang Zhou;Zhipeng Li;Guichun Liu;Xiangyu Pan;Ru Zhang;Zeshan Lin;Lei Chen;Qiang Qiu;Yong E.Zhang;Wen Wang-.Ruminant-specific genes identified using high-quality genome data and their roles in rumen evolution)[J].科学通报（英文版）,2022(08):825-835

Ruminant,Ruminants,publically,predating,SPRRII

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