摘要
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.Ruminantspecific genes shared similar evolutionary and expression patterns with new genes found in other mammals,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.
反刍动物是世界上最成功的哺乳动物类群之一,具有显著的形态特征比如瘤胃.新基因在物种的表型演化中有重要的作用.为研究新基因在反刍动物新器官演化中的作用,结合新组装的鼷鹿和林麝的高质量基因组,以及以前发表的其他反刍动物科的高质量基因组,以牛科的绵羊基因注释为主,本工作鉴定了1064个反刍动物特异的新基因.结果显示,反刍动物新基因和其他哺乳动物中的新基因具有相似的演化和表达模式.有一部分新基因在瘤胃的演化中有作用.但大部分瘤胃表达的新基因招募自原先在其他组织表达的基因.如,在瘤胃不同发育时期有表达波动的反刍特异性PRD-SPRRⅡ基因家族成员受到正选择作用,可能在瘤胃的表皮发育中有重要功能.该工作的研究结果为理解反刍动物新基因的起源进化模式和哺乳动物新器官的演化提供了新的见解.
作者
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
陈春燕;殷源;黎浩榕;周博童;周炯;周小芳;李志鹏;刘贵春;潘香羽;张如;林泽山;陈垒;邱强;张勇;王文(School of Ecology and Environment,Northwestern Polytechnical 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)
基金
supported by the National Natural Science Foundation of China(32030016)
the Natural Science Foundation of Shaanxi Province(2020JQ-149)
the State Key Laboratory of Genetics Resources and Evolution(GREKF19-11)
the Innovation Foundation for Doctor Dissertation of Northwestern Polytechnical University to Zeshan Lin
the Shaanxi Program for Support of Topnotch Young Professionals to Lei Chen。