Ruminant-specific genes identified using high-quality genome data and their roles in rumen evolution

基于高质量系统发育基因组学数据鉴定的反刍动物特异性基因及其在瘤胃演化中的作用

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.