Gene losses may contribute to subterranean adaptations in naked mole-rat and blind mole-rat

	Gene losses may contribute to subterranean adaptations in naked mole-rat and blind mole-rat
	Zheng, Zhizhong; Hua, Rong; Xu, Guoqiang; Yang, Hui; Shi, Peng
	2022
发表期刊	BMC BIOLOGY
卷号	20 期号:1
摘要	Background Naked mole-rats (Heterocephalus glaber, NMRs) and blind mole-rats (Spalax galili, BMRs) are representative subterranean rodents that have evolved many extraordinary traits, including hypoxia tolerance, longevity, and cancer resistance. Although multiple candidate loci responsible for these traits have been uncovered by genomic studies, many of them are limited to functional changes to amino acid sequence and little is known about the contributions of other genetic events. To address this issue, we focused on gene losses (unitary pseudogenes) and systematically analyzed gene losses in NMRs and BMRs, aiming to elucidate the potential roles of pseudogenes in their adaptation to subterranean lifestyle. Results We obtained the pseudogene repertoires in NMRs and BMRs, as well as their respective aboveground relatives, guinea pigs and rats, on a genome-wide scale. As a result, 167, 139, 341, and 112 pseudogenes were identified in NMRs, BMRs, guinea pigs, and rats, respectively. Functional enrichment analysis identified 4 shared and 2 species-specific enriched functional groups (EFGs) in subterranean lineages. Notably, the pseudogenes in these EFGs might be associated with either regressive (e.g., visual system) or adaptive (e.g., altered DNA damage response) traits. In addition, several pseudogenes including TNNI3K and PDE5A might be associated with specific cardiac features observed in subterranean lineages. Interestingly, we observed 20 convergent gene losses in NMRs and BMRs. Given that the functional investigations of these genes are generally scarce, we provided functional evidence that independent loss of TRIM17 in NMRs and BMRs might be beneficial for neuronal survival under hypoxia, supporting the positive role of eliminating TRIM17 function in hypoxia adaptation. Our results also suggested that pseudogenes, together with positively selected genes, reinforced subterranean adaptations cooperatively. Conclusions Our study provides new insights into the molecular underpinnings of subterranean adaptations and highlights the importance of gene losses in mammalian evolution.
收录类别	sci
语种	英语
文献类型	期刊论文
条目标识符	http://ir.kiz.ac.cn/handle/152453/13124
专题	科研部门_进化与功能基因组学（施鹏）遗传资源与进化国家重点实验室
推荐引用方式 GB/T 7714	Zheng, Zhizhong,Hua, Rong,Xu, Guoqiang,et al. Gene losses may contribute to subterranean adaptations in naked mole-rat and blind mole-rat[J]. BMC BIOLOGY,2022,20(1).
APA	Zheng, Zhizhong,Hua, Rong,Xu, Guoqiang,Yang, Hui,&Shi, Peng.(2022).Gene losses may contribute to subterranean adaptations in naked mole-rat and blind mole-rat.BMC BIOLOGY,20(1).
MLA	Zheng, Zhizhong,et al."Gene losses may contribute to subterranean adaptations in naked mole-rat and blind mole-rat".BMC BIOLOGY 20.1(2022).

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