{"title":"Chromosome-level genome assembly of the kiang (Equus kiang) illuminates genomic basis for its high-altitude adaptation.","authors":"Chuang Zhou, Xiaofeng Zheng, Kexin Peng, Kaize Feng, Bisong Yue, Yongjie Wu","doi":"10.1111/1749-4877.12795","DOIUrl":null,"url":null,"abstract":"<p><p>The kiang (Equus kiang) can only be observed in the Qinghai-Tibet Plateau (QTP). The kiang displayed excellent athletic performance in the high-altitude environment, which attracted wide interest in the investigation of the potential adaptive mechanisms to the extreme environment. Here, we assembled a chromosome-level genome of the kiang based on Hi-C sequencing technology. A total of 324.14 Gb clean data were generated, and the chromosome-level genome with 26 chromosomes (25 + X) and scaffold N50 of 101.77 Mb was obtained for the kiang. The genomic synteny analysis revealed large-scale chromosomal rearrangement during the evolution process of Equus species. Phylogenetic and divergence analyses revealed that the kiang was the sister branch to the ass and diverged from a common ancestor at approximately 13.5 Mya. The expanded gene families were mainly related to the hypoxia response, metabolism, and immunity. The kiang suffered a significant loss of olfaction-related genes, which might indicate decreased olfactory sensibility. Positively selected genes (PSGs) detected in the kiang were mainly associated with hypoxia response. Especially, there were two species-specific missense amino acid mutations in the PSG STAT3 annotated in the hypoxia-inducible factor 1 signal pathway, which may play an important role in the high-altitude adaptation of the kiang. Moreover, structure variations in the kiang genome were also identified, which possibly contributed to the high-altitude adaptation of the kiang. Comparative analysis revealed a lot of species-specific insertions and deletions in the kiang genome, such as PIK3CB and AKT with 3258 and 189 bp insertions in the intron region, respectively, possibly affecting the expression and regulation of hypoxia-related downstream pathways. This study provided valuable genomic resources, and our findings help a better understanding of the underlying adaptive strategies to the high-altitude environment in the kiang.</p>","PeriodicalId":13654,"journal":{"name":"Integrative zoology","volume":null,"pages":null},"PeriodicalIF":3.5000,"publicationDate":"2023-12-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Integrative zoology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1111/1749-4877.12795","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"ZOOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
The kiang (Equus kiang) can only be observed in the Qinghai-Tibet Plateau (QTP). The kiang displayed excellent athletic performance in the high-altitude environment, which attracted wide interest in the investigation of the potential adaptive mechanisms to the extreme environment. Here, we assembled a chromosome-level genome of the kiang based on Hi-C sequencing technology. A total of 324.14 Gb clean data were generated, and the chromosome-level genome with 26 chromosomes (25 + X) and scaffold N50 of 101.77 Mb was obtained for the kiang. The genomic synteny analysis revealed large-scale chromosomal rearrangement during the evolution process of Equus species. Phylogenetic and divergence analyses revealed that the kiang was the sister branch to the ass and diverged from a common ancestor at approximately 13.5 Mya. The expanded gene families were mainly related to the hypoxia response, metabolism, and immunity. The kiang suffered a significant loss of olfaction-related genes, which might indicate decreased olfactory sensibility. Positively selected genes (PSGs) detected in the kiang were mainly associated with hypoxia response. Especially, there were two species-specific missense amino acid mutations in the PSG STAT3 annotated in the hypoxia-inducible factor 1 signal pathway, which may play an important role in the high-altitude adaptation of the kiang. Moreover, structure variations in the kiang genome were also identified, which possibly contributed to the high-altitude adaptation of the kiang. Comparative analysis revealed a lot of species-specific insertions and deletions in the kiang genome, such as PIK3CB and AKT with 3258 and 189 bp insertions in the intron region, respectively, possibly affecting the expression and regulation of hypoxia-related downstream pathways. This study provided valuable genomic resources, and our findings help a better understanding of the underlying adaptive strategies to the high-altitude environment in the kiang.
期刊介绍:
The official journal of the International Society of Zoological Sciences focuses on zoology as an integrative discipline encompassing all aspects of animal life. It presents a broader perspective of many levels of zoological inquiry, both spatial and temporal, and encourages cooperation between zoology and other disciplines including, but not limited to, physics, computer science, social science, ethics, teaching, paleontology, molecular biology, physiology, behavior, ecology and the built environment. It also looks at the animal-human interaction through exploring animal-plant interactions, microbe/pathogen effects and global changes on the environment and human society.
Integrative topics of greatest interest to INZ include:
(1) Animals & climate change
(2) Animals & pollution
(3) Animals & infectious diseases
(4) Animals & biological invasions
(5) Animal-plant interactions
(6) Zoogeography & paleontology
(7) Neurons, genes & behavior
(8) Molecular ecology & evolution
(9) Physiological adaptations