Long-Read Genome Sequencing Provides Molecular Insights into Scavenging and Societal Complexity in Spotted Hyena Crocuta crocuta.
Yong Shao, Xiao-Bo Wang, Mei-Ling Zhang, Yan Liu, Sheng Wang, Bao-Lin Zhang, Min-Min Yang, Ming-Hai Yang, Ting Jia, Tian-Chun Pu, Yan Lu, He Liu, Zhe Xu, Bo Li, Ning Liu, Violet Magoma Onsongo, Dong-Dong Wu, Cheng-Lin Zhang, Jue Ruan, Yan Li
Author Information
Yong Shao: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Xiao-Bo Wang: Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Mei-Ling Zhang: Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China.
Yan Liu: Beijing Zoo, Beijing, China.
Sheng Wang: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Bao-Lin Zhang: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Min-Min Yang: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Ming-Hai Yang: Beijing Zoo, Beijing, China.
Ting Jia: Beijing Zoo, Beijing, China.
Tian-Chun Pu: Beijing Zoo, Beijing, China.
Yan Lu: Beijing Zoo, Beijing, China.
He Liu: Beijing Zoo, Beijing, China.
Zhe Xu: Beijing Zoo, Beijing, China.
Bo Li: Beijing Zoo, Beijing, China.
Ning Liu: Beijing Zoo, Beijing, China.
Violet Magoma Onsongo: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Dong-Dong Wu: State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. ORCID
Cheng-Lin Zhang: Beijing Zoo, Beijing, China.
Jue Ruan: Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China.
Yan Li: State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China.
The spotted hyena (Crocuta crocuta) is a large and unique terrestrial carnivore. It is a particularly fascinating species due to its distinct phenotypic traits, especially its complex social structure and scavenging lifestyle, with associated high dietary exposure to microbial pathogens. However, the underlying molecular mechanisms related to these phenotypes remain elusive. Here, we sequenced and assembled a high-quality long-read genome of the spotted hyena, with a contig N50 length of ∼13.75 Mb. Based on comparative genomics, immunoglobulin family members (e.g., IGKV4-1) showed significant adaptive duplications in the spotted hyena and striped hyena. Furthermore, immune-related genes (e.g., CD8A, LAG3, and TLR3) experienced species-specific positive selection in the spotted hyena lineage. These results suggest that immune tolerance between the spotted hyena and closely related striped hyena has undergone adaptive divergence to cope with prolonged dietary exposure to microbial pathogens from scavenging. Furthermore, we provided the potential genetic insights underlying social complexity, hinting at social behavior and cognition. Specifically, the RECNE-associated genes (e.g., UGP2 and ACTR2) in the spotted hyena genome are involved in regulation of social communication. Taken together, our genomic analyses provide molecular insights into the scavenging lifestyle and societal complexity of spotted hyenas.
