The genome of African manatee Trichechus senegalensis reveals secondary adaptation to the aquatic environment
Xin Huang,
Guixin Dong,
Huizhong Fan,
Wenliang Zhou,
Guangping Huang,
Dengfeng Guan,
Delu Zhang,
Fuwen Wei
Affiliations
Xin Huang
Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
Guixin Dong
Guangdong Chimelong Group, Co., Ltd., Guangzhou 511400, China
Huizhong Fan
CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
Wenliang Zhou
Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
Guangping Huang
CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Jiangxi Provincial Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China
Dengfeng Guan
CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
Delu Zhang
Chimelong Ocean Kingdom, Zhuhai 519000, China
Fuwen Wei
Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Jiangxi Provincial Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China; Corresponding author
Summary: Sirenians exhibit unique aquatic adaptations, showcasing both convergent adaptive features shared with cetaceans and unique characteristics such as cold sensitivity and dense bones. Here, we report a chromosome-level genome of the African manatee (Trichechus senegalensis) with high continuity, completeness, and accuracy. We found that genes associated with osteopetrosis have undergone positive selection (CSF1R and LRRK1) or pseudogenized (FAM111A and IGSF23) in the African manatee, potentially contributing to the dense bone formation. The loss of KCNK18 may have increased their sensitivity to cold water temperatures. Moreover, we identified convergent evolutionary signatures in 392 genes among fully aquatic mammals, primarily enriched in skin or skeletal system development and circadian rhythm, which contributed to the transition from terrestrial to fully aquatic lifestyles. The African manatee currently possesses a small effective population size and low genome-wide heterozygosity. Overall, our study provides genetic resources for understanding the evolutionary characteristics and conservation efforts of this species.
