The genome of African manatee reveals secondary adaptation to the aquatic environment.

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 () with high continuity, completeness, and accuracy. We found that genes associated with osteopetrosis have undergone positive selection ( and ) or pseudogenized ( and ) in the African manatee, potentially contributing to the dense bone formation. The loss of 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.