Abstract
Trichechus manatus and Trichechus inunguis are the two Sirenia species that occur in the Americas. Despite their increasing extinction risk, many aspects of their biology remain understudied, including the repetitive DNA fraction of their genomes. Here we used the sequenced genome of T. manatus and TAREAN to identify satellite DNAs (satDNAs) in this species. We report the first description of TMAsat, a satDNA comprising ~0.87% of the genome, with ~684bp monomers and centromeric localization. In T. inunguis, TMAsat showed similar monomer length, chromosome localization and conserved CENP-B box-like motifs as in T. manatus. We also detected this satDNA in the Dugong dugon and in the now extinct Hydrodamalis gigas genomes. The neighbor-joining tree shows that TMAsat sequences from T. manatus, T. inunguis, D. dugon, and H. gigas lack species-specific clusters, which disagrees with the predictions of concerted evolution. We detected a divergent TMAsat-like homologous sequence in elephants and hyraxes, but not in other mammals, suggesting this sequence was already present in the common ancestor of Paenungulata, and later became a satDNA in the Sirenians. This is the first description of a centromeric satDNA in manatees and will facilitate the inclusion of Sirenia in future studies of centromeres and satDNA biology.
Highlights
The order Sirenia encompasses four extant herbivorous aquatic mammals
Dugong dugon occurs across coastal waters in the Indo-West Pacific Ocean, and T. senegalensis is restricted to the west coast of Africa, making T. manatus, the West Indian manatee, and T. inunguis, the Amazonian manatee, the only sirenians to occur in the Americas
These studies showed that the T. m. manatus populations from the Caribbean and up to the Amazon River mouth are phylogenetically closer to the populations of T. m. latirostris from the United States than to the Brazilian T. m. manatus populations south of the Amazon River mouth (Vianna et al, 2006; Barros et al, 2017; Lima et al, 2019, 2021)
Summary
The order Sirenia encompasses four extant herbivorous aquatic mammals. The Dugongidae family includes the Dugong dugon and the Steller’s sea cow Hydrodamalis gigas, the latter extinct due to overhunting, and the Trichechidae family includes three manatee species: Trichechus manatus, Trichechus inunguis, and Trichechus senegalensis (Domning, 2018). Dugong dugon occurs across coastal waters in the Indo-West Pacific Ocean, and T. senegalensis is restricted to the west coast of Africa, making T. manatus, the West Indian manatee, and T. inunguis, the Amazonian manatee, the only sirenians to occur in the Americas. The West Indian manatee occurs in Caribbean waters and the Atlantic coast ranging from Florida to the northeast of Brazil, and T. inunguis is found along the Amazon River basin (Bonvicino et al, 2020). Recent morphological and genetic analyses suggest the need for a revision in the T. manatus taxonomy considering the influence of the Amazon River as a barrier to gene flow. These studies showed that the T. m. Hybrids between T. manatus and T. inunguis have been reported on the sympatric area at the Amazon River mouth (Vianna et al, 2006; Lima et al, 2019; Luna et al, 2021)
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