Complete mitochondrial genome of the Florida manatee (Trichechus manatus latirotris, Sirenia)

Abstract

The Florida manatee (Trichechus manatus latirostris) is an endangered subspecies of the West Indian manatee (T. manatus), which inhabits inland and marine waters of southeastern United States. In this study, we assembled the mitochondrial genome (mtDNA) of the Florida manatee from whole genome shotgun reads. As a result, we show that the currently annotated T. manatus mtDNA belongs to a different species, the Amazonian manatee (T. inunguis). The newly assembled Florida manatee mtDNA is 16,881 bp in length, with 13 protein-coding genes, two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and one non-coding control region (D-loop). Phylogenetic analysis based on the control region indicates the newly assembled mtDNA is haplotype A01, characteristic of T. m. latirostris, while the current mtDNA associated with the Florida manatee genome assembly has a Ti02 haplotype that is found in Amazonian manatees and hybrids.

The evolutionary history of manatees told by their mitogenomes

“…One of the first studies that discussed trichechid diversification compared tooth and skeletal characteristics from extant Trichechus species with fossil taxa, and concluded that T. manatus and T. senegalensis have similar morphological characteristics-which could be the consequence of a close relationship, and that T. inunguis has more derived characteristics 3 . Other studies using molecular data found divergent results: a study using only the cyt-b sequence suggested a sister relationship between T. manatus and T. senegalensis 9 , while other studies using mitochondrial D-loop as a genetic marker found T. senegalensis as the sister group of T. manatus and T. inunguis with high support values 13,46 , similar to our data. The divergence time estimates based on our mitogenomic data in the Family Trichechidae (approximately 7 Ma) are consistent with the fossil record for the genus in South America-register from Early Miocene and Late Miocene 3,47 .…”

“…We first created two custom BLAST databases on these genomes. Then we used the mtDNA from T. manatus (GenBank access numbers AM904728, and MN105083), as query in BLAST + v. 2.9.0 to search T. inunguis and T. manatus mtDNAs 13,25 . We subsequently used a custom Python 3 script 26 to retrieve BLAST hits and did the assembly with Geneious R9 (https ://www.genei ous.com).…”

TLR4 and TLR8 variability in Amazonian and West Indian manatee species from Brazil

“…This hybrid individual was studied by Luna ( 2013 ) and, although it had morphological characteristics of a West Indian manatee, its mitochondrial DNA is of an Amazonian manatee, while its karyotype had an intermediate number of chromosomes (n=50) between West Indian (n=48) and Amazonian (n-56) manatee. Although no conclusion may be drawn from only one hybrid individual, it reminds us of the importance of studying hybridization in manatees ( Vilaça et al, 2019 ; Vilaça and Santos, 2020 ) and to evaluate the relative contribution of TLR polymorphism on the adaptation of those hybrids. As has been evidenced in some studies, TLR genes are to a great extent subjected to purifying selection ( Alcaide and Edwards, 2011 ; Areal et al, 2011 ; Shen et al, 2012 ; Ishengoma and Agaba, 2017 ).…”

“…An additional study using craniomorphometric characteristics and cytogenetics ( Barros et al, 2016 ) indicates that West Indian manatees in the Brazilian coast must be a distinct species from the Antillean manatee. To complicate things further, evidence of hybrids of West Indian and Amazonian manatees reveals that those two species interbreed in transient habitats in the mouth of the Amazon river ( Vilaça et al, 2019 ; Vilaça and Santos, 2020 ), with unknown consequences for adaptation and for the gene pool of the species involved.…”