Abstract
<title>Abstract</title> <p> This study presents the first draft genome for the Amazonian manatee ( <italic>Trichechus inunguis</italic> ), the only exclusively freshwater sirenian species, contributing to the understanding of genomic evolution, adaptation to the freshwater environment and species conservation. The genome was sequenced using Illumina technology, employing 151 bp paired-end reads and achieving approximately 37× coverage. Initial assemblies were highly fragmented; however, reference-guided scaffolding with RagTag using the chromosome-level genome of <italic>T. senegalensi</italic> s increased BUSCO completeness to 98.8% for the female and 96.7% for the male. The genome sizes were 2.89 Gb (female) and 2.75 Gb (male), smaller than those of <italic>T. manatus</italic> (3.10 Gb) and <italic>T. senegalensis</italic> (3.19 Gb). A total of 19,001 protein-coding genes were identified in <italic>T. inunguis</italic> , with 89.1% of BUSCO genes annotated as complete. Repetitive elements accounted for 48.52% of the female genome and 46.54% of the male genome, with a predominance of retroelements and LINE-1/L1-CIN4, which corresponded to 13.46% of the genome. Comparative analysis revealed an expansion of gene families associated with G-protein-coupled receptor signaling, ion channels, oxidative metabolism and transport, potentially linked to adaptation to the Amazonian environment. This genome serves as a fundamental resource for evolutionary, population and conservation studies. </p>