The first genomic resource for the ‘near threatened’ Neotropical otter Lontra longicaudis (Carnivora: Mustelidae): mitochondrial genome characterisation and insights into phylomitogenomic relationships in the family Mustelidae

Abstract

ABSTRACT The Neotropical otter Lontra longicaudis is a top predator in aquatic ecosystems from North, Central, and South America and is subjected to substantial environmental distress due to historic and contemporary anthropogenic disturbance. Currently, L. longicaudis is considered ‘near threatened’ by the International Union for Conservation of Nature Red List of Threatened Species. This study renders the first genomic resource for L. longicaudis; its mitochondrial genome was assembled and characterised in detail. The AT-rich mitochondrial genome of L. longicaudis was 16,436 bp in length and encoded 13 protein coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a 994 bp long putative control region (CR). The heavy use of CTA (Leu), ATA (Met), and ATC (Ile) codons in PCGs contributes to the AT-rich nature of this genome. Out of 22 tRNAs, tRNA-Ser (AGY) (trnS1) lacked a typical ‘cloverleaf’ secondary structure. In the CR, numerous microsatellites and two tandem repeats were detected as well as multiple ‘hairpin’ structures. Ka/Ks values estimated for all but one PCG were < 1, indicating purifying selection in most PCGs. atp8 experienced neutral selection. A phylogenomic analysis based on PCGs confirms the monophyly of the family Mustelidae and also supports the monophyletic status of the subfamilies Guloinae, Helictidinae, Melinae, Mustelinae and Lutrinae; Ictonychinae was found to be polyphyletic. In the Lutrinae, L. longicaudis had an early branching position. The characterisation of a complete mitochondrial genome in the Neotropical otter L. longicaudis constitutes the first step towards supporting conservation efforts using genomic tools in this and other mustelids inhabiting aquatic neotropical environments under considerable contemporary anthropogenic disturbance.