Characterisation and comparative analysis of the complete mitochondrial genomes of two whiprays, <i>Himantura leoparda</i> and <i>H. uarnak,</i> occurring in the Southwest Indian Ocean

Abstract

The genus <i>Himantura</i>, Müller and Henle 1837 (Myliobatiformes: Dasyatidae) comprises benthic stingrays inhabiting tropical and subtropical waters, including the biodiversity-rich Southwest Indian Ocean (SWIO). Despite their ecological significance and susceptibility to anthropogenic pressures, the genetic diversity and evolutionary relationships of <i>Himantura</i> species remain poorly understood. This study sequenced and characterised the complete mitochondrial genomes of the SWIO variants of <i>Himantura leoparda</i> (17,682 bp) and <i>Himantura uarnak</i> (17,670 bp), the latter representing the first mitogenome for this species. Each mitogenome exhibited the typical vertebrate structure: 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a control region. Codon usage was strongly AT-biased, with leucine (CTA) and isoleucine (ATC) predominating. Elevated single nucleotide polymorphism diversity in <i>ND4</i> suggests ongoing divergence with adaptive implications. Phylogenetic analysis of concatenated PCGs confirmed the monophyly of <i>Himantura</i> within Dasyatidae, with distinct separation between the two SWIO mitogenomes supporting recognition of two separate species. The SWIO <i>H. leoparda</i> variant was most closely related to the Indo-Pacific <i>H. leoparda</i> variant. These findings address taxonomic ambiguities within the genus and highlight the need for species-specific conservation strategies, providing essential mitogenomic data to support future <i>Himantura</i> research in the SWIO.