Analysis of the Entire Mitogenome of the Threatened Freshwater Stingray Potamotrygon leopoldi (Myliobatiformes: Potamotrygonidae) and Comprehensive Phylogenetic Assessment in the Xingu River, Brazilian Amazon

Abstract

The present study characterizes the complete mitochondrial genome of Potamotrygon leopoldi, commonly referred to as the "white blotched stingray", a member of the Potamotrygonidae family that are a group of stingrays that live exclusively in freshwater environments. Potamotrygon leopoldi, endemic to the Xingu River in the Amazon region, are exploited by commercial fisheries for food and commonly exploited by the ornamental industry, and this has a significant impact on the populations. Here, newly assembled PacBio long-read sequencing assesses the complete mitogenome of P. leopoldi and performs a comparative investigation into the evolutionary connections to other extant taxa of elasmobranchs. The mitogenome has 17,504 bp, containing 13 protein-coding, 22 tRNA, and 2 rRNA genes. The mitogenome comprises A: 32.32%, T: 24.41%, C: 12.84%, and G: 30.42%, with an AT content of 56.73%. The values of AT and GC skewness were 0.13 and -0.40, respectively. Our phylogenetic analyses with mitogenome sequences of 40 elasmobranch species support the monophyly for the Potamotrygonidae family and indicate a close relationship to the Dasyatidae family and a sister relationship with Potamotrygon orbignyi and Potamotrygon falkneri. We also detected various amino acid sites in positive selection exclusively in P. leopoldi. This extensive comparative mitogenomic investigation offers novel and significant insights into the evolutionary lineage of neotropical freshwater stingrays and their closely related taxa. It is an indispensable resource for facilitating ongoing and prospective investigations into the molecular evolution of elasmobranchs.

Keywords: arraia Negra do Xingu; mitochondrial genome; phylogeny; positive selection.

Figure 1

Circular genome map of the P. leopoldi mitochondrial genome, showing 13 PCGs (in green and yellow), 2 rRNA (in red) genes, 22 tRNA genes (in blue), and the control region D-loop (in gray).

Figure 2

Secondary structure of tRNAs in the mitogenome of P. leopoldi visualized in the Forna web server.

Figure 3

Arrangement of genes encoding rRNAs and proteins of P. leopoldi and other species of Potamotrygon genus. Heavy (+) and light (−) strands. Red arrows represent the changes between Potamotrygon leopoldi and the other species that were used in the gene arrangement comparison.

Figure 4

Relative Synonymous Codon Usage (RSCU) of the protein-coding genes of P. leopoldi and species from the Potamotrygonidae family and the C. milii as outgroup.

Figure 5

Organization of the CR in the complete mitogenomes of P. leopoldi, other four species from the Potamotrygon genus, and the outgroup C. milii.

Figure 6

(A) Phylogenetic tree using the complete mitochondrial genome of species of order Myliobatiformes. GenBank Accession IDs are in brackets. The nodal support indicates the posterior probability in BI. (B) Divergence time estimates in the class Chondrichthyes. The value above the node represents the time to present in My.