Assembly and analysis of the complete mitochondrial genome of the Bogotá Robber Frog, Pristimantis bogotensis

Mitochondrial genomes are widely used in evolutionary studies due to their maternal inheritance, high mutation rate, and utility for inferring phylogeographic and phylogenetic relationships. The Neotropical frog genus, Pristimantis (Anura: Craugastoridae), with over 620 described species, represents the most species-rich anuran genera in the world, yet no mitogenome assemblies are available from this group. Here we use long-read DNA sequencing to assemble the complete mitogenome of Pristimantis bogotensis, a high-elevation Andean frog endemic to the Eastern Cordillera of Colombia. This mitogenomic characterization represents a valuable resource within this group of direct-developing anurans.

The complete mitochondrial genome of P. bogotensis was sequenced using Oxford Nanopore Technologies and assembled de novo. The mitogenome assembly was unusually large at 19,565 bp, yet exhibited the structure typical of vertebrate mitochondrial genomes, with a GC content of 40.2% and containing 13 protein-coding genes, 2 rRNA genes, 1 light-strand origin of replication, the control region containing the heavy-strand origin of replication and D-loop, and 22 tRNA genes. Notably, the tRNA-Cys lacked the D-arm. A phylogenetic analysis of previously published complete and partial anuran mitogenomes confirmed the placement of P. bogotensis within Pristimantis and supported a previous claim that the loss of the D-arm in tRNA-Cys might serve as a potential synapomorphy for this speciose clade.

To our knowledge, this is the first complete mitochondrial genome reported for the family Craugastoridae, and represents an important resource for phylogeography, metabarcoding, and phylogenetic studies in frogs, with direct applications in conservation and taxonomy.