Genetic chronicle of the capybara: the complete mitochondrial genome of Hydrochoerus hydrochaeris

Abstract

The capybara, Hydrochoerus hydrochaeris, is a rodent that inhabits the wetlands of South America. Despite being widely distributed and having the nuclear genomes available, there has been a lack of information regarding the mitochondrial genome. To address this, we conducted the assembly and annotation of the capybara’s mitochondrial genome and reconstructed the phylogeny of Parvorder Caviomorpha. The assembly was conducted under the de novo method with GetOrganelle, while the annotation was performed with MitoZ. Analysis of relative codon synonymous usage was conducted in the mitochondrial genomes of the capybara and two other Caviidae species: Cavia porcellus and Cavia aperea. The phylogenetic inference was conducted under the Maximum Likelihood method, using the 13 protein-coding genes, including the capybara as well as other 42 Caviomorpha mitochondrial genomes. The resulting capybara mitochondrial genome consisted of 16,681 bp, 37 genes (22 tRNAs, 2 rRNAs, and 13 protein-coding genes) and a control region. The number of genes and their arrangement corresponds to the pattern observed in most mammalian species. The capybara was recovered as a sister group of Cavia. Caviidae was reconstructed as a monophyletic group that is closely related to Cuniculidae. Overall, this study provides valuable insights into the mitochondrial evolution and evolutionary relationships of the capybara.