The complete mitochondrial genome of H. hydrochaeris assembled in this study presented a circular topology with 16,681 base pairs (bp) in length and a GC content of 39.48%. Thirty-seven genes were annotated, including 22 tRNAs, 13 PCGs, two rRNAs and one control region (Supplementary Table ST01-02). This pattern, together with the gene arrangement observed in the capybara’s mitogenome (Fig. 1), is considered to be conserved in mammals (Prada and Boore 2019; Montaña-Lozano et al. 2022; Rackham and Filipovska 2022).
Concerning the PCGs, excluding ND6, which was encoded in the light strand (L-strand), all others were encoded in the heavy strand (H-strand). Minimal variation was observed regarding the gene length compared to the mitochondrial genomes of Cavia aperea (Cao and Xia 2016) and Cavia porcellus (Lord et al. 2018). As for the start codons, ATG was the most prevalent, present in ND1, ND4L, ND4, ND6, COX1, COX2, COX3, ATP6, ATP8 and CYTB. While ATT was observed in ND2, ND3 and ND5. As for the stop codons, TAA and TAG were predominant, with TAA appearing in ATP6, ATP8, ND4L, ND5 and COX2, while TAG was observed in ND1, ND2, ND3, ND6 and COX1. Additionally, ND4 and COX3 had T– as the stop codon, and CYTB was the only PCG with AGA. See Supplementary Table ST01-03 for more information.
All 22 tRNAs exhibited conserved structures and features, with no deviation in the anticodons. As expected for vertebrates, tRNA-Leu and tRNA-Ser were duplicated, with one of the tRNA-Ser with no D-arm (Supplementary Table ST01-S04). Concerning the rRNAs, 12S rRNA was 955 bp in length, while 16S had 1,569 bp, which showed a small variation in size when compared to Cavia species.
Regarding the phylogenetic relationships, H. hydrochaeris was recovered as a sister group of Cavia aperea and Cavia porcellus (Fig. 2). Together, they constitute the Caviidae clade. The observed phylogeny is congruent with the current Caviidae taxonomy, since this clade was recovered in previous studies with the family (Rowe and Honeycutt 2002; Pérez and Pol 2012; Honeycutt 2013; Madozzo-Jaén 2019). Cuniculus paca (Cuniculidae) was reconstructed as the sister group of Caviidae and the first group of Cavioidea to diverge. However, Dasyproctidae was not sampled in this study due to the unavailability of mitochondrial genomes and we were not able to access the family position within Cavioidea. Therefore, the description of novel mitochondrial genomes will greatly improve phylogenetic studies with mtDNA data, which can be helpful in reconstructing the evolutionary history of Cavioidea. Moreover, Coendou insidiosus (Erethizontoidea: Erethizontidae) was recovered as the sister group of Cavioidea, which was also previously recovered (Honeycutt 2013). This clade was reconstructed as the sister group of a major clade composed of Chinchillidae (Chinchilloidea) and Octodontidae, Ctenomyidae and Echimyidae (Octodontoidea).
The successful completion of the sequencing and annotation of the capybara mitochondrial genome represents a noteworthy scientific milestone, underscoring the inherent significance of dedicated research in elucidating the complex genetic landscape of this species. This achievement not only contributes to the advancement of knowledge in the fields of evolutionary biology, population genetics, and conservation science but also provides a solid foundation for future investigations, fostering a deeper understanding of capybara biology and facilitating informed conservation strategies.