Structural evolution of the whole mitochondrial genome and phylogenetic inference in snakes (Squamata: Serpentes), including the undescribed mitogenome of the Brazilian endemic and critically endangered pitviper Bothrops insularis.

Evolutionary analyses of mitogenomes have provided insights into species evolution and conservation. Studies on snakes revealed a higher diversity especially involving variation in tRNA clusters. However, despite the increase in assemblies in databases, the available information for Brazilian species remains scarce in mitogenomic surveys. Based on this, we sequenced and provided the first description of the mitogenome of Bothrops insularis, a critically endangered taxon. We also used the B. insularis assembly and 128 molecules available in databases up to March 2022 to explore rearrangements and evolution of the mtDNA under a phylogenomic perspective. Comparative analyses revealed 24 mitotypes due to rearrangements within four tRNA clusters and within control regions. Mitotype 1 (M1) and Mitotype 2 (M2) are restricted to Scolecophidia and M3 is highly distributed within Alethinophidia. In addition, the M3 is suggested as the most likely ancestral mitotype during the mitogenome evolution. Regarding Bothrops, we recovered the same mitotype for B. jararaca and B. insularis, which structure differs from other Bothrops species. Nucleotide variation suggests 1.5% divergence between B. jararaca and B. insularis. Therefore, we suggest that B. insularis can be considered an evolutionary significant unit, and the data generated herein can be valuable for insights into genome evolution and conservation.