Background: Mitochondrial DNA sequences have long been used in phylogenetic studies. However, little attentionhas been paid to the changes in gene arrangement patterns in the snake’s mitogenome. Here, we analyzed thecomplete mitogenome sequences and structures of 65 snake species from 14 families and examined their structuralpatterns, organization and evolution. Our purpose was to further investigate the evolutionary implications andpossible rearrangement mechanisms of the mitogenome within snakes.

Results: In total, eleven types of mitochondrial gene arrangement patterns were detected (Type I, II, III, III-A, III-B,III-B1, III-C, III-D, III-E, III-F, III-G), with mitochondrial genome rearrangements being a major trend in snakes, especiallyin Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss,translocation and duplication. Within Scolecophidia, the O L was lost several times in Typhlopidae andLeptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region andtranslocation of the tRNA Leu gene are two visible features in Alethinophidian mitochondrial genomes. Independentlyand stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in threefamilies, indicating that the presence of P* was a polytopic event in the mitogenome.

Conclusions: The WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots formitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenomestructural diversity.