Abstract
BackgroundMitochondrial DNA sequences have long been used in phylogenetic studies. However, little attention has been paid to the changes in gene arrangement patterns in the snake’s mitogenome. Here, we analyzed the complete mitogenome sequences and structures of 65 snake species from 14 families and examined their structural patterns, organization and evolution. Our purpose was to further investigate the evolutionary implications and possible rearrangement mechanisms of the mitogenome within snakes.ResultsIn 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, especially in Alethinophidia. In snake mitogenomes, the rearrangements mainly involved three processes, gene loss, translocation and duplication. Within Scolecophidia, the OL was lost several times in Typhlopidae and Leptotyphlopidae, but persisted as a plesiomorphy in the Alethinophidia. Duplication of the control region and translocation of the tRNALeu gene are two visible features in Alethinophidian mitochondrial genomes. Independently and stochastically, the duplication of pseudo-Pro (P*) emerged in seven different lineages of unequal size in three families, indicating that the presence of P* was a polytopic event in the mitogenome.ConclusionsThe WANCY tRNA gene cluster and the control regions and their adjacent segments were hotspots for mitogenome rearrangement. Maintenance of duplicate control regions may be the source for snake mitogenome structural diversity.
Highlights
Mitochondrial DNA sequences have long been used in phylogenetic studies
Types of mitogenome arrangement In the present study, the mitogenome size for Lycodon ruhstrati, L. rufozinatum and L. flavozonatum were found to range between 17,153-17,188 bp, respectively (Additional file 2: Table S1)
The mitogenomes contained 2 rRNAs, 22 tRNAs, 13 protein-coding genes (PCGs), 2 control regions (CR1 and CR2), and a pseudopro (P*, which is absent in L. ruhstrati) (Additional file 2: Table S1)
Summary
Mitochondrial DNA sequences have long been used in phylogenetic studies. little attention has been paid to the changes in gene arrangement patterns in the snake’s mitogenome. Deviations from the typical organization pattern have been found in many animal groups, such as fish [13, 14], amphibians [3, 5], reptiles [6, 10, 15,16,17,18,19], birds [7, 20], and mammals [21, 22] Such deviations involve shuffling of tRNA gene clusters, translocations and/or duplications of genes, loss of genes, and some gene inversions [3, 5,6,7, 13, 20, 23,24,25].
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