Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes

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.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4717-7) contains supplementary material, which is available to authorized users.

Phylogeny of caucasian rock lizards (Darevskia) and other true lizards based on mitogenome analysis: Optimisation of the algorithms and gene selection

“…Sequences of complete mitochondrial DNAs of Darevskia species were deposited in GenBank with accession numbers MH481130-37; MG704915-21. In all the species we have > 20X ; the observed lengths of the protein coding genes were similar to those found in other reptile mitochondrial genomes [38,40,41,62]. (Fig 2A and 2B).…”

Complete mitochondrial genome of Siamese cobra (Naja kaouthia) determined using next-generation sequencing

“…Mitogenomes contained 37 genes and two putative control regions (CRs). Gene arrangement patterns were identical to those of snakes (Yan et al 2008;Qian et al 2018). The ND6 gene and eight tRNA genes were encoded by the L-strand, with the remaining genes encoded by the H-strand.…”

“…The ND6 gene and eight tRNA genes were encoded by the L-strand, with the remaining genes encoded by the H-strand. The two putative CRs (1,028 bp and 1,027 bp in length) were located between tRNA-Ile and tRNA-Leu for CR1 and between tRNA-Pro and tRNA-Phe for CR2, respectively, with three conserved sequence blocks: CSB-1, CSB-2, and CSB-3 in the two CRs of snake mitogenomes (Yan et al 2008;Qian et al 2018). No tandem repeat was found in either of the two CRs, a result similar to common snake mitogenomes (Qian et al 2018).…”

“…The two putative CRs (1,028 bp and 1,027 bp in length) were located between tRNA-Ile and tRNA-Leu for CR1 and between tRNA-Pro and tRNA-Phe for CR2, respectively, with three conserved sequence blocks: CSB-1, CSB-2, and CSB-3 in the two CRs of snake mitogenomes (Yan et al 2008;Qian et al 2018). No tandem repeat was found in either of the two CRs, a result similar to common snake mitogenomes (Qian et al 2018). Comparison of overall nucleotide diversity among elapid snake mitogenomes was determined at 18.15 ± 0.66% and among Naja at 3.88%, suggesting sequence divergence in the same genus.…”

Phylogeny of Eryx Jayakari Isolated from Ha’il Province

“…Mitogenome or mitochondrial DNA (MtDNA) of vertebrates is distinguished by cellular abundancy, rapid evolution, intronless sequence, and highly conserved content and order. Therefore, mitogenome represented a valuable tool for molecular taxonomy, phylogeny, and evolutional studies (Qian et al, 2018). Snake mitogenome is unusual for vertebrates; in having unique duplicated control regions (CRs), higher evolutionary rate than nuclear DNA, shorter tRNA genes, and other shortened genes; that make it an ideal model for exploring potential links between mitogenomic structure, function, and evolution (Douglas and Gower, 2010;Eberhard and Wright, 2016).…”