The complete mitochondrial DNA sequence and the phylogenetic position of Achalinus meiguensis (Reptilia: Squamata)

Wang, Guangli; He, Shunping; Huang, Song; He, Ming; Zhao, Ermi

doi:10.1007/s11434-009-0160-0

Cited by 19 publications

(9 citation statements)

References 56 publications

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“…However, the resultant Bayesian tree showed that Homalopsidae was nested within Elapidae and Colubridae (Additional file 3 : Figure S2). Thus, the topology of our phylogenetic tree is similar to previous studies [ 12 , 18 , 39 , 46 , 47 ] and in agreement with the results from nucelar gene analyses [ 45 , 48 ].…”

Section: Resultssupporting

confidence: 91%

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

et al. 2018

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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.

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Section: Resultssupporting

confidence: 91%

“…These unique characteristics are the duplicated control regions, an elevated evolutionary rate relative to nuclear DNA. and shorter tRNA genes, and other shortened genes [ 12 , 25 , 39 , 40 ].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2018

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“…They are located between the tRNA Phe and ND1 genes and are separated by the tRNA Val gene, as observed in other snakes. The base composition of the 12S rRNA gene is 18.6% T, 28% C, 34.5% A, and 18.9% G, while the 16S rRNA composition is 20.2% T, 25.6% C, 38.1% A, and 16.2% G. The total length of rRNAs is 2404 bp, which is similar to that of other colubroid (Jiang et al 2007) and Achalinus (Wang et al 2009) snakes but shorter than that of members of Scolecophidia, Henophidia, and Acrochordus (Jiang et al 2007).…”

Section: Pro Genessupporting

confidence: 53%

The complete mitochondrial genome of the Sichuan hot-spring keel-back (Thermophis zhaoermii; Serpentes: Colubridae) and a mitogenomic phylogeny of the snakes

Feng

Zhao³

2010

Mitochondrial DNA

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The complete mitochondrial genome sequence of the Sichuan hot-spring keel-back (Thermophis zhaoermii) was determined in the present study. The genome is 17,322 bp in size, containing 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes, 22 transfer RNA (tRNA) genes, and 2 control regions, similar to other alethinophidian snakes. A special 40 bp non-coding region, which was highly homologous to the start of control regions I (CR I) and II (CR II), containing a 16 bp C-rich segment, was identified upstream of the pseudo-tRNA Pro gene that had been observed across Colubridae and Homalopsidae. Twelve concatenated heavy-strand encoded protein-coding genes were used for phylogenetic reconstruction employing Bayesian and maximum likelihood inference. Both analyses yielded identical topologies, demonstrating that T. zhaoermii can solidly be placed within Colubridae as a sister group to Colubrinae. The paraphyly of Scolecophidia and monophyly of Henophidia and Caenophidia were also supported. A relaxed clock molecular divergence time analysis was carried out to estimate the temporal origin of each clade. Our results indicate that the Alethinophidia began to diverge from the paraphyletic Scolecophidia approximately 130 million years ago in the early Cretaceous; the divergence of living alethinophidian snakes, the radiation of the Caenophidia, and the separation between Acrochordus and the Colubroidea might have been caused by the K/T event.

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“…Although there are nine species in the genus Achalinus presently, a few sequences of this genus have been determined. Two of these sequences are the complete mitochondrial genome of Achalinus meiguensis (Wang et al 2009) and Achalinus rufescens (Zhang et al 2017). In this article, we determined and described the mitogenome of A. spinalis in order to obtain basic genetic information about this species.…”

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Mitochondrial genome of the Common burrowing snake Achalinus spinalis (Reptilia: Xenodermatidae)

Peng

Yang

Duan

et al. 2017

Mitochondrial DNA Part B

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Common burrowing snake Achalinus spinalis is the type species of Achalinus. The complete mitochondrial genome (mitogenome) sequence of A. spinalis was determined by using a PCR-based method. The total length of mitogenome is 17,165 bp and contains 13 protein-coding genes, 22 tRNA genes, 2 ribosome RNA genes and 2 control regions (CR). All the protein-coding genes in A. spinalis were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The phylogenetic tree of A. spinalis and 12 other closely species was built. The DNA data presented here will be useful to study the evolutionary relationships and genetic diversity of A. spinalis.

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The complete mitochondrial DNA sequence and the phylogenetic position of Achalinus meiguensis (Reptilia: Squamata)

Cited by 19 publications

References 56 publications

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

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

The complete mitochondrial genome of the Sichuan hot-spring keel-back (Thermophis zhaoermii; Serpentes: Colubridae) and a mitogenomic phylogeny of the snakes

Mitochondrial genome of the Common burrowing snake Achalinus spinalis (Reptilia: Xenodermatidae)

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