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

Abstract

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.

Reclassification of Oligodon ningshaanensis Yuan, 1983 (Ophidia: Colubridae) into a New Genus, Stichophanes gen. nov. with Description on Its Malacophagous Behavior

“…Vidal et al (2000) suggested an Asian-North American origin of xenodontines (meaning differently from dipsadines) in the early Tertiary. This result is also mentioned by He et al (2010) that the divergence time of Thermophis from other xenodontine snakes is ~10-28 mya. The topologies of our results may agree with an Asian origin of the American Dipsadinae.…”

Sequencing and analysis of the mitochondrial genome of Pituophis catenifer sayi (Squamata: Colubridae)

“…Eight tRNA genes and ND6 are encoded on the light strand; the remaining genes are encoded on the heavy strand. Previous work reported the presence of a pseudo-tRNA-Pro gene adjacent to CRII in some Colubridae snakes (He et al 2010;Yan et al 2014). Our analysis of the P. catenifer sayi mitogenome does not indicate the presence of this DNA sequence, similar to results in E. schrenckii (Liu & Zhao 2015).…”

The complete mitochondrial genome of the Amur rat-snake Elaphe schrenckii (Squamata: Colubridae)

“…The complete mtDNA is 17,165 bp in length and contains 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and two control regions (CRI and CRII), which is similar to that of other reported Colubridae snakes (Chen et al, 2014;He et al, 2010;Jang & Hwang, 2011;Li et al, 2014a,b;Wan et al, 2014;Yan et al, 2014). The accurate annotated mitochondrial genome sequence was submitted to GenBank with accession number KP888955.…”