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

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 (tRNA) 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.