The complete mitochondrial genome of Geoemyda spengleri its phylogenetic implications

Abstract

In this study, we determined the entire mitochondrial genome of Geoemyda spengleri. The complete mitogenome sequence was 17,448 bp in length, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA) genes; it also featured a control region (D-Loop). The overall nucleotide composition was as follows: A, 33.7%; T, 27.6%; C, 25.6%; and G, 13.1%, with a total A + T content of 61.3%. The phylogenetic analysis demonstrated a close relationship between G. spengleri, Sacalia quadriocellata, Sacalia bealei, Cyclemys oldhamii, and other species in Geoemydidae.

Keywords:

• Geoemyda spengleri
• mitogenome
• conservation genetics
• taxonomy

Black-breasted leaf turtle (Geoemyda spengleri) belongs to Order Testudines, Family Geoemydidae (Cai et al. 2015). It is an important reptilia distributed in Hunan, Guangdong, Guangxi, Hainan of China and parts of Viet Nam. Threatened by the levels of trade and scarcity of this species, G. spengleri has been listed in the national second-class national-protected wild animal which belongs to the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) in Appendix III (China). Many researchers hold different opinions on the classification status of this species (Shen et al. 1998; Cai et al. 2015; IUCN Red List of Threatened Species 2017). In this study, we report the complete mitochondrial genome of G. spengleri based on the Sanger sequencing data and compared it with those of 20 other species mitochondrial genomes available from the Testudines.

Tissue samples of G. spengleri were provided by Heilongjiang Province Museum, and the specimen of G. spengleri was stored in the amphibians and reptiles specimen room of Heilongjiang Province Museum. The total genomic DNA was extracted from the muscle of the specimen using Tissue DNA Extract kit (Tiangen Biotech Inc., Beijing, China) following the manufacturer’s protocol. The mitogenomes were amplified using eighteen primers, and PCR products were determined by the method of Sanger sequencing. The sequencing results were then assembled using the DNAman software package version 6.0.3 (Lynnon Biosoft, Vaudreuil, Canada). The transfer RNA (tRNA) genes were initially identified using the tRNAscan-SE version 1.21 program (Lowe and Eddy 1997) and they were then checked manually. The protein-coding genes (PCGs) and ribosomal RNA (rRNA) genes of the mitochondrial genomes were annotated using the MITOS Web server (Bernt et al. 2013).

The complete mitogenome sequence of G. spengleri was 17,448 bp in length and it was deposited in GenBank under accession number MH748151. The sequence contained 13 PCGs, 22 tRNA genes, 2 rRNA (12SrRNA and 16SrRNA) genes, an origin of replication on the light-strand (OL), and a control region (D-Loop). The overall base composition was as follows: A, 33.7%; T, 27.6%; C, 25.6%; and G, 13.1%, with an A + T bias (61.3%), which was similar to Sacalia bealei, Cuora aurocapitata, and other tortoises in Geoemydidae.

The phylogenetic tree was constructed with MEGA5.0 based on 20 complete mitochondrial genome sequences of Tesudines with Palea steindachneri as an outgroup (Figure 1). The phylogenetic position of G. spengleri was clustered with tortoises in Geoemydidae, and G. spengleri formed a sister relationship with Cuora, Mauremys, Cyclemys, and Sacalia in the Geoemydidae family, with 100% bootstrap support values.

Figure 1. Maximum Likelihood tree based on 20 complete mitochondrial genome sequences of Tesudines with Palea steindachneri as an outgroup. Alphanumeric terms indicate the GenBank accession numbers.

Acknowledgements

The authors thank anonymous reviewers for providing valuable comments on the manuscript.

Disclosure statement

The authors report no declaration of interest. The authors alone are responsible for the content and writing of this article.

Additional information

Funding

This work was supported by the National Natural Science Foundation of China [No. 31702152].