Abstract
The spotted pond turtle Geoclemys hamiltonii (Gray, 1830) is widely distributed in the Indus, Ganges, and Brahmaputra river basins. In this study, the complete mitochondrial genome (mitogenome) of G. hamiltonii was sequenced using the next-generation sequencing (NGS) and Sanger sequencing, and the essential characteristics, gene arrangement, and phylogenetic relationship were analyzed. The results showed that the G. hamiltonii mitogenome was 16,505 bp in length (A: 33.6%, C: 27.1%, G: 13.4%, T: 25.8%) and consisted of 22 tRNAs, 13 protein-coding genes, two ribosomal RNA genes, and a non-coding control region (GenBank accession ON243873). The genome composition of G. hamiltonii presented a slight A + T bias (59.4%), and showed a positive AT skew (0.131) and a negative GC skew (− 0.338). All tRNAs had the typical clover structure, except trnS1 (GCT). The gene order of the G. hamiltonii mitogenome was the same as other Geoemydidae mitogenomes. A phylogenetic analysis based on the complete mitogenome indicated that the G. hamiltonii grouped independently of other species in the family Geoemydidae, supporting the species’ placement in the monotypic genus Geoclemys. Our results describe a novel genome at the species level. As the first complete mitogenome of G. hamiltonii, it provided valuable molecular information for phylogenetic and conservation genetics analyses of G. hamiltonii.
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Data Availability
The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at [https://www.ncbi.nlm.nih.gov] (https://www.ncbi.nlm.nih.gov/) under the accession number ON243873. The associated SRA number is SRR20592023.
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Acknowledgements
We are grateful to Dr. Yuan Xu (College of Animal Science and Technology, Northeast Agricultural University, Harbin, China) for his help with the sequence annotations. Cynthia Kulongowski with Liwen Bianji (Edanz) (www.liwenbianji.cn) assisted with editing the language of a draft of this manuscript.
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This work was supported by the Education Department of Hainan Province under Grant Hnky2021-25.
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Conceived and designed the experiments: GM, ZZ, XZ, XZ, and JW; Performed the experiments: ZZ, XZ, and XZ; Analyzed the data: ZZ XZ; Wrote the paper: GM and ZZ; Helped to proofread the paper: GM, ZZ, XZ, and JW; All authors agree to be accountable for all aspects of the work.
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This work was approved by the Animal Research Ethics Committee of Hainan Provincial Education Center for Ecology and Environment, Hainan Normal University (HNECEE2022-006), China.
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10528_2023_10562_MOESM1_ESM.tif
Predicted secondary structures of the 22 tRNA genes of the Geoclemys hamiltonii mitogenome. Supplementary file1 (TIF 3134 kb)
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Ma, G., Zuo, Z., Zhou, X. et al. The Characterization of Mitochondrial Genome of Spotted Pond Turtle (Geoclemys hamiltonii). Biochem Genet (2023). https://doi.org/10.1007/s10528-023-10562-y
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DOI: https://doi.org/10.1007/s10528-023-10562-y