Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China.
Biochem Genet. 2024 Aug;62(4):2946-2957. doi: 10.1007/s10528-023-10562-y. Epub 2023 Dec 5.
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.
斑点池龟（Geoclemys hamiltonii）广泛分布于印度河、恒河和雅鲁藏布江流域。本研究采用下一代测序（NGS）和 Sanger 测序技术对 G. hamiltonii 的完整线粒体基因组（mitogenome）进行了测序，并分析了其特征、基因排列和系统发育关系。结果表明，G. hamiltonii 的线粒体基因组长 16505bp（A:33.6%，C:27.1%，G:13.4%，T:25.8%），由 22 个 tRNA、13 个蛋白质编码基因、两个核糖体 RNA 基因和一个非编码控制区（GenBank 登录号 ON243873）组成。G. hamiltonii 的基因组组成表现出轻微的 A+T 偏好（59.4%），具有正的 AT 倾斜（0.131）和负的 GC 倾斜（-0.338）。所有 tRNA 均具有典型的三叶草结构，除 trnS1（GCT）外。G. hamiltonii 线粒体基因组的基因排列与其他 Geoemydidae 线粒体基因组相同。基于完整线粒体基因组的系统发育分析表明，G. hamiltonii 与 Geoemydidae 科的其他物种独立分组，支持该物种被归入单型属 Geoclemys。本研究结果描述了一个新的物种水平基因组。作为 G. hamiltonii 的第一个完整线粒体基因组，它为 G. hamiltonii 的系统发育和保护遗传学分析提供了有价值的分子信息。
