Complete Mitochondrial Genomes of Four Pelodiscus sinensis Strains and Comparison with Other Trionychidae Species

SIMPLE SUMMARY: The Chinese soft-shelled turtle (Pelodiscus sinensis) is an economically important aquatic reptile species with rich nutrition and medicinal value. However, the wild resources of P. sinensis have been depleting due to natural and artificial factors in recent decades. Herein, we report the complete mitochondrial genomes of four P. sinensis strains and analyzed the nucleotide composition and variable site for the four mitogenomes. Using Ka/Ks and sliding window analyses, we explored the genetic diversity and selection pressures of different mitochondrial genes in the four P. sinensis strains. Through comparative analysis, the present study described the structural variation of 22 tRNAs, replication origin region of the L-strand, and control region, indicating the genetic variations among the four P. sinensis strains. Furthermore, the evolutionary relationship of P. sinensis strains and other Trionychidae species was determined by phylogenetic analysis. Taken together, our findings provide genetic information and an essential basis for understanding the genetic variations and evolutionary relationship of P. sinensis strains, which will play an important role in bioprospecting and conservation of P. sinensis. ABSTRACT: The Chinese soft-shelled turtle (Pelodiscus sinensis) is an important aquaculture reptile with rich nutritional and medicinal values. In recent decades, the wild resources of P. sinensis have been depleting due to natural and artificial factors. Herein, we report the complete mitochondrial genome of four P. sinensis strains, including the Japanese (RB) strain, Qingxi Huabie (HB) strain, Jiangxi (JB) strain, and Qingxi Wubie (WB) strain. The nucleotide composition within the complete mitogenomes was biased towards A + T with a variable frequency ranging from 59.28% (cox3) to 70.31% (atp8). The mitogenomes of all four strains contained 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, 1 control region, and a replication origin region of the L-strand replication (OL), which was consistent with most vertebrates. Additionally, the atp8, nad4l, nad6, and nad3 genes possessed high genetic variation and can be used as potential markers for the identification of these P. sinensis strains. Additionally, all PCGs genes were evolving primarily under purifying selection. Through comparative analysis, it was revealed that most of the tRNAs were structurally different in the TψC stem, DHU stem, and acceptor stem. The length of the tandem repeats in the control region was variable in the four P. sinensis strains, ranging from 2 bp to 50 bp. Phylogenetic analysis indicated that all P. sinensis strains clustered into one branch and were closely related to other Trionychinae species. Overall, this study provides mitochondrial genome information for different P. sinensis strains to support further species identification and germplasm resource conservation.