Dataset Information

Complete mitochondrial genome of the razor-backed musk turtle (Sternotherus carinatus, testudines: emydidae) in Korea.

ABSTRACT: Sternotherus carinatus has been considered as a potential invasive species in Korea. However, the mitochondrial genome information of S. carinatus which can be used to control its effect on ecosystem is lacking. In this study, the complete mitochondrial genome of S. carinatus in Korea was sequenced and characterized. The mitochondrial genome consists of 37 genes (13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes) and a noncoding region. Phylogenetic analysis based on the mitochondrial genome sequences showed that S. carinatus from Korea is separated from other turtles which are the invasive species in Korea. Sequence divergence calculations indicated near-zero divergence between S. carinatus populations in Korea, the USA, and China, suggesting limited genetic differentiation. In the context of the broader issue of invasive species disrupting ecosystems, this research contributes to the identification of mitochondrial genomes for various freshwater turtle species, emphasizing the need for extended data collection to discern genetic mixing trends between native and non-native species. This study is a significant step toward managing S. carinatus as a potential invasive species in Korea.

SUBMITTER: Park J

PROVIDER: S-EPMC10768728 | biostudies-literature | 2023

REPOSITORIES: biostudies-literature

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Publications

Complete mitochondrial genome of the razor-backed musk turtle (Sternotherus carinatus, testudines: emydidae) in Korea.

Park Jaehong J Cheon Seung-Ju SJ Choi Jae-Hyuk JH Park Seung-Min SM Sung Ha-Cheol HC Lee Dong-Hyun DH

Mitochondrial DNA. Part B, Resources 20231218 12

Sternotherus carinatus has been considered as a potential invasive species in Korea. However, the mitochondrial genome information of S. carinatus which can be used to control its effect on ecosystem is lacking. In this study, the complete mitochondrial genome of S. carinatus in Korea was sequenced and characterized. The mitochondrial genome consists of 37 genes (13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes) and a noncoding region. Phylogenetic a ...[more]

PMID: 38189026

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Project description:The characterization of a complete mitogenome is widely used in genomics studies for systematics and evolutionary research. However, the sequences and structural motifs contained within the mitogenome of Testudines taxa have rarely been examined. The present study decodes the first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (16,657 bp) by using next-generation sequencing. This denovo assembly encodes 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA, and one control region (CR). Most of the genes were encoded on majority strand, except for one PCG (NADH dehydrogenase subunit 6) and eight tRNAs. Most of the PCGs were started with an ATG initiation codon, except for Cytochrome oxidase subunit 1 with "GTG" and NADH dehydrogenase subunit 5 with "ATA." The termination codons, "TAA" and "AGA" were observed in two subunits of NADH dehydrogenase gene. The relative synonymous codon usage analysis revealed the maximum abundance of alanine, isoleucine, leucine, and threonine. The nonsynonymous/synonymous ratios were <1 in all PCGs, which indicates strong negative selection among all Geoemydid species. The study also found the typical cloverleaf secondary structure in most of the tRNA genes, except for serine with the lack of the conventional DHU arm. The comparative study of Geoemydid mitogenomes revealed the occurrence of tandem repeats was frequent in the 3' end of CR. Further, two copies of a unique tandem repeat "TTCTCTTT" were identified in P. tentoria. The Bayesian and maximum-likelihood phylogenetic trees using concatenation of 13 PCGs revealed the close relationships of P. tentoria with Batagur trivittata in the studied dataset. All the Geoemydid species showed distinct clustering with high bootstrap support congruent with previous evolutionary hypotheses. We suggest that the generations of more mitogenomes of Geoemydid species are required, to improve our understanding of their in-depth phylogenetic and evolutionary relationships.

Dataset Information

Complete mitochondrial genome of the razor-backed musk turtle (Sternotherus carinatus, testudines: emydidae) in Korea.

Publications

Complete mitochondrial genome of the razor-backed musk turtle (<i>Sternotherus carinatus</i>, testudines: emydidae) in Korea.

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