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The complete mitochondrial genome of the endangered Chinese black-necked pond turtle, Mauremys nigricans.

ABSTRACT: The complete mitochondrial genome of the endangered Chinese black-necked pond turtle, Mauremys nigricans, was determined in this study. The mitogenome was 16?779?bp in length, and the GC content was 39.07%. The genomes encoded 37 genes typically found in other vertebrates. In the control region, three CSBs were identified, followed by long tandem repeats of (ATATCATATT)₁₀(ATATC)(ATATATC)₇(TA)₁₀₂. The mitochondiral genome sequence would be useful for the phylogenetic and conservation studies of Asian endangered turtles.

SUBMITTER: Zhao J

PROVIDER: S-EPMC7800554 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature

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The complete mitochondrial genome of the endangered Chinese black-necked pond turtle, Mauremys nigricans.

Zhao Jian J Zhang Xincheng X Li Wei W Zhang Dandan D Zhu Xinping X

Mitochondrial DNA. Part B, Resources 20160201 1

The complete mitochondrial genome of the endangered Chinese black-necked pond turtle, Mauremys nigricans, was determined in this study. The mitogenome was 16 779 bp in length, and the GC content was 39.07%. The genomes encoded 37 genes typically found in other vertebrates. In the control region, three CSBs were identified, followed by long tandem repeats of (ATATCATATT)10(ATATC)(ATATATC)7(TA)102. The mitochondiral genome sequence would be useful for the ph ...[more]

PMID: 33473409

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Project description:The characterization of mitochondrial genome has been evidenced as an efficient field of study for phylogenetic and evolutionary analysis in vertebrates including turtles. The aim of this study was to distinguish the structure and variability of the Trionychidae species mitogenomes through comparative analysis. The complete mitogenome (16796 bp) of an endangered freshwater turtle, Nilssonia nigricans was sequenced and annotated. The mitogenome encoded for 37 genes and a major non-coding control region (CR). The mitogenome was A + T biased (62.16%) and included six overlapping and 19 intergenic spacer regions. The Relative synonymous codon usage (RSCU) value was consistent among all the Trionychidae species; with the exception of significant reduction of Serine (TCG) frequency in N. nigricans, N. formosa, and R. swinhoei. In N. nigricans, most of the transfer RNAs (tRNAs) were folded into classic clover-leaf secondary structures with Watson-Crick base pairing except for trnS1 (GCT). The comparative analysis revealed that most of the tRNAs were structurally different, except for trnE (TTC), trnQ (TTG), and trnM (CAT). The structural features of tRNAs resulted ≥ 10 mismatched or wobble base pairings in 12 tRNAs, which reflects the nucleotide composition in both H- and L-strands. The mitogenome of N. nigricans also revealed two unique tandem repeats (ATTAT)8, and (TATTA)20 in the CR. Further, the conserved motif 5'-GACATA-3' and stable stem-loop structure was detected in the CRs of all Trionychidae species, which play an significant role in regulating transcription and replication in the mitochondrial genome. Further, the comparative analysis of Ka/Ks indicated negative selection in most of the protein coding genes (PCGs). The constructed Maximum Likelihood (ML) phylogeny using all PCGs showed clustering of N. nigricans with N. formosa. The resulting phylogeny illustrated the similar topology as described previously and consistent with the taxonomic classification. However, more sampling from different taxonomic groups of Testudines and studies on their mitogenomics are desirable for better understanding of the phylogenetic and evolutionary relationships.

Project description:Heavy metals are among the most ubiquitous environmental pollutants of recent decades. Copper is commonly used to control algal blooms or macrophyte and waste infestations, its ambient concentration has increased significantly, indicating possible environmental risk. To investigate the effects of copper exposure on bioaccumulation, antioxidant defense, immune response, and apoptosis in the Chinese Striped-necked Turtle Mauremys sinensis, three experimental groups, control (0.0 mg/L), Cu2 (2 mg/L) and Cu4 (4 mg/L) were designed, and sampled at 14 and 28 days. Results showed that copper accumulates in different organs depending on the concentration and exposure time, Liver > Kidney > Gut > Heart > Brain > Muscle and the time order was 28 days > 14 days. The liver enzymes AST, ALT, and ALP decreased when the turtles were exposed to copper stress, while the contents of bilirubin TBIL, DBIL, IBIL, and LDH showed a significant upward trend. Similarly, the mRNA expression level of acetylcholinesterase AChE in the brain was significantly downregulated upon copper exposure. An upward trend was noticed in the liver Metallothionein MT mRNA expression levels compared to the control group. The mRNA expression levels of antioxidant enzymes CAT, SOD, MnSOD, and GSH-PX1 in the liver increased initially and then significantly decreased. Furthermore, the relative mRNA expression levels of inflammatory cytokines IL-1β, IL-8, TNF-α, and IFN-γ involved in inflammatory response significantly upregulated. Copper significantly increased the hepatic mRNA transcription of heat shock proteins HSP70 and HSP90 at different exposure durations. In addition, the relative mRNA levels of caspase3, caspase8, and caspase9 related to the caspase-dependent apoptotic pathway significantly increased under copper stress. These results explain that copper toxicity causes bioaccumulation, promotes oxidative stress, obstructs immunity, and induces inflammation and apoptosis by altering their gene expression levels in M. sinensis.

Project description:Background:The mutualistic symbiosis between the gut microbial communities (microbiota) and their host animals has attracted much attention. Many factors potentially affect the gut microbiota, which also varies among host animals. The native Chinese three-keeled pond turtle (Chinemys reevesii) and the invasive red-eared slider turtle (Trachemys scripta elegans) are two common farm-raised species in China, with the latter generally considered a more successful species. However, supporting evidence from the gut microbiota has yet to be collected. Methods:We collected feces samples from these two turtle species raised in a farm under identical conditions, and analyzed the composition and relative abundance of the gut microbes using bacterial 16S rRNA sequencing on the Roach/454 platform. Results:The gut microbiota was mainly composed of Bacteroidetes and Firmicutes at the phylum level, and Porphyromonadaceae, Bacteroidaceae and Lachnospiraceae at the family level in both species. The relative abundance of the microbes and gene functions in the gut microbiota differed between the two species, whereas alpha or beta diversity did not. Microbes of the families Bacteroidaceae, Clostridiaceae and Lachnospiraceae were comparatively more abundant in C. reevesii, whereas those of the families Porphyromonadaceae and Fusobacteriaceae were comparatively more abundant in T. s. elegans. In both species the gut microbiota had functional roles in enhancing metabolism, genetic information processing and environmental information processing according to the Kyoto Encyclopedia of Genes and Genomes database. The potential to gain mass is greater in T. s. elegans than in C. reevesii, as revealed by the fact that the Firmicutes/Bacteroidetes ratio was lower in the former species. The percentage of human disease-related functional genes was lower in T. s. elegans than in C. reevesii, presumably suggesting an enhanced potential to colonize new habitats in the former species.

Dataset Information

The complete mitochondrial genome of the endangered Chinese black-necked pond turtle, Mauremys nigricans.

Publications

The complete mitochondrial genome of the endangered Chinese black-necked pond turtle, <i>Mauremys nigricans</i>.

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