Complete mitochondrial genome of the Cumberland slider (Trachemys scripta troostii, Testudienes: Emydidae) in Korea.
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ABSTRACT:
SUBMITTER: Ryu G
PROVIDER: S-EPMC7995875 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The complete mitochondrial (mt) genome of Trachemys scripta elegans in Korea was sequenced and characterized. The mt genome is constituted of 37 genes (13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes) and a noncoding control region. Phylogenetic analysis based on the complete mt genome showed that T. s. elegans Korea has closer relationship with T. scripta Canada than T. s. elegans China. This is the first complete mt genome from T. s. elegans in Korea, which provides information for biogeographical studies and management plan for invasive species.
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Project description:The complete mitochondrial (mt) genome of Trachemys scripta ssp. in Korea was sequenced and characterized. The mt genome is constituted of 37 genes (13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes) and a control region. Phylogenetic analysis based on the complete mt genome showed that the unidentified turtle had the mt genome closely related to that of T. s. elegans, though it had distinct morphology compared to T. s. elegans. This study can provide information for biogeographical studies and management plan for invasive species.
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Project description:The bony shell of the turtle is an evolutionary novelty not found in any other group of animals, however, research into its formation has suggested that it has evolved through modification of conserved developmental mechanisms. Although these mechanisms have been extensively characterized in model organisms, the tools for characterizing them in non-model organisms such as turtles have been limited by a lack of genomic resources. We have used a next generation sequencing approach to generate and assemble a transcriptome from stage 14 and 17 Trachemys scripta embryos, stages during which important events in shell development are known to take place. The transcriptome consists of 231,876 sequences with an N50 of 1,166 bp. GO terms and EC codes were assigned to the 61,643 unique predicted proteins identified in the transcriptome sequences. All major GO categories and metabolic pathways are represented in the transcriptome. Transcriptome sequences were used to amplify several cDNA fragments designed for use as RNA in situ probes. One of these, BMP5, was hybridized to a T. scripta embryo and exhibits both conserved and novel expression patterns. The transcriptome sequences should be of broad use for understanding the evolution and development of the turtle shell and for annotating any future T. scripta genome sequences.
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Project description:Among vertebrates, turtles have many unique characteristics providing biologists with opportunities to study novel evolutionary innovations and processes. We present here a high-quality, partially phased, and chromosome-level Red-Eared Slider (Trachemys scripta elegans, TSE) genome as a reference for future research on turtle and tetrapod evolution. This TSE assembly is 2.269?Gb in length, has one of the highest scaffold N50 and N90 values of any published turtle genome to date (N50?=?129.68?Mb and N90?=?19?Mb), and has a total of 28,415 annotated genes. We introduce synteny analyses using BUSCO single-copy orthologs, which reveal two chromosome fusion events accounting for differences in chromosome counts between emydids and other cryptodire turtles and reveal many fission/fusion events for birds, crocodiles, and snakes relative to TSE. This annotated chromosome-level genome will provide an important reference genome for future studies on turtle, vertebrate, and chromosome evolution.
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Project description:The red-eared slider (RES) ranavirus (RESRV) was isolated from a free-ranging RES turtle that died with evidence of respiratory disease. The RESRV genome sequence (106,878?bp) was determined, and phylogenetic analysis revealed that it is a common midwife toad virus (CMTV) strain. This study is the first report of CMTV in RES.
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Project description:Background:How species colonize new environments is still a fundamental question in ecology and evolution, assessable by evaluating range characteristics of invasive species. Here we propose a model approach to evaluate environmental conditions and species features to predict niche changes in non-equilibrium contexts. It incorporates potentially range-limiting processes (fundamental niche), hence allowing for better predictions of range shifts, differentiation of analog and non-analog conditions between the native and non-native (invaded) ranges, and identification of environmental conditions not currently available but likely in the future. We apply our approach with the worldwide invasive slider-turtle Trachemys scripta. Methods:We estimated the native and non-native realized niches of T. scripta and built its fundamental niche based on key features of the turtle's temperature physiological tolerance limits and survival-associated factors. We next estimated response functions adjusted to the physiological predictor variables and estimated habitat suitability values, followed by a comprehensive set of analyses and simulations to compare the environmental conditions occupied by T. scripta (at its native and non-native ranges). Results:Climatic space analysis showed that the T. scripta's non-native realized niche is 28.6% greater than the native one. Response curves showed that it does not use its entire range of temperature tolerances (density curves for native: 5.3-23.7 °C and non-native: 1.7-28.4 °C ranges). Whether considering the mean temperature of the warmest or the coldest quarter, it occupies a wider range of temperatures along its non-native distribution. Results of the response curves for worldwide (global) and across Mexico (regional) comparisons showed it occupies analog and non-analog conditions between its native and invaded ranges, exhibiting also unoccupied suitable climatic conditions. Discussion:We demonstrate that T. scripta occupies a wider subset of its fundamental niche along its non-native range (within its physiological tolerances), revealing that the species observed niche shift corresponds to a different subset of its fundamental niche (niche unfilling). We also identified suitable environmental conditions, globally and regionally, where the slider turtle could potentially invade. Our approach allows to accurately predict niche changes in novel or non-equilibrium contexts, which can improve our understanding about ecological aspects and geographic range boundaries in current and potential invasions.
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Project description:The complete mitochondrial genome of Pseudemys concinna in Korea was sequenced and characterized. The mitochondrial genome is constituted of 37 genes (13 protein-coding genes, 22 transfer RNA (tRNA) genes, and two ribosomal RNA (rRNA) genes) and a noncoding region. Phylogenetic analysis based on the complete mitochondrial genome showed that P. concinna has closer relationship with Chrysemys picta than Trachemys scripta elegans. This is the first case for complete mitochondrial genome from P. concinna in Korea, which will provide information for biogeographical studies and management plan for invasive species.
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Project description:The complete mitochondrial genome of Chrysemys dorsalis in Korea was sequenced and characterized. The mitochondrial genome is 17,258 bp in length and the GC content is 39%. It is constituted of 37 genes, 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and a noncoding region. Phylogenetic analysis reveals that C. dorsalis forms a monophyletic group with C. picta turtles but is distinctly separated from them, aligning with previous findings. In Korea, C. dorsalis forms a discrete clade, separate from both native and invasive turtle species. No evidence of genetic disturbance or intermingling is observed. This is the first case of a complete mitochondrial genome from C. dorsalis and provides crucial data for understanding C. dorsalis and managing invasive species effectively, emphasizing the need for continued mitochondrial genome data accumulation.
| S-EPMC10786420 | biostudies-literature
Project description:The red-eared slider (Trachemys scripta elegans), identified as one of the 100 most invasive species in the world, is a freshwater turtle originally from the eastern United States and northeastern Mexico. Field investigations have shown that T. s. elegans can survive and lay eggs in saline habitats. In order to understand the molecular mechanisms of salinity adaptation, high-throughput RNA-Seq was utilized to identify the changes in gene expression profiles in the liver of T. s. elegans in response to elevated salinity. We exposed individuals to 0, 5, or 15 psu (practical salinity units) for 30 days. A total of 157.21 million reads were obtained and assembled into 205138 unigenes with an average length of 620 bp and N50 of 964 bp. Of these, 1019 DEGs (differentially expressed genes) were found in the comparison of 0 vs. 5 psu, 1194 DEGs in 0 vs. 15 psu and 1180 DEGs in 5 vs. 15 psu, which are mainly related to macromolecule metabolic process, ion transport, oxidoreductase activity and generation of precursor metabolites and energy by GO (Gene Ontology) enrichment analyses. T. s. elegans can adapt itself into salinity by balancing the entry of sodium and chloride ions via the up-regulation expression genes of ion transport (potassium voltage-gated channel subfamily H member 5, KCNH5; erine/threonine-protein kinase 32, STK32; salt-inducible kinase 1, SIK1; adiponectin, ACDC), and by accumulating plasma urea and free amino acid via the up-regulation expression genes of amino acid metabolism (ornithine decarboxylase antizyme 3, OAZ3; glutamine synthetase, GLUL; asparaginase-like protein 1b, ASRGL; L-amino-acid oxidase-like, LAAO; sodium-dependent neutral amino acid transporter B, SLC6A15s; amino acid permease, SLC7A9) in response to osmotic regulation. An investment of energy to maintain their homeostatic balance is required to salinity adaptation, therefore, the genes related to energy production and conversion (F-ATPase protein 6, ATP6; cytochrome c oxidase subunit I, COX1; cytochrome c oxidase subunit III, COX3; cytochrome b, CYTb; cytochrome P450 17A1, CYP17A1) were up-regulated with the increase of gene expression associated with lipid metabolism (apolipoprotein E precursor, APoE; coenzyme Q-binding protein, CoQ10; high-density lipoprotein particle, SAA) and carbohydrate metabolism (HK, MIP). These findings improve our understanding of the underlying molecular mechanisms involved in salinity adaptation and provide general guidance to illuminate the invasion potential of T. s. elegans into saline environments.
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Project description:In many cases, the DNA-binding activity of a transcription factor does not change, while its transcriptional activity is greatly influenced by the make-up of bound proteins. In this study, we assessed the protein composition and DNA-binding ability of the E2F transcription factor complex to provide insight into cell cycle control in an anoxia tolerant turtle through the use of a modified ELISA protocol. This modification also permits the use of custom DNA probes that are tailored to a specific DNA binding region, introducing the ability to design capture probes for non-model organisms. Through the use of EMSA and ELISA DNA binding assays, we have successfully determined the in vitro DNA binding activity and complex dynamics of the Rb/E2F cell cycle regulatory mechanisms in an anoxic turtle, Trachemys scripta elegans. Repressive cell cycle proteins (E2F4, Rb, HDAC4 and Suv39H1) were found to significantly increase at E2F DNA-binding sites upon anoxic exposure in anoxic turtle liver. The lack of p130 involvement in the E2F DNA-bound complex indicates that anoxic turtle liver may maintain G1 arrest for the duration of stress survival.
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