Structural Variation of the Turtle Mitochondrial Control Region

Bernacki, Lucas E.; Kilpatrick, C. William

doi:10.1007/s00239-020-09962-0

Cited by 10 publications

(2 citation statements)

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“…The total length of G. hamiltonii CR was 989 bp (India) and 985 bp (China), within the range of 947 bp ( B. trivittata ) and 1,151 bp ( P. tentoria ) in other Batagurinae species. The CR of G. hamiltonii was also typically constructed with three functional domains: the termination associated sequence (TAS), the conserved sequence block (CSB), and the central conserved (CD), as illustrated in other Testunines ( Bernacki & Kilpatrick, 2020 ). Species-specific structural variations were observed in the TAS, CSB-F, and CSB-2 domains ( Fig.…”

Section: Resultsmentioning

confidence: 99%

Matrilineal phylogeny and habitat suitability of the endangered spotted pond turtle (Geoclemys hamiltonii; Testudines: Geoemydidae): a two-dimensional approach to forecasting future conservation consequences

Kundu,

Mukherjee,

Kamalakannan

et al. 2023

PeerJ

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The spotted pond turtle (Geoclemys hamiltonii) is a threatened and less explored species endemic to Bangladesh, India, Nepal, and Pakistan. To infer structural variation and matrilineal phylogenetic interpretation, the present research decoded the mitogenome of G. hamiltonii (16,509 bp) using next-generation sequencing technology. The mitogenome comprises 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one AT-rich control region (CR) with similar strand symmetry in vertebrates. The ATG was identified as a start codon in most of the PCGs except Cytochrome oxidase subunit 1 (cox1), which started with the GTG codon. The non-coding CR of G. hamiltonii was determined to have a unique structure and variation in different domains and stem-loop secondary structure as compared with other Batagurinae species. The PCGs-based Bayesian phylogeny inferred strong monophyletic support for all Batagurinae species and confirmed the sister relationship of G. hamiltonii with Pangshura and Batagur taxa. We recommend generating more mitogenomic data for other Batagurinae species to confirm their population structure and evolutionary relationships. In addition, the present study aims to infer the habitat suitability and habitat quality of G. hamiltonii in its global distribution, both in the present and future climatic scenarios. We identify that only 58,542 km2 (7.16%) of the total range extent (817,341 km2) is suitable for this species, along with the fragmented habitats in both the eastern and western ranges. Comparative habitat quality assessment suggests the level of patch shape in the western range is higher (71.3%) compared to the eastern range. Our results suggest a massive decline of approximately 65.73% to 70.31% and 70.53% to 75.30% under ssp245 and ssp585 future scenarios, respectively, for the years between 2021–2040 and 2061–2080 compared with the current distribution. The present study indicates that proper conservation management requires greater attention to the causes and solutions to the fragmented distribution and safeguarding of this endangered species in the Indus, Ganges, and Brahmaputra (IGB) river basins.

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Section: Resultsmentioning

confidence: 99%

Matrilineal phylogeny and habitat suitability of the endangered spotted pond turtle (Geoclemys hamiltonii; Testudines: Geoemydidae): a two-dimensional approach to forecasting future conservation consequences

Kundu,

Mukherjee,

Kamalakannan

et al. 2023

PeerJ

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“…The effectiveness of SynGenes was evaluated through research conducted on GenBank and PubMedCentral, focusing on the COI, CYTB genes and the Control Region, which are frequently employed in phylogenetic and population studies [14,[23][24][25][26]. The investigation encompassed 944 chordate families (Additional file 1).…”

Section: Search Data In Genbank and Pubmedcentralmentioning

confidence: 99%

SynGenes: a Python class for standardizing nomenclatures of mitochondrial and chloroplast genes and a web form for enhancing searches for evolutionary analyses

Rabelo,

Sodré,

de Sousa

et al. 2024

BMC Bioinformatics

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Background The reconstruction of the evolutionary history of organisms has been greatly influenced by the advent of molecular techniques, leading to a significant increase in studies utilizing genomic data from different species. However, the lack of standardization in gene nomenclature poses a challenge in database searches and evolutionary analyses, impacting the accuracy of results obtained. Results To address this issue, a Python class for standardizing gene nomenclatures, SynGenes, has been developed. It automatically recognizes and converts different nomenclature variations into a standardized form, facilitating comprehensive and accurate searches. Additionally, SynGenes offers a web form for individual searches using different names associated with the same gene. The SynGenes database contains a total of 545 gene name variations for mitochondrial and 2485 for chloroplasts genes, providing a valuable resource for researchers. Conclusions The SynGenes platform offers a solution for standardizing gene nomenclatures of mitochondrial and chloroplast genes and providing a standardized search solution for specific markers in GenBank. Evaluation of SynGenes effectiveness through research conducted on GenBank and PubMedCentral demonstrated its ability to yield a greater number of outcomes compared to conventional searches, ensuring more comprehensive and accurate results. This tool is crucial for accurate database searches, and consequently, evolutionary analyses, addressing the challenges posed by non-standardized gene nomenclature. Graphical abstract

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Comparative Analysis of the Complete Mitochondrial Genomes of Three Sisoridae (Osteichthyes, Siluriformes) and the Phylogenetic Relationships of Sisoridae

Wang,

Chen,

Liu

et al. 2024

Biochem Genet

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BackgroundAt present, the phylogenetic relationship of the Sisoridae is relatively chaotic. ObjectiveThis study systematically investigated the mitochondrial genomes (mitogenomes) of three species Creteuchiloglanis kamengensis, Glaridoglanis andersonii, and Exostoma sp., reconstruct the phylogenetic relationships of the family and to determine the phylogenetic position of Exostoma sp. within Sisoridae. MethodThe sample of three Sisoridae were collected and DNA were extracted. After sequencing, NOVOPlasty was used for sequence assembly. Annotate sequences with MITOS WebServer, tRNAscan-SE2.0, and NCBI database. MEGA was used for sequence analysis and Phylosuite was used for phylogenetic tree construction. ResultsThe lengths of the mitogenomes' sequences of C. kamengensis, G. andersonii, and Exostoma sp were 16,589, 16,531, and 16,529 bp, respectively. They contained one identical control region (D-loop), two ribosomal RNAs (rRNAs), 13 protein-coding genes (PCGs) and 22 transfer RNA (tRNA) genes among the three species. We applied two approaches, Bayesian Inference (BI) and Maximum Likelihood (ML), to build phylogenetic trees. Our ndings revealed that the topological structure of both ML and BI trees exhibited signi cant congruence. Speci cally, the monophyly of Sisorinae and Glyptosternoids was robustly supported in the ML tree. ConclusionIt also proves that the current phylogenetic relationship of Sisoridae is relatively chaotic, and provides new molecular biology data support for the reconstruction of the phylogenetic relationship of Sisoridae. This study will be of great scienti c value to the study of phylogeny and the genetic variation of Sisoridae.

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Structural Variation of the Turtle Mitochondrial Control Region

Cited by 10 publications

References 73 publications

Matrilineal phylogeny and habitat suitability of the endangered spotted pond turtle (Geoclemys hamiltonii; Testudines: Geoemydidae): a two-dimensional approach to forecasting future conservation consequences

Matrilineal phylogeny and habitat suitability of the endangered spotted pond turtle (Geoclemys hamiltonii; Testudines: Geoemydidae): a two-dimensional approach to forecasting future conservation consequences

SynGenes: a Python class for standardizing nomenclatures of mitochondrial and chloroplast genes and a web form for enhancing searches for evolutionary analyses

Comparative Analysis of the Complete Mitochondrial Genomes of Three Sisoridae (Osteichthyes, Siluriformes) and the Phylogenetic Relationships of Sisoridae

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