The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): Characterization and comparative analysis

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 mitochon...

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Bibliographic Details
Published in:Ecology and evolution 2019-09, Vol.9 (18), p.10854-10868
Main Authors: Kundu, Shantanu, Kumar, Vikas, Tyagi, Kaomud, Chakraborty, Rajasree, Chandra, Kailash
Format: Article
Language:English
Subjects:
Alanine
Batagur trivittata
Bayesian analysis
Biodiversity
Biological evolution
Climate change
Clustering
Codons
Comparative analysis
Comparative studies
Cuora trifasciata
Cyclemys atripons
Cyclemys dentata
Cytochrome
Cytochromes
Dehydrogenase
Deoxyribonucleic acid
DNA
Endangered & extinct species
Evolution
Field study
freshwater turtles
Gene sequencing
Genes
Genomes
Genomics
Isoleucine
Kachuga tentoria
Leucine
Mauremys annamensis
Mitochondria
Mitochondrial DNA
mitogenome
Morphology
NADH
NADH dehydrogenase
Negative selection
Nicotinamide adenine dinucleotide
Notochelys platynota
Original Research
Pangshura
Pangshura sylhetensis
Pangshura tentoria
Phylogenetics
Phylogeny
Protein structure
Reptiles & amphibians
Ribonucleic acid
RNA
rRNA
Sacalia bealei
Secondary structure
Serine
Species
Systematics
Testudines
Threonine
Transfer RNA
tRNA Ser
Turtles
Vijayachelys silvatica
Wildlife conservation
Zoology
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Summary: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
ISSN:2045-7758
2045-7758
DOI:10.1002/ece3.5606