Sequencing and characterization of the complete mitochondrial genome of Critically Endangered Black Soft-shell Turtle (<i>Nilssonia nigricans</i>)

Kundu, Shantanu; Kumar, Vadlapudi; Tyagi, Kaomud; Chakraborty, Rajasree; Singha, Devkant; Rahaman, Iftikar; Pakrashi, Avas; Chandra, Kailash

doi:10.1101/361501

Cited by 1 publication

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References 35 publications

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“…However, to understand the robust evolutionary relationship, reconcile of phylogeny by in-depth molecular data is necessitated. Comparative mitochondriomics has demonstrated its utility in elucidating the phylogenetic relationships of many taxa, including turtles (Amer & Kumazawa, 2009;Chen et al, 2013;Jiang et al, 2016;Li et al, 2017;Kundu et al, 2018b). Originally, the genus Pangshura was erected by Gray, 1856 within Batagur, a genus contained Pangshura, Batagur, Kachuga and Morenia species.…”

Section: Phylogeny Of Geoemydid Mitogenomesmentioning

confidence: 99%

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Supplemental Information 2: Figure S2 a Pictorial Overview of the Methodologies Used for Sequencing and Analysis OfP. Tentor

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Complete mitochondrial genomes of Indian tent turtle, Pangshura tentoria was sequenced and annotated as 16,657 bp in length. This first assembly was encoded by 37 genes: 13 protein coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs) as similar to the typical vertebrate mitochondrial gene arrangement. The complete mitogenome has a base composition of A (33.30%), G (13.54%), C (27%), and T (26.13%). Most of the genes were encoded on major strand, except for the eight tRNAs and one PCG (nad6). Almost all PCGs were starting with an ATG initiation codon, except for cytochrome oxidase subunit 1 (cox1) with 'GTG' and NADH dehydrogenase subunit 5 (nad5) with 'ATA'. The typical termination codons, 'TAA' and 'AGA' has been observed in NADH dehydrogenase subunit 4l (nad4l) and NADH dehydrogenase subunit 6 (nad6) respectively; and others were used incomplete stop codons. The Relative Synonymous Codon Usage (RSCU) analysis revealed the maximum abundance of Alanine, Isoleucine, Leucine, and Threonine in P. tentoria. Codon distribution per thousand codon (CDsPT) values for all the amino acids showed the maximum values were present for Leucine in all geoemydid turtles. Further, the PCGs showed non-synonymous (Ka)/synonymous (Ks) values were <1 that indicated a strong negative selection among the studied species. The tRNAs were folded into classic cloverleaf secondary structures, except for trnS (GCT), lacking of the conventional DHU arm or stem. Further, the 10 tRNAs showed G-T mismatches and forming weak bonds. In the control region (CR) of P. tentoria, a single tandem repeat of eight base pairs (TTCTCTTT) was resulted with two copy numbers. The comparative study of CR with other geoemydid turtles revealed the numbers of tandem repeats were frequent in the 3´ end and structural characteristic were species-specific. The Maximum Likelihood (ML) phylogeny showed 32 geoemydid turtles were clustered distinctly with high bootstrap support and congruent with the previous phylogenetic hypothesis. Further, the representative mitogenome sequences of other family/suborder were depicted discrete clades in the ML tree. The study argued the complete mitochondrial genome sequence of

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Section: Phylogeny Of Geoemydid Mitogenomesmentioning
confidence: 99%

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Supplemental Information 2: Figure S2 a Pictorial Overview of the Methodologies Used for Sequencing and Analysis OfP. Tentor
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Sequencing and characterization of the complete mitochondrial genome of Critically Endangered Black Soft-shell Turtle (Nilssonia nigricans)

Cited by 1 publication

References 35 publications

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