The complete mitochondrial genome of the endangered Assam Roofed Turtle, Pangshura sylhetensis (Testudines: Geoemydidae): Genomic features and phylogeny

Abstract

The Assam Roofed Turtle, Pangshura sylhetensis is an endangered and least studied species endemic to India and Bangladesh. The present study decodes the first complete mitochondrial genome of P. sylhetensis (16,568 bp) by using next-generation sequencing. The assembly encodes 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). Most of the genes were encoded on the majority strand, except NADH dehydrogenase subunit 6 (nad6) and eight tRNAs. All PCGs start with an ATG initiation codon, except for Cytochrome oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 5 (nad5), which both start with GTG codon. The study also found the typical cloverleaf secondary structures in most of the predicted tRNA structures, except for serine (trnS1) which lacks of conventional DHU arm and loop. Both Bayesian and maximum-likelihood phylogenetic inference using 13 concatenated PCGs demonstrated strong support for the monophyly of all 52 Testudines species within their respective families and revealed Batagur trivittata as the nearest neighbor of P. sylhetensis. The mitogenomic phylogeny with other amniotes is congruent with previous research, supporting the sister relationship of Testudines and Archosaurians (birds and crocodilians). Additionally, the mitochondrial Gene Order (GO) analysis indicated plesiomorphy with the typical vertebrate GO in most of the Testudines species.

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

“…Both conventional and molecular taxonomy have demonstrated the separate lineage of G. hamiltonii from other Batagurinae species ( Spinks et al, 2004 ; Le, McCord & Iverson, 2007 ; Thomson, Spinks & Shaffer, 2021 ). The mitogenomic data has been effectively employed to infer the evolutionary relationships of many Testudines species, adding the members of the Batagurinae subfamily ( Feng et al, 2017 ; Kundu et al, 2019 , 2020 ; Kumar et al, 2021 ).…”

“…Among the Batagurinae subfamily, seven mitogenomes (including the previously generated mitogenome for G. hamiltonii ) of six species have been generated so far. The genomic features and phylogeny have been elaborated for Batagur trivittata ( Feng et al, 2017 ), Pangshura tentoria ( Kundu et al, 2019 ), and Pangshura sylhetensis ( Kundu et al, 2020 ), and the mitogenomes of two Batagur turtles ( B. kachuga and B. dhongoka ) were also recently analyzed ( Kumar et al, 2021 ). Lastly, the mitogenomes of G. hamiltonii and Batagur affinis have been generated from China (outside range, vouchered at the Turtle Research and Conservation Center of Hainan Normal University) and Malaysia, respectively (animal in captivity), but neither rendered any structural variations or phylogenetic interpretation.…”

Characterization of the complete mitochondrial genome of the critically endangered Southern River Terrapin, Batagur affinis affinis (Reptilia: Geoemydidae)

“… 2017 ), Pangshura sylhetensis MK580979 (Kundu et al. 2020 ), Pangshura tentoria MH795989 (Kundu et al. 2019 ), and Amyda cartilaginea MT039230 (Cui et al.…”

De novo mitochondrial genome sequencing of Cladonia subulata and phylogenetic analysis with other dissimilar species

“…An ML analysis was performed using IQ-tree [ 61 ] incorporated in PhyloSuite under the Edge-linked partition model with 5000 ultrafast bootstraps replicates. Subsequently, Bayesian analyses were conducted using the Markov chain Monte Carlo (MCMC) method in MrBayes v.3.1.2 according to the Kundu [ 62 ] with the following conditions: the partition model was chosen ( S4 Table ), then the tree was then run for 10,000,000 generations with 25% burn in, with trees saved saving at every 100 generations. MCMC analysis was used to generate the convergence metrics until the standard deviation (SD) of split frequencies fell below 0.01 and the potential scale reduction factor (PSRF) for all parameters approached 1.0.…”