Comparative Mitogenomics of Two Critically Endangered Turtles, Batagur Kachuga and Batagur Dhongoka (Testudines: Geoemydidae): Implications in Phylogenetics of Freshwater Turtles

Abstract

The Red-crowned roofed turtle (Batagur kachuga) and Three-striped roofed turtle (B. dhongoka) are ‘critically endangered’ turtles in the Geoemydidae family. Herein, we generated the novel mitochondrial genome sequence of B. kachuga (16,155) and B. dhongoka (15,620) and compared it with other turtles species. Batagur mitogenome has 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), and one control region (CR). The genome composition was biased toward A + T, with positive AT-skew and negative GC-skew. In the examined species, all 13 PCGs were started by ATG codons, except COI gene, which was initiated by GTG. The majority of mito-genes were encoded on the heavy strand, except eight tRNAs and the ND6 region. We observed a typical cloverleaf structure for all tRNA, excluding tRNASer (AGN), where the base pairs of the dihydrouridine (DHU) arm were abridged. Bayesian Inference (BI) based phylogenetic analysis was constructed among 39 species from six Testudines families, exhibited a close genetic relationship between Batagur and Pangshura with a high supporting value (PP ~ 0.99). It provides additional mitogenomic resources for further study of the Testudines evolutionary patterns.

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.…”