Complete mitochondrial genome of the Cyclemys dentata and phylogenetic analysis of the major family Geoemydidae

Abstract

ABSTRACT. In the present study, the complete mitochondrial (mt) genome of Cyclemys dentata was determined using PCR reactions. The structural organization and gene order of C. dentata were equivalent to those of most other vertebrates. The mt genome was 16,489 bp in length, has rich A+T content, consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region (D-loop). All protein-coding genes started with ATG, many genes have complete stop codons, except ND2, COX3, ND3, and cyt-b genes had incomplete stop codons of T. The light-strand replication origin (O L ) of C. dentata might fold into a stable stem-loop secondary structure, and its loop had 2 nt less than that of the Cyclemys atripons O L sequence. The D-Loop of C. dentata contained a central domain (CD), 2 extended termination associated sequences (ETAS1, ETAS2) and 3 conserved sequence blocks (CSB1, CSB2, CSB3). The average length of 20 turtles' mt genomes was 16,692.5 bp, including 34.1% A, 27.0% T, 26.0% C and 12.9% G. The C. dentata mitochondrial genome (2015) mtDNA of C. dentata and phylogeny of family Geoemydidae.could provide useful data for further studies on phylogenetics and conservation genetics of this species. The phylogenetic relationships of the family Geoemydidae were analyzed by maximum-likelihood (ML) and neighbor-joining (NJ) based on concatenated sequences of 13 protein-coding genes from 20 turtle species. The ML and NJ trees had homologous topologies. The results support the existing classification of the genera of Geoemydidae, that C. dentata was a sister species of C. atripons, Pyxidea nested in Cuora, and Chinemys was synonymous with Mauremys.

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

“…Currently, 31 mitogenomes of species comprising seven Geoemydidae genera ( Mauremys , Cuora , Heosemys , Sacalia , Notochelys , Cyclemys , and Batagur ) are available in GenBank. Among them, only four mitogenomes (, , , and ) of four species ( Batagur trivittata , Cuora mouhotii , Cuora trifasciata , and Cyclemys dentata ) are published (Feng, Yang, Zhang, & Zhao, ; Huang et al, ; Li, Zhang, Zhao, Shi, & Zhu, ; Zhang, Nie, Cao, & Zhan, ). However, no complete mitogenome of any species of Pangshura is available.…”

Intraspecific variations in Cyt b and D-loop sequences of Testudine species, Lissemys punctata from south Karnataka

“…1 ) revealed that the open reading frame begins with 'ATG' (Methionine) and terminates with 'TAA' was similar to other reported Trionychidae species in database, except Pelodiscus sinensis from Republic of Korea (AY962573.1) reported 'ATT' start codon for Cyt b [26] . The AT rich (60%) nucleotide composition of Cyt b gene in current study reflects the characteristic vertebrate mitogenome composition [27] . 'TGA' (or UGA) believed to be a universal termination codon for nuclear genes appeared in the current Cyt b sequence stretch but, here it codes for Tryptophan as in all vertebrate mtDNA [28] .…”

“…3 . The overall nucleotide composition consist 33–34% (A), 30–32% (T), 11–12% (G) and 21–22% (C), highlighting AT rich vertebrate mtDNA composition [27] . D-loop sequences (∼1000 bp) analyzed in MEGA v6.06 [21] for intraspecific variations revealed 189 variable sites, 51 parsimony informative sites and only 89 conserved sites.…”

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

“…Similar results have also been reported in several turtles, such as Pangshura spps. (Kundu et al, 2019;2020), Cyclemys dentata (Huang et al, 2015), Pyxidea mouhotii (Zhang et al, 2008b), Cuora trifasciata (Li et al, 2015), and B. trivittata (Feng et al, 2017).…”