Research Article

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

Published: April 13, 2015
Genet. Mol. Res. 14 (2) : 3234-3243 DOI: https://doi.org/10.4238/2015.April.13.2
Cite this Article:
(2015). Complete mitochondrial genome of the Cyclemys dentata and phylogenetic analysis of the major family Geoemydidae. Genet. Mol. Res. 14(2): gmr4355. https://doi.org/10.4238/2015.April.13.2
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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 (OL) 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 OL 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 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.

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 (OL) 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 OL 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 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.