Complete sequence and organization of the mitochondrial genome of Cyclemys atripons (Testudines, Geoemydidae)

Zhang, Li; Nie, Liuwang; Zhang, Ying; Rui, Jinlong; Zhang, Yanyun

doi:10.1590/s1415-47572008000400027

Cited by 8 publications

(7 citation statements)

References 18 publications

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“…However, the base numbers of the stem or loop were among the different species. The stem and loop primarily contained 9 to 11 and 7 to 10 nt, respectively (Zhang et al, 2008b). The O L of C. dentata contained a 10-bp stem and 8-nt loop, which was different from that of C. atripons (i.e., 10-bp stem and 10-nt loop).…”

Section: Discussionmentioning

confidence: 88%

“…The complete mtDNA sequence of C. dentata was submitted to GenBank. Structure analysis of the control region was conducted in accordance with previously published methods (Sbisà et al, 1997;Zhang et al, 2008b).…”

Section: Discussionmentioning

confidence: 99%

“…Because of its maternal inheritance, relative lack of recombination, and a higher rate of base substitution than most nuclear genes, the mt genome has been widely used to study taxonomy, phylogeny, genetic structure, and biological identification (Jiang et al, 2011). It has been employed as a marker in turtle science (Avise et al, 1992;Bowen et al, 1994;Shaffer et al, 1997;Kumazawa and Nishida 1999;Cao et al, 2000;van der Kuyl et al, 2002;Spinks et al, 2004;Krenz et al, 2005;Parham et al, 2006;Fritz et al, 2008;Stuart and Fritz, 2008;Zhang et al, 2008b;Wiens et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

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

Huang¹,

Li²,

Jiang³

et al. 2015

Genet. Mol. Res.

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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 (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.

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Section: Discussionmentioning

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Huang¹,

Li²,

Jiang³

et al. 2015

Genet. Mol. Res.

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“…The NADH3 gene always has an insertion, which has been reported in most turtles with the exception of Pelodiscus sinensis and Kinosternon flavescens (Zardoya and Meyer, 1998a;Peng et al, 2005;Pu et al, 2005;Zhang et al, 2008). It is generally thought that the base could be related to a TAA stop codon frameshift which can cause a premature termination of protein translation if not corrected by RNA editing or other mechanisms (Mindell et al, 1998(Mindell et al, , 1999.…”

Section: Features Of C Insculpta Mtdna Geneticsmentioning

confidence: 99%

The mitochondrial genome complete sequence and organization of the Pig-nosed Turtle Carettochelys insculpta (Testudines, Carettochelyidae) and its phylogeny position in Testudines

Xiong

Zhou

et al. 2010

Amphib Reptilia

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The Pig-nosed Turtle Carettochelys insculpta (Testudines; Cryptodira; Carettochelyidae) is the sole living representative of the Carettochelyidae. The phylogenetic position of C. insculpta within Testudines has not yet been determined unequivocally. To address this issue, we sequenced the whole mitochondrial DNA (mtDNA) of C. insculpta using the long-and-accurate PCR (LA-PCR) method. The results show that the length of C. insculpta mtDNA is 16 439 bp and its structure is conserved compared to those of other turtles and other vertebrates except the NADH4 gene beginning with an ATC start codon. The 3 -side of the control region in mtDNA has two tandem repeat motifs, each consisting of nine 5 -CA-3 units and sixteen 5 -AT-3 units. To assess the phylogenetic position of C. insculpta, Maximum parsimony (MP), Maximum likelihood (ML) and Bayesian (BI) analyses were conducted based on complete mtDNA from 22 taxa. MP analyses robustly supported that the earliest phylogenetic tree splits separated into three basal branches: the Pelomedusidae (Pelomedusa subrufa), the Carettochelyidae (C. insculpta) and an assemblage of 18 cryptodiran turtle species; while ML and BI analyses suggested that Carettochelyidae and Trionychidae formed a clade, and that this clade was the sister taxon to all other cryptodiran turtles.

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“…D-loop is the predominant regulatory most variable region of mtDNA, used to identify genetically discrete populations, foraging ground, and nesting behavior of turtles, intraspecific variability, and phylogenetic relationship [10] , [11] , [12] , [13] . D-loop mutation has promoted longevity in centenarians [14] and occurrence of tandem repeats (VNTRs) is regarded as valuable molecular marker in turtle species studies [15] .…”

Section: Introductionmentioning

confidence: 99%

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

Lalitha

Chandavar

2018

Journal of Advanced Research

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Complete sequence and organization of the mitochondrial genome of Cyclemys atripons (Testudines, Geoemydidae)

Cited by 8 publications

References 18 publications

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

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

The mitochondrial genome complete sequence and organization of the Pig-nosed Turtle Carettochelys insculpta (Testudines, Carettochelyidae) and its phylogeny position in Testudines

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

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