http://informahealthcare.com/mdn ISSN: 2470-1394 (print), 2470-1408 (electronic) Mitochondrial DNA Part A, 2016; 27(6): 4226–4227 ! 2015 Informa UK Limited, trading as Taylor & Francis Group. DOI: 10.3109/19401736.2015.1022751
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of Gekko chinensis (Squamata, Gekkonidae) Shuangli Hao, Jun Ping, and Yongpu Zhang College of Life and Environmental Science, Wenzhou University, Wenzhou, China
Abstract
Keywords
We sequenced the complete mitochondrial genome of Gekko chinensis, which is an endemic species to China. The complete mitogenome is 17,906 bp in size, containing 37 genes coding for 13 proteins, two ribosomal RNAs, 22 transfer RNAs, and a control region. The A + T content of the overall base composition of H-strand is 61.1% (T: 27.6%, C: 25.5%, A: 33.5%, and G: 13.4%). The major non-coding region (control region) is 2530 bp in length and the A + T content is 67.9%. Besides, four tandem repeats were found within the control region. In Bayesian inference (BI), maximum likelihood (ML) and maximum parsimony (MP) trees, we found G. chinensis is a sister clade to Gekko swinhonis.
Gekkonidae, Gekko chinensis, mitogenome
The Gekkonidae is widely distributed around the world and contains more than 90 genera and over 1000 named species (Han et al., 2004). In this study, we sequenced the complete mitochondrial genome of the Chinese endemic species, Gekko chinensis, living in the wild or the structure gaps in Fujian, Guangdong, Hainan, Guangxi provinces (Zhao, 1999). The genome was sequenced using muscle tissue taken from a specimen collected from Quanzhou, Fujian province. The accession number of this sequence is KP666135 in GenBank. Total DNA was extracted using the DNeasy Tissue Kit (Qiagen, Valencia, CA). Short fragments were first amplified and sequenced with primers rPhe-1L and H1858, rND1-3L and rND2-2H, rCO1-4L and uCO2-1H, uLys-lL and uCO3-1H, rND4L-2L and rND4-2H, and rND5-3L and rGlu-1H (Kumazawa & Endo, 2004). From these short sequences, specific primers were designed for accurate polymerase chain reaction (PCR). All PCRs were carried out using the Veriti 96 Well Thermal Cycler (Applied Biosystems, Foster City, CA). TaKaRa r-Taq and LA-Taq Kits (Takara Biomedical, Dalian, China) were used for normal and long PCRs. The G. chinensis mitochondrial genome consists of 17,906 bp with 13 protein-coding genes, two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and a control region. The gene content and the arrangement are identical to other known species of Gekkonidae (Li et al., 2013; Qin et al., 2011; Yan et al., 2014).
History Received 13 February 2015 Revised 16 February 2015 Accepted 21 February 2015 Published online 22 May 2015
The whole base composition of H-strand is T: 27.6%, C: 25.5%, A: 33.5%, and G: 13.4% and the A + T content: 61.1%. Except COI and ND5 genes, which start with the start codon GTG, all the remained protein-coding genes (PCG) in this mitogenome appear to start with the conventional start codon ATN (nine ATGs; one ATT and one ATA). Five genes (ND1, ATP8, ATP6, ND4L, and ND4) end with a stop codon TAA, ND6 end with TAG, and COI end with AGA. The remaining six genes (ND3 and Cyt b with TA–, ND2, COII, COIII, and ND5 with T– –) have incomplete stop codons. The tRNA genes range in size from 63 to 76 nucleotides, of which the secondary structures were predicted by tRNAscan-SE online server, and all the tRNAs could form typical cloverleaf structure except for tRNASer (AGC). The control region located between the tRNAPhe and tRNAPro genes is 2530 bp in length with the A + T content of 67.9% and four tandem repeats are found in it. We constructed the Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) trees (Figure 1) to confirm the phylogenetic relationship of Gekkonidae in addition to G. chinensis, another 20 known mt genomes from Genbank. Hemitheconyx taylori and H. caudicinctus were selected as outgroups. BI was performed with MrBayes 3.1.2 (Huelsenbeck & Ronquist, 2001), MP and ML were performed using PAUP* 4.0b10 (Swofford, 2002). In BI, ML and MP trees, we found G. chinensis is a sister clade to G. swinhonis.
Correspondence: Prof. Yongpu Zhang, College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China. Tel: +577 86689079. Fax: +577 86689257. E-mail:
[email protected]
DOI: 10.3109/19401736.2015.1022751
Complete mitogenome of G.chinensis
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Figure 1. Phylogenetic tree of the relationships among 21 species of Gekkonidae based on the nucleotide dataset of the 12 mitochondrial protein-coding genes except ATP6 gene with the first and second codon positions of 6023 nucleotides. Branch lengths and topology are from the Bayesian analysis. Numbers above branches specify posterior probabilities from Bayesian inference (BI), bootstrap percentages from maximum likelihood (ML, 1000 replications), and maximum parsimony (MP, 1000 replications) analyses. The GenBank numbers are shown as below: Hemitheconyx taylori (AB610503), Hemitheconyx caudicinctus (AB610502), Teratoscincus keyserlingii (AY753545), Cnemaspis limi (HQ896026), Heteronotia binoei (EF626816), Phyllodactylus unctus (HQ896027), Uroplatus ebenaui (AB738950), Uroplatus fimbriatus (AB612276), Hemidactylus bowringii (KM508815), Hemidactylus frenatus (GQ245970), Stenodactylus petrii (AB738952), Tropiocolotes steudneri (AB738944), Tropiocolotes tripolitanus (AB661661), Lepidodactylus lugubris (AB738945), Gekko vittatus (AB178897), Gekko swinhonis (JQ906550), Gekko gecko LW1 (HM370130), Gekko gecko (AY282753), Phelsuma guimbeaui (AB661664), and Phelsuma laticauda (HQ896029).
Acknowledgements The authors thank Dr. Danna Yu (Zhejiang Normal University) for providing experimental guidance in this project and helpful corrections and comments for this manuscript.
Declaration of interest This work was supported by the grants from the National Natural Science Foundation of China (31170376). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of this article.
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