http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.926506

MITOGENOME ANNOUNCEMENT

Complete mitochondrial genome of disc coral Turbinaria peltata (Scleractinia, Dendrophylliidae) Xiaofeng Shi1, Peng Tian1, Rongcheng Lin1, Wenlu Lan2, Wentao Niu1, and Xinqing Zheng1 Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, P.R. China and 2Marine Environmental Monitoring Center of Guangxi, Beihai, P.R. China

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Abstract

Keywords

To date, no complete nucleotide sequences of the mitochondrial genome of Dendrophylliidae are yet available. In our study, the entire mitochondrial nucleotide sequence was determined for the Dendrophylliidae species Turbinaria peltata. The sequence was 18,966 bp in length and contained thirteen protein-coding genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), two transfer RNA genes (tRNAMet and tRNATrp) and a putative control region locating between Cyt b and ND2. The overall base composition of the mitogenome was 25.6% A, 37.4% T, 23.5% G, and 13.5% C, with a high AT content of 63%, indicating an obvious anti-guanine bias. It shared 93.7%, 87% and 84.8 % mitogenome sequence with Goniopora columna, Acropora robusta and Euphyllia ancora, respectively.

Genetics, mitogenome, scleractinian, Turbinaria peltata

The mitogenomes of Anthozoans distinctly differ from the standard knowledge of mitochondrial characterization in several important respects such as much fewer transfer RNA (tRNA) genes and the introns spanning within some genes (Chen et al., 2008b). These unique features have attracted more and more interest in the studies of evolution of corals (Chen et al., 2002; Park et al., 2012; Tseng et al., 2005). Furthermore, high levels of extensive phenotypic plasticity as well as introgressive hybridization have resulted in equivocal taxonomic determinations and controversial phylogenies among scleractinians (Huang et al., 2009). And recent studies have demonstrated the great utility of mitogenome in tracing the evolution of coral taxa (Chen et al., 2008a; Lin et al., 2012). Up to date, however, only 2% scleractinian corals have a sequenced mitogenome (Wang et al., 2012). Further evaluation of complete scleractinian mt genomes is urgently needed. The family Dendrophylliidae comprises mostly ahermatypic genera and only three hermatypic genera. No complete mitochondrial genome sequences of this family are yet available. As a representative hermatypic species of genus Turbinaria within Dendrophylliidae, Turbinaria peltata is widespread in the IndoPacific and primarily inhabited from east Africa to French Polynesia. And it generally increases in abundance with increasing latitude, as opposed to most other corals (Veron, 2000). Few studies, to date, have focused on this species. In this study, the complete mitogenome of T. peltata was obtained with PCR approach using the primer pairs designed by

Correspondence: R. Lin, Third Institute of Oceanography, State Oceanic Administration, 178 Daxue Road, Xiamen 361005, Fujian, P.R. China. Tel: +86-592-2195578. Fax: +86-592-2195578. E-mail: linrongcheng@ tio.org.cn

History Received 2 May 2014 Accepted 9 May 2014 Published online 18 June 2014

Lin et al. (2012). The DNA sequence was deposited in GenBank under the accession number KJ725201. The complete mitochondrial DNA sequence (18,966 bp in length) consisted of two ribosomal RNA (rRNA) genes (12S rRNA and 16S rRNA), two tRNA genes (tRNAMet and tRNATrp), thirteen protein-coding genes and a putative control region (Table 1). The overall base composition of the mitogenome was 25.6% A, 37.4% T, 23.5% G, and 13.5% C, respectively, with a high A + T content (63%), indicating an obvious anti-guanine bias. Most of the protein-coding genes began with an ATG start codon, except for ND5, ND4L and ND3, which started with GTG. The complete termination codons for the protein-coding genes were either TAA or TAG. All of the seventeen genes were encoded on the heavy strand with a typical scleractinian coral mitochondrial gene arrangement (Brugler & France, 2007; Van Oppen et al., 2002). And there were no peculiar structures such as an idiosyncratic ATP8 or a duplicated tRNATrp (Chen et al., 2008b). The ND5 gene was interrupted by a large group I intron (11,331 bp) which contained ten protein-coding genes and 12S rRNA. And the COI gene was also interrupted by a 964 bp intron. There were no overlapping nucleotides between adjacent genes and the number of non-coding nucleotides between different genes varied from 15 to 628 bp. The putative control region bound by Cyt b and ND2 was 628 bp in length. Using MEGA 4.0 (Tamura et al., 2007) for sequence alignment, the mitogenome sequence of T. peltata was 93.7%, 87.0% and 84.8% similar to that of Goniopora columna, Acropora robusta and Euphyllia ancora, respectively.

Declaration of interest This study was supported by the Scientific Research Foundation of Third Institute of Oceanography, SOA (No. 2013025), Public Science and Technology Research Funds Projects of Ocean (No. 201105012) and the

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X. Shi et al.

Mitochondrial DNA, Early Online: 1–2

Table 1. Characteristics of the mitochondrial genome of T. peltata. Position Gene

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Met

tRNA 16S rRNA ND5 5’ ND1 Cyt b ND2 ND6 ATP6 ND4 12S rRNA COIII COII ND4L ND3 ND5 30 tRNATrp ATP8 COI

Codon

From

To

Length (bp)

A + T (%)

Anticodon

1 107 2667 3715 4810 6602 7733 8409 9437 11,026 12,327 13,151 13,948 14,263 14,718 15,875 15,977 16,315 18,173

71 2379 3385 4698 5973 7699 8326 9107 10,912 12,090 13,115 13,894 14,247 14,619 15,834 15,944 16,192 17,208 18,856

71 2273 719 984 1164 1098 594 699 1476 1065 789 744 300 357 1117 70 216 894 684

42.2 61.6 62.3 61.6 71.7 61.6 64.7 65.4 62.9 59.1 62.9 64.5 69.6 64.4 63.2 48.6 69 62

CAT

Start

GTG ATG ATG ATG ATA ATG ATG

Stop

TAA TAA TAA TAA TAG TAA

ATG ATG GTG GTG

TAG TAG TAA TAG TAG

ATG ATG

TAA

TCA

Intergenic nucleotides* 110 35 287 329 111 628 33 82 329 113 236 35 53 15 98 40 32 122

TAA

*Data correspond to the number of nucleotides between the given gene and its previous gene.

project of Marine Development Institute of Xiamen in 2014 (No. K140301). The authors report no conflict of interest. The authors alone are responsible for the content and writing of the paper.

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Complete mitochondrial genome of disc coral Turbinaria peltata (Scleractinia, Dendrophylliidae).

To date, no complete nucleotide sequences of the mitochondrial genome of Dendrophylliidae are yet available. In our study, the entire mitochondrial nu...
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