Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis

ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20

Complete mitochondrial genome of leaf coral Pavona decussata (Scleractinia, Agariciidae) Xiaofeng Shi, Rongcheng Lin, Xinqing Zheng, Xinming Liu & Wentao Niu To cite this article: Xiaofeng Shi, Rongcheng Lin, Xinqing Zheng, Xinming Liu & Wentao Niu (2015): Complete mitochondrial genome of leaf coral Pavona decussata (Scleractinia, Agariciidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1007296

Published online: 29 Jan 2015.

Submit your article to this journal

Article views: 11

View related articles

View Crossmark data

Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [York University Libraries]

Date: 06 November 2015, At: 16:41

http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1007296

MITOGENOME ANNOUNCEMENT

Complete mitochondrial genome of leaf coral Pavona decussata (Scleractinia, Agariciidae) Xiaofeng Shi1, Rongcheng Lin1, Xinqing Zheng1, Xinming Liu2, and Wentao Niu1 1

Laboratory of Marine Biology and Ecology, Third Institute of Oceanography, State Oceanic Administration, Xiamen, P.R. China and Guangxi Academy of Oceanography, Nanning, P.R. China

Downloaded by [York University Libraries] at 16:41 06 November 2015

2

Abstract

Keywords

The leaf coral Pavona decussate is a wide-spread shallow-water species of genus Pavona within Agariciidae. In our study, the entire mitochondrial nucleotide sequence of P. decussate was determined. The sequence was 18,378 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes (small and large mitochondrial ribosomal RNA) and 2 transfer RNA genes (tRNAMet and tRNATrp). The overall base composition of the mitogenome was 23.8% A, 35.4% T, 25.4% G, and 15.4% C, with a high AT content of 59.3%, which is typical for invertebrate mtDNA. It shared 97.9%, 96.2% and 89.3% mitogenome sequence with P. clavus, Agaricia humilis and Astreopora myriophthalma, respectively.

Genetics, mitogenome, Pavona decussata, scleractinian

Recent phylogenetic analyses have demonstrated the limits of traditional coral taxonomy due to extensive phenotypic plasticity. Moreover, introgressive hybridization has also resulted in equivocal taxonomic determinations and controversial phylogenies among scleractinians. A more reliable classification system based on genetic information in addition to the morphological approach is required (Uda et al., 2011), but molecular taxonomy is hampered by the scarcity of available markers (Flot et al., 2007). Complete mitochondrial genome sequences are useful tool for molecular taxonomy and enable phylogenetic reconstruction in tracing the evolution of scleractinian taxa (Meyer et al., 1990; Normark et al., 1991). The combined information from several mitochondrial genes will also help to estimate evolutionary relationships and deep divergence times in anthozoan lineages that could not be achieved with fewer individual genes (Medina et al., 2006). However, more sequenced mitogenomes as well as further evaluation of complete scleractinian mt genomes are needed to determine appropriate mtDNA sequences for species and/or population-level phylogenies. The distinction between Pavona and Leptoseris, both of which belong to the family Agariciidae of scleractinia, has been reported to be uncertain with some species (Dai et al., 2009; Veron, 1986). In this study, we determined the complete mitochondrial genome sequence of P. decussata, as a widespread shallow-water species of genus Pavona within Agariciidae (Erhardt et al., 2005; Veron, 1986). A PCR-based approach using the primer pairs on the basis of 74 universal primers designed by Lin et al. (2011) was performed and the

History Received 20 December 2014 Accepted 30 December 2014 Published online 29 January 2015

DNA sequence was annotated with the aid of web-based tools DOGMA and tRNAscan-SE v.1.21 (Cheng et al., 2012). The complete nucleotide sequence was deposited in GenBank under the accession number KP231535. The complete mitochondrial DNA sequence (18,378 bp in length) consisted of 2 ribosomal RNA (rRNA) genes (small and large mitochondrial rRNA), 2 tRNA genes (tRNAMet and tRNATrp) and 13 protein-coding genes (Table 1). The overall base composition of the mitogenome was 23.8% A, 35.4% T, 25.4% G, and 15.4% C, respectively, with a high A + T content (59.3%), which is typical for invertebrate mtDNA (Brugler et al., 2007; van Oppen et al., 2002). Most of the protein-coding genes began with ATG or GTG start codon, except for ND2, which started with ATA. The complete termination codons for the protein-coding genes were either TAA or TAG. All of the 17 genes were encoded on the heavy strand with the typical scleractinian coral mitochondrial gene arrangement (Lin et al., 2011; van Oppen et al., 2002). And there were no peculiar structures such as an idiosyncratic ATP8 or a duplicated tRNATrp (Chen et al., 2008). The ND5 gene was interrupted by a large group I intron (11 129 bp) which contained 10 protein-coding genes and small mitochondrial ribosomal RNA. There was an overlapping nucleotides between the adjacent genes of ATP8 and COI. No introns were observed in the COI gene. Using MEGA 5.2 (Tamura et al., 2011) for sequence alignment, the mitogenome sequence of P. decussata was 97.9%, 96.2% and 89.3% similar to that of P. clavus (DQ643836.1), Agaricia humilis (DQ643831.1) and Astreopora myriophthalma (KJ634272.1), respectively.

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: [email protected]

2

X. Shi et al.

Mitochondrial DNA, Early Online: 1–2

Table 1. Characteristics of the mitochondrial genome of P. decussate. Position Gene

Downloaded by [York University Libraries] at 16:41 06 November 2015

0

ND5 5 ND1 Cyt b ND2 ND6 ATP6 ND4 rns* COIII COII ND4L ND3 ND5 30 tRNATrp ATP8 COI tRNAMet rrnL*

Codon

From

To

Length (bp)

A + T(%)

1 1060 2086 3694 4813 5461 6370 7901 9459 10,276 11,054 11,380 11,850 12,993 13,095 13,259 15,890 15,962

720 2043 3237 4791 5418 6159 7848 9069 10,247 11,019 11,353 11,736 12,965 13,062 13,313 14,905 15,960 18,262

720 984 1152 1098 606 699 1479 1169 789 744 300 357 1116 70 219 1611 71 2301

59.8 58.6 58.7 59.9 62.1 60.5 58.2 60.1 61.3 66.0 60.2 59.9 48.6 69.9 60.1 42.3 58.7

Anticodon

Start

Stop

Intergenic nucleotidesy

GTG ATG ATG ATA GTG ATG ATG

TAA TAG TAA TAA TAG TAG

339 42 236 21 42 210 52 389 28 34 26 113 27 32 19 984 1

GTG ATG GTG ATG

TAG TAA TAA TAA TAG

GTG ATG

TAA TAA

TCA CAT

yData correspond to the number of nucleotides between the given gene and its previous gene. *rrnS and rrnL represent genes of small and large mitochondrial ribosomal RNA subunits, respectively.

Declarations of interest The authors report no conflict of interest. The authors alone are responsible for the content and writing of the paper. This study was supported by Basic Science Research Fund of the Third Institute of Oceanography, SOA (No. 2013025) and the Ocean Public Welfare Scientific Research Project of China (No. 201105012), Project 41406166 supported by NSFC and ‘‘Study on the Response and Acclimation of CTI Coral Reef Ecosystem to Global Change’’ supported by the International Cooperation and Performance of China.

References Brugler MR, France SC. (2007). The complete mitochondrial genome of the black coral Chrysopathes formosa (Cnidaria: Anthozoa: Antipatharia) supports classification of antipatharians within the subclass Hexacorallia. Mol Phylogenet Evol 42:776–88. Chen C, Dai CF, Plathong S, Chiou CY, Chen CA. (2008). The complete mitochondrial genomes of needle corals, Seriatopora spp. (Scleractinia: Pocilloporidae): An idiosyncratic atp8, duplicated trnW gene, and hypervariable regions used to determine species phylogenies and recently diverged populations. Mol Phylogenet Evol 46:19–33. Cheng J, Ma GQ, Song N, Gao TX. (2012). Complete mitochondrial genome sequence of bighead croaker Collichthys niveatus (Perciformes, Sciaenidae): A mitogenomic perspective on the phylogenetic relationships of Pseudosciaeniae. Gene 491:210–23. Dai C, Horng S. (2009). Scleractinia Fauna of Taiwan I: The complex group. Taipei, Taiwan: National Taiwan University. Erhardt H, Knop D. (2005). Corals: Indo-Pacific field guide. Frankfurt, Germany: IKAN-Unterwasserarchiv.

Flot JF, Tillier S. (2007). The mitochondrial genome of Pocillopora (Cnidaria: Scleractinia) contains two variable regions: The putative D-loop and a novel ORF of unknown function. Gene 401:80–7. Lin MF, Luzon KS, Licuanan WY, Ablan-Lagman MC, Chen CA. (2011). Seventy-four universal primers for characterizing the complete mitochondrial genomes of scleractinian corals (Cnidaria; Anthozoa). Zool Stud 50:513–24. Medina M, Collins AG, Takaoka TL, Kuehl JV, Boore JL. (2006). Naked corals: Skeleton loss in Scleractinia. P Natl Acad Sci USA 103: 9096–100. Meyer A, Kocher TD, Basasibwaki P, Wilson AC. (1990). Monophyletic origin of Lake Victoria cichlid fishes suggested by mitochondrial DNA sequences. Nature 347:550–3. Normark BB, Mccune AR, Harrison RG. (1991). Phylogenetic relationships of neopterygian fishes, inferred from mitochondrial DNA sequences. Mol Biol Evol 8:819–34. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. (2011). MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–9. Uda K, Komeda Y, Koyama H, Koga K, Fujita T, Iwasaki N, Suzuki T. (2011). Complete mitochondrial genomes of two Japanese precious corals, Paracorallium japonicum and Corallium konojoi (Cnidaria, Octocorallia, Coralliidae): Notable differences in gene arrangement. Gene 476:27–37. Van Oppen MJ, Catmull J, Mcdonald BJ, Hislop NR, Hagerman PJ, Miller DJ. (2002). The mitochondrial genome of Acropora tenuis (Cnidaria; Scleractinia) contains a large group I intron and a candidate control region. J Mol Evol 55:1–13. Veron J. (1986). Corals of Australia and the Indo-Pacific (2nd Revised edition). Hawaii, America: University of Hawaii Press.

Complete mitochondrial genome of leaf coral Pavona decussata (Scleractinia, Agariciidae).

The leaf coral Pavona decussate is a wide-spread shallow-water species of genus Pavona within Agariciidae. In our study, the entire mitochondrial nucl...
432KB Sizes 2 Downloads 4 Views