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
The complete mitochondrial genome of the Epinephelus polyphekadion (Teleostei, Serranidae) Guoqing Zhang, Mengmeng Chen, Jian Luo & Guohua Chen To cite this article: Guoqing Zhang, Mengmeng Chen, Jian Luo & Guohua Chen (2015): The complete mitochondrial genome of the Epinephelus polyphekadion (Teleostei, Serranidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1028033
Published online: 10 Jun 2015.
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Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [University of California, San Diego]
Date: 11 November 2015, At: 08:17
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1028033
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the Epinephelus polyphekadion (Teleostei, Serranidae) Guoqing Zhang, Mengmeng Chen, Jian Luo, and Guohua Chen
Downloaded by [University of California, San Diego] at 08:17 11 November 2015
Key Laboratory of Tropical Biological Resources, Ministry of Education, College of Ocean, Hainan University, Haikou, P.R. China
Abstract
Keywords
In this study, the complete mitochondrial genome of the Epinephelus polyphekadion has been sequenced by the next-generation sequencing (NGS) techniques strategy. The mitochondrial genome is 16,691 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The nucleotide compositions of the light strand are 27.90% A, 29.05% T, 27.48% G and 15.58% C. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy-strand (H-strand). All the tRNAs have clover secondary structure with conservative anticodon arm, T C arm and D arm except for tRNASer(GCT) and tRNA-Pro(TGG), which D arm consists of 13 bp and 7 bp single-base, respectively. Phylogenetic tree showed that E. latifasciatus, E. polyphekadion, E. epistictus, E. akaara and E. stictus of the Epinephelus formed a monophyletic group, whereas E. latifasciatus, E. polyphekadion and E. epistictus formed a sister group.
DNA maker, Epinephelus polyphekadion, mitochondrial genome
Epinephelus polyphekadion is one of the commercially important species, frequently occurring along the nearshore coral reef area in the southern part of the Red Sea coast of Saudi Arabia. It is also widely distributed in the tropical and subtropical IndoWest Pacific region from the Red Sea and east coast of Africa to French Polynesia and in the western Pacific region from southern Japan to southern Queensland and Lord Howe Island (Rhodes et al., 2003). In recent years, the studies on species of the genus Epinephelus are already focused on growth performance, feeding and considered as important mariculture organisms (James et al., 1997). Nevertheless, there is no information about its genetic characteristics. In this study, we determined to sequence the complete mitochondrial genome of E. polyphekadion using the next-generation sequencing (NGS) techniques strategy, with purpose of finding new DNA marker for the studies on population genetics of E. polyphekadion. The samples supplied by Chenhai Aquatic Products Co. (Sanya, Hainan, China) were collected from the South China Sea. Fin samples were clipped and preserved in 95% ethanol. Total genomic DNA was isolated using phenol chloroform extraction method (Han et al., 2014). The mitogenome length of E. polyphekadion is 16,691 bp (GenBank accession number KP684520). Genome content
Correspondence: Professor Guohua Chen, Key Laboratory of Tropical Biological Resources, Ministry of Education, College of Ocean, Hainan University, Haikou 570228, China. E-mail: [email protected]
History Received 27 January 2015 Revised 28 February 2015 Accepted 8 March 2015 Published online 10 June 2015
consists of 13 protein-coding genes, 2 ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA genes (tRNA) and 1 control region. The gene order is similar to the typical teleostean fishes (Boore, 1999). Eight tRNA genes (Gln, Ala, Asn, Cys, Try, Ser(TGA), Glu, Pro) and the NADH dehydrogenase subunit 6 (ND6) are encoded on the light-strand (L-strand), the rest of the genes are on the heavy-strand (H-strand). The nucleotide compositions of the L-strand are 27.90% A, 29.05% T, 27.48% G and 15.58% C. The nucleotide composition shows a nucleotide bias against G and especially in the 12 protein-coding genes encoded by the H-strand. Among the protein-coding genes, initiation codons of COXI and ATP6 are GTG and CTG, respectively, and ATG for other 10 protein-coding genes. The usage of termination codons includes TAG(ND1), TAA(COXI, ATP8, ND4L, ND5 and ND6), TA(ATP6 and COXIII) and T(ND2, COXII, ND3, ND4 and Cytb). The 22 tRNA genes vary from 68 to 76 bp in length, all the tRNAs have clover secondary structure with conservative anticodon arm, T C arm and D arm except for tRNA-Ser(GCT) and tRNA-Pro(TGG), in which D arm consists of 13 and 7 bp single-base, respectively. The 12S and 16S rRNA genes are located between the tRNAPhe(GAA) and tRNA-Leu(TAA), and are separated by the tRNAVal(TAC) gene. The D-loop region is 987 bp in length, located between tRNA-Pro(TGG) and tRNA-Phe(GAA) genes. It is an AT rich region and also the most variable region in mtDNA, the nucleotide composition of D-loop region is 34.58% A, 37.39% T, 12.16% G and 15.60% C. In addition, we discuss the phylogenetic relationship among 18 fish species, for which complete mitochondrial genome sequences are available in the public databases. The Neighbor-Joining (NJ) molecular phylogenetic family-tree was constructed using the
2
G. Zhang et al.
Figure 1. Phylogenetic tree derived from Epinephelus polyphekadion and the other 17 kinds of fish mtDNA genome nucleotide sequences. Genbank accession numbers: (E. lanceolatus, KM386619.1; E. fasciatomaculosus, NC_020782.1; E. areolatus, NC_020785.1; E. akaara, NC_011113.1; E. quayanus, NC_021450.1; E. bruneus, FJ594964.1; E. tukula, NC_024039.1; E. latifasciatus, NC_020784.1; E. fuscoguttatus, NC_020046.1; E. sexfasciatus, NC_021765.1; E. stictus, NC_021133.1; E. merra, AP005991.1; E. epistictus, NC_021462.1; E. coioides, NC_011111.1; E. moara, NC_017891.1; E. polyphekadion, KP684520; Danio rerio, AC024175.3; Oryzias latipes, AP008948.1).
Mitochondrial DNA, Early Online: 1–2
Epinephelus polyphekadion
96
Epinephelus epistictus Epinephelus areolatus
99
99
Epinephelus stictus Epinephelus fasciatomaculosus
85 100
83
Epinephelus akaara Epinephelus quayanus Epinephelus merra
99
99 99
Epinephelus tukula Epinephelus moara Epinephelus bruneus
99
99
Downloaded by [University of California, San Diego] at 08:17 11 November 2015
Epinephelus latifasciatus
94 93
Epinephelus lanceolatus Epinephelus coioides
99
Epinephelus fuscoguttatus 100
Epinephelus sexfasciatus Danio rerio Foryzias latipes
0.2
Bootstrap method (No. of Bootstrap Replications: 1000). Phylogenetic tree (Figure 1) showed that Epinephelus polyphekadion and other 17 kinds of fish have a higher homology sequence. The result indicated that E. latifasciatus, E. polyphekadion, E. epistictus, E. akaara and E. stictus of the Epinephelus formed a monophyletic group, whereas E. latifasciatus, E. polyphekadion and E. epistictus formed a sister group.
Declaration of interest This work was supported by China 863 project (NO. 2012AA10A407) and Produce-Learn-Research Projects of Hainan Province (CXY20130045).
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Han Y, Chen G, Luo J, Wen X, Li W, Wang J. (2014). The complete mitochondrial genome of Cheilinus undulates based on high-throughput sequencing technique. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.971276. James CM, Al-Thobaiti SA, Rasem BM, Carlos MH. (1997). Breeding and larval rearing of the camouflage grouper Epinephelus polyphekadion (Bleeker) in the hypersaline waters of the Red Sea coast of Saudi Arabia. Aquac Res 28:671–81. Rhodes KL, Lewis RI, Chapman RW, Sadovy Y. (2003). Genetic structure of camouflage grouper, Epinephelus polyphekadion (Pisces: Serranidae), in the western central Pacific. Mar Biol 142:771–6.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of the Epinephelus polyphekadion (Teleostei, Serranidae) Guoqing Zhang, Mengmeng Chen, Jian Luo & Guohua Chen To cite this article: Guoqing Zhang, Mengmeng Chen, Jian Luo & Guohua Chen (2015): The complete mitochondrial genome of the Epinephelus polyphekadion (Teleostei, Serranidae), Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2015.1028033
Published online: 10 Jun 2015.
Submit your article to this journal
Article views: 7
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: [University of California, San Diego]
Date: 11 November 2015, At: 08:17
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1028033
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the Epinephelus polyphekadion (Teleostei, Serranidae) Guoqing Zhang, Mengmeng Chen, Jian Luo, and Guohua Chen
Downloaded by [University of California, San Diego] at 08:17 11 November 2015
Key Laboratory of Tropical Biological Resources, Ministry of Education, College of Ocean, Hainan University, Haikou, P.R. China
Abstract
Keywords
In this study, the complete mitochondrial genome of the Epinephelus polyphekadion has been sequenced by the next-generation sequencing (NGS) techniques strategy. The mitochondrial genome is 16,691 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The nucleotide compositions of the light strand are 27.90% A, 29.05% T, 27.48% G and 15.58% C. With the exception of ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy-strand (H-strand). All the tRNAs have clover secondary structure with conservative anticodon arm, T C arm and D arm except for tRNASer(GCT) and tRNA-Pro(TGG), which D arm consists of 13 bp and 7 bp single-base, respectively. Phylogenetic tree showed that E. latifasciatus, E. polyphekadion, E. epistictus, E. akaara and E. stictus of the Epinephelus formed a monophyletic group, whereas E. latifasciatus, E. polyphekadion and E. epistictus formed a sister group.
DNA maker, Epinephelus polyphekadion, mitochondrial genome
Epinephelus polyphekadion is one of the commercially important species, frequently occurring along the nearshore coral reef area in the southern part of the Red Sea coast of Saudi Arabia. It is also widely distributed in the tropical and subtropical IndoWest Pacific region from the Red Sea and east coast of Africa to French Polynesia and in the western Pacific region from southern Japan to southern Queensland and Lord Howe Island (Rhodes et al., 2003). In recent years, the studies on species of the genus Epinephelus are already focused on growth performance, feeding and considered as important mariculture organisms (James et al., 1997). Nevertheless, there is no information about its genetic characteristics. In this study, we determined to sequence the complete mitochondrial genome of E. polyphekadion using the next-generation sequencing (NGS) techniques strategy, with purpose of finding new DNA marker for the studies on population genetics of E. polyphekadion. The samples supplied by Chenhai Aquatic Products Co. (Sanya, Hainan, China) were collected from the South China Sea. Fin samples were clipped and preserved in 95% ethanol. Total genomic DNA was isolated using phenol chloroform extraction method (Han et al., 2014). The mitogenome length of E. polyphekadion is 16,691 bp (GenBank accession number KP684520). Genome content
Correspondence: Professor Guohua Chen, Key Laboratory of Tropical Biological Resources, Ministry of Education, College of Ocean, Hainan University, Haikou 570228, China. E-mail: [email protected]
History Received 27 January 2015 Revised 28 February 2015 Accepted 8 March 2015 Published online 10 June 2015
consists of 13 protein-coding genes, 2 ribosomal RNA genes (12S rRNA and 16S rRNA), 22 transfer RNA genes (tRNA) and 1 control region. The gene order is similar to the typical teleostean fishes (Boore, 1999). Eight tRNA genes (Gln, Ala, Asn, Cys, Try, Ser(TGA), Glu, Pro) and the NADH dehydrogenase subunit 6 (ND6) are encoded on the light-strand (L-strand), the rest of the genes are on the heavy-strand (H-strand). The nucleotide compositions of the L-strand are 27.90% A, 29.05% T, 27.48% G and 15.58% C. The nucleotide composition shows a nucleotide bias against G and especially in the 12 protein-coding genes encoded by the H-strand. Among the protein-coding genes, initiation codons of COXI and ATP6 are GTG and CTG, respectively, and ATG for other 10 protein-coding genes. The usage of termination codons includes TAG(ND1), TAA(COXI, ATP8, ND4L, ND5 and ND6), TA(ATP6 and COXIII) and T(ND2, COXII, ND3, ND4 and Cytb). The 22 tRNA genes vary from 68 to 76 bp in length, all the tRNAs have clover secondary structure with conservative anticodon arm, T C arm and D arm except for tRNA-Ser(GCT) and tRNA-Pro(TGG), in which D arm consists of 13 and 7 bp single-base, respectively. The 12S and 16S rRNA genes are located between the tRNAPhe(GAA) and tRNA-Leu(TAA), and are separated by the tRNAVal(TAC) gene. The D-loop region is 987 bp in length, located between tRNA-Pro(TGG) and tRNA-Phe(GAA) genes. It is an AT rich region and also the most variable region in mtDNA, the nucleotide composition of D-loop region is 34.58% A, 37.39% T, 12.16% G and 15.60% C. In addition, we discuss the phylogenetic relationship among 18 fish species, for which complete mitochondrial genome sequences are available in the public databases. The Neighbor-Joining (NJ) molecular phylogenetic family-tree was constructed using the
2
G. Zhang et al.
Figure 1. Phylogenetic tree derived from Epinephelus polyphekadion and the other 17 kinds of fish mtDNA genome nucleotide sequences. Genbank accession numbers: (E. lanceolatus, KM386619.1; E. fasciatomaculosus, NC_020782.1; E. areolatus, NC_020785.1; E. akaara, NC_011113.1; E. quayanus, NC_021450.1; E. bruneus, FJ594964.1; E. tukula, NC_024039.1; E. latifasciatus, NC_020784.1; E. fuscoguttatus, NC_020046.1; E. sexfasciatus, NC_021765.1; E. stictus, NC_021133.1; E. merra, AP005991.1; E. epistictus, NC_021462.1; E. coioides, NC_011111.1; E. moara, NC_017891.1; E. polyphekadion, KP684520; Danio rerio, AC024175.3; Oryzias latipes, AP008948.1).
Mitochondrial DNA, Early Online: 1–2
Epinephelus polyphekadion
96
Epinephelus epistictus Epinephelus areolatus
99
99
Epinephelus stictus Epinephelus fasciatomaculosus
85 100
83
Epinephelus akaara Epinephelus quayanus Epinephelus merra
99
99 99
Epinephelus tukula Epinephelus moara Epinephelus bruneus
99
99
Downloaded by [University of California, San Diego] at 08:17 11 November 2015
Epinephelus latifasciatus
94 93
Epinephelus lanceolatus Epinephelus coioides
99
Epinephelus fuscoguttatus 100
Epinephelus sexfasciatus Danio rerio Foryzias latipes
0.2
Bootstrap method (No. of Bootstrap Replications: 1000). Phylogenetic tree (Figure 1) showed that Epinephelus polyphekadion and other 17 kinds of fish have a higher homology sequence. The result indicated that E. latifasciatus, E. polyphekadion, E. epistictus, E. akaara and E. stictus of the Epinephelus formed a monophyletic group, whereas E. latifasciatus, E. polyphekadion and E. epistictus formed a sister group.
Declaration of interest This work was supported by China 863 project (NO. 2012AA10A407) and Produce-Learn-Research Projects of Hainan Province (CXY20130045).
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Han Y, Chen G, Luo J, Wen X, Li W, Wang J. (2014). The complete mitochondrial genome of Cheilinus undulates based on high-throughput sequencing technique. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.971276. James CM, Al-Thobaiti SA, Rasem BM, Carlos MH. (1997). Breeding and larval rearing of the camouflage grouper Epinephelus polyphekadion (Bleeker) in the hypersaline waters of the Red Sea coast of Saudi Arabia. Aquac Res 28:671–81. Rhodes KL, Lewis RI, Chapman RW, Sadovy Y. (2003). Genetic structure of camouflage grouper, Epinephelus polyphekadion (Pisces: Serranidae), in the western central Pacific. Mar Biol 142:771–6.
