http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1022756
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the Synanceia verrucosa (Scorpaeniformes: Synanceiidae) Qian Wang, Jun Wang, Jian Luo, and Guohua Chen
Mitochondrial DNA Downloaded from informahealthcare.com by University of Virginia on 04/12/15 For personal use only.
Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Ocean, Hainan University, Haikou, PR China
Abstract
Keywords
The complete mitochondrial genome of the Synanceia verrucosa has been sequenced. The mitochondrial genome is 16,506 bp in length, containing 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The gene order and the composition of S. verrucosa mitochondrial genome were similar to that of most other vertebrates. The overall nucleotides base composition of the heavy strand is A (31.01%), G (15.06%), C (25.60%), and T (28.34%). With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The tRNA-Ser2 gene lacked DHC arm and could not fold into a typical clover-leaf secondary structure. Seen from the phylogenetic tree, a stonefish (S. verrucosa), two lionfishes, and eight rockfishes from the same order (Scorpaeniformes) clustered into one branch.
Mitochondrial genome, Synanceia verrucosa, Synanceiidae
The Synanceia verrucosa (Scorpaeniformes: Synanceiidae) is one of the most venomous known fish in the stonefish family, and lives on reef bottoms camouflaged as a rock, which mainly distributes in the Pacific and the Indian Oceans (Chuang & Shiao, 2014). However, little information about its genetic characteristic has been reported. Therefore, the purpose of this study was to sequence the complete mitochondrial genome of S. verrucosa by using the next-generation sequencing (NGS) techniques strategy (Han et al., 2014), which can be used to unveil taxonomic problems and phylogenetic relationships in Synanceiidae. One specimen of S. verrucosa was collected from the South China Sea. The total genomic DNA was extracted from the fin of the fresh fish using the salting-out procedure (Howe et al., 1997). The complete mitochondrial genome of S. verrucosa (Genbank accession number KP789313.1) is 16,506 bp in length, containing 13 protein-coding genes, two ribosomal RNA genes (12 S rRNA and 16 S rRNA), 22 transfer RNA genes (tRNA), and one control region, which is the same as the typical vertebrates (Wang et al., 2008). Most of the genes are encoded on the heavy strand, with only the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes [Gln, Ala, Asn, Cys, Try, Glu, Pro, and Ser (TGA)] encoded on the light strand. The overall nucleotides base composition of the heavy strand is 31.01% of A, 15.06% of G, 25.60% of C, and 28.34% of T, with an A + T bias.
Correspondence: Prof. Guohua Chen, College of Ocean, Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, PR China. Tel: +86 898 66279184. Fax: +86 898 66279184. E-mail: [email protected]
History Received 18 February 2015 Accepted 21 February 2015 Published online 26 March 2015
In the 13 identified protein-coding genes, except for COX1 was initiated by GTG, the remaining genes were initiated by the ATG codon. The ND1, COX1, ATP8, ND4L, ND5, and ND6 were terminated with TAA codon, while the other proteincoding genes were stopped by incomplete codon TA (ND2, ATP6, and COX3) or T (COX2, ND3, ND4, and CYTB). The 12 S and 16 S rRNA genes are located between the tRNA-Phe (GAA) and tRNA-Leu (TAA) genes, and are separated by the tRNA-Val (TAC) gene with the same situation found in other vertebrates. Most genes are either abutted or overlapped. The 22 tRNA genes vary from 66 to 74 bp in length, and could be folded into the typical cloverleaf secondary structure although numerous non-complementary and T–G base pairs exist in the stem regions, except tRNA-Ser2, in which the dihydrouridine (DHU) arm is replaced by a simple loop with 12 unpaired nucleotides. The control region was 855 bp in length, located between tRNA-Pro (TGG) and tRNA-Phe (GAA) gene. The nucleotide composition of control region was 33.33% of A, 21.17% of C, 15.20% of G, and 30.29% of T. The maximum likelihood tree (by RAxML 8.1.5, Heidelberg, Germany) (Stamatakis, 2014) based on the mitochondrial genome nucleotide sequences of the S. verrucosa and the other 12 kinds of fish were constructed under the mutation model of GTR + G (by jModelTest 2.1.7, Vigo, Spain) (Darriba et al., 2012). Seen from the phylogenetic tree (Figure 1), a stonefish (S. verrucosa), two lionfishes (Pterois volitans and Pterois miles), and eight rockfishes (Sebastes pachycephalus, Sebastes koreanus, Sebastes oblongus, Sebastes owstoni, Sebastes inermis, Helicolenus hilgendorfi, Helicolenus avius, and Sebastiscus marmoratus) from the same order (Scorpaeniformes) clustered into one branch. Among the three fish family within the order, Sebastidae (rockfish) and Scorpaenidae (lionfish) have a closer relationship and formed a sub-branch.
Mitochondrial DNA Downloaded from informahealthcare.com by University of Virginia on 04/12/15 For personal use only.
2
Q. Wang et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Maximum likelihood tree based on the mitochondrial genome nucleotide sequences of the Synanceia verrucosa (KP789313.1) and the other 12 kinds of fish under the mutation model of GTR + G. Genbank accession numbers of the sequences were used for the tree as follows: Sebastes pachycephalus, KF836442.1; Sebastes koreanus, KF561237.1; Sebastes oblongus, KF836441.1; Sebastes owstoni, KJ834063.1; Sebastes inermis, KF725093.1; Helicolenus hilgendorfi, AP002948.1; Helicolenus avius, AB734123.1; Sebastiscus marmoratus, GU452728.1; Pterois volitans, KM488633.1; Pterois miles, LK022697.1; Oryzias latipes, NC_004387.1; Takifugu obscurus, NC_011626.1.
Declaration of interest The authors report no declaration of interest. The authors alone are responsible for the content and writing of this article. This work is supported by the National 863 Program of China (No. 2012AA10A414) and Produce-Learn-Research Projects of Hainan Province (CXY20130045).
References Chuang PS, Shiao JC. (2014). Toxin gene determination and evolution in scorpaenoid fish. Toxicon 88:21–33. Darriba D, Taboada GL, Doallo R, Posada D. (2012). jModelTest 2: More models, new heuristics and parallel computing. Nat Methods 9:772.
Han YL, Chen GH, Luo J, Wen X, Li WS, Wang J. (2014). The complete mitochondrial genome of Cheilinus undulates based on high-throughput sequencing echnique. Mitochondrial DNA 20:1–3. Howe JR, Klimstra DS, Cordon-Cardo C. (1997). DNA extraction from paraffin-embedded tissues using a salting-out procedure: A reliable method for PCR amplification of archival material. Histol Histopathol 12:595–601. Stamatakis A. (2014). RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–13. Wang C, Chen Q, Lu G, Xu J, Yang Q, Li S. (2008). Complete mitochondrial genome of the grass carp (Ctenophar yngodon idella, Teleostei): Insight into its phylogenic position within Cyprinidae. Gene 424:96–101.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the Synanceia verrucosa (Scorpaeniformes: Synanceiidae) Qian Wang, Jun Wang, Jian Luo, and Guohua Chen
Mitochondrial DNA Downloaded from informahealthcare.com by University of Virginia on 04/12/15 For personal use only.
Key Laboratory of Tropical Biological Resources of Ministry of Education, College of Ocean, Hainan University, Haikou, PR China
Abstract
Keywords
The complete mitochondrial genome of the Synanceia verrucosa has been sequenced. The mitochondrial genome is 16,506 bp in length, containing 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and one control region. The gene order and the composition of S. verrucosa mitochondrial genome were similar to that of most other vertebrates. The overall nucleotides base composition of the heavy strand is A (31.01%), G (15.06%), C (25.60%), and T (28.34%). With the exception of the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The tRNA-Ser2 gene lacked DHC arm and could not fold into a typical clover-leaf secondary structure. Seen from the phylogenetic tree, a stonefish (S. verrucosa), two lionfishes, and eight rockfishes from the same order (Scorpaeniformes) clustered into one branch.
Mitochondrial genome, Synanceia verrucosa, Synanceiidae
The Synanceia verrucosa (Scorpaeniformes: Synanceiidae) is one of the most venomous known fish in the stonefish family, and lives on reef bottoms camouflaged as a rock, which mainly distributes in the Pacific and the Indian Oceans (Chuang & Shiao, 2014). However, little information about its genetic characteristic has been reported. Therefore, the purpose of this study was to sequence the complete mitochondrial genome of S. verrucosa by using the next-generation sequencing (NGS) techniques strategy (Han et al., 2014), which can be used to unveil taxonomic problems and phylogenetic relationships in Synanceiidae. One specimen of S. verrucosa was collected from the South China Sea. The total genomic DNA was extracted from the fin of the fresh fish using the salting-out procedure (Howe et al., 1997). The complete mitochondrial genome of S. verrucosa (Genbank accession number KP789313.1) is 16,506 bp in length, containing 13 protein-coding genes, two ribosomal RNA genes (12 S rRNA and 16 S rRNA), 22 transfer RNA genes (tRNA), and one control region, which is the same as the typical vertebrates (Wang et al., 2008). Most of the genes are encoded on the heavy strand, with only the NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes [Gln, Ala, Asn, Cys, Try, Glu, Pro, and Ser (TGA)] encoded on the light strand. The overall nucleotides base composition of the heavy strand is 31.01% of A, 15.06% of G, 25.60% of C, and 28.34% of T, with an A + T bias.
Correspondence: Prof. Guohua Chen, College of Ocean, Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, PR China. Tel: +86 898 66279184. Fax: +86 898 66279184. E-mail: [email protected]
History Received 18 February 2015 Accepted 21 February 2015 Published online 26 March 2015
In the 13 identified protein-coding genes, except for COX1 was initiated by GTG, the remaining genes were initiated by the ATG codon. The ND1, COX1, ATP8, ND4L, ND5, and ND6 were terminated with TAA codon, while the other proteincoding genes were stopped by incomplete codon TA (ND2, ATP6, and COX3) or T (COX2, ND3, ND4, and CYTB). The 12 S and 16 S rRNA genes are located between the tRNA-Phe (GAA) and tRNA-Leu (TAA) genes, and are separated by the tRNA-Val (TAC) gene with the same situation found in other vertebrates. Most genes are either abutted or overlapped. The 22 tRNA genes vary from 66 to 74 bp in length, and could be folded into the typical cloverleaf secondary structure although numerous non-complementary and T–G base pairs exist in the stem regions, except tRNA-Ser2, in which the dihydrouridine (DHU) arm is replaced by a simple loop with 12 unpaired nucleotides. The control region was 855 bp in length, located between tRNA-Pro (TGG) and tRNA-Phe (GAA) gene. The nucleotide composition of control region was 33.33% of A, 21.17% of C, 15.20% of G, and 30.29% of T. The maximum likelihood tree (by RAxML 8.1.5, Heidelberg, Germany) (Stamatakis, 2014) based on the mitochondrial genome nucleotide sequences of the S. verrucosa and the other 12 kinds of fish were constructed under the mutation model of GTR + G (by jModelTest 2.1.7, Vigo, Spain) (Darriba et al., 2012). Seen from the phylogenetic tree (Figure 1), a stonefish (S. verrucosa), two lionfishes (Pterois volitans and Pterois miles), and eight rockfishes (Sebastes pachycephalus, Sebastes koreanus, Sebastes oblongus, Sebastes owstoni, Sebastes inermis, Helicolenus hilgendorfi, Helicolenus avius, and Sebastiscus marmoratus) from the same order (Scorpaeniformes) clustered into one branch. Among the three fish family within the order, Sebastidae (rockfish) and Scorpaenidae (lionfish) have a closer relationship and formed a sub-branch.
Mitochondrial DNA Downloaded from informahealthcare.com by University of Virginia on 04/12/15 For personal use only.
2
Q. Wang et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Maximum likelihood tree based on the mitochondrial genome nucleotide sequences of the Synanceia verrucosa (KP789313.1) and the other 12 kinds of fish under the mutation model of GTR + G. Genbank accession numbers of the sequences were used for the tree as follows: Sebastes pachycephalus, KF836442.1; Sebastes koreanus, KF561237.1; Sebastes oblongus, KF836441.1; Sebastes owstoni, KJ834063.1; Sebastes inermis, KF725093.1; Helicolenus hilgendorfi, AP002948.1; Helicolenus avius, AB734123.1; Sebastiscus marmoratus, GU452728.1; Pterois volitans, KM488633.1; Pterois miles, LK022697.1; Oryzias latipes, NC_004387.1; Takifugu obscurus, NC_011626.1.
Declaration of interest The authors report no declaration of interest. The authors alone are responsible for the content and writing of this article. This work is supported by the National 863 Program of China (No. 2012AA10A414) and Produce-Learn-Research Projects of Hainan Province (CXY20130045).
References Chuang PS, Shiao JC. (2014). Toxin gene determination and evolution in scorpaenoid fish. Toxicon 88:21–33. Darriba D, Taboada GL, Doallo R, Posada D. (2012). jModelTest 2: More models, new heuristics and parallel computing. Nat Methods 9:772.
Han YL, Chen GH, Luo J, Wen X, Li WS, Wang J. (2014). The complete mitochondrial genome of Cheilinus undulates based on high-throughput sequencing echnique. Mitochondrial DNA 20:1–3. Howe JR, Klimstra DS, Cordon-Cardo C. (1997). DNA extraction from paraffin-embedded tissues using a salting-out procedure: A reliable method for PCR amplification of archival material. Histol Histopathol 12:595–601. Stamatakis A. (2014). RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–13. Wang C, Chen Q, Lu G, Xu J, Yang Q, Li S. (2008). Complete mitochondrial genome of the grass carp (Ctenophar yngodon idella, Teleostei): Insight into its phylogenic position within Cyprinidae. Gene 424:96–101.
