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
Mitochondrial genome of the Torpedo scad Megalaspis cordyla (Perciformes: Carangidae): genome characterization and phylogenetic consideration Min Li, Yufang Li & Zuozhi Chen To cite this article: Min Li, Yufang Li & Zuozhi Chen (2014): Mitochondrial genome of the Torpedo scad Megalaspis cordyla (Perciformes: Carangidae): genome characterization and phylogenetic consideration, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.971258
Published online: 16 Oct 2014.
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Date: 05 November 2015, At: 16:10
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.971258
MITOGENOME ANNOUNCEMENT
Mitochondrial genome of the Torpedo scad Megalaspis cordyla (Perciformes: Carangidae): genome characterization and phylogenetic consideration Min Li1,2, Yufang Li1,2, and Zuozhi Chen1 Downloaded by [University of California, San Diego] at 16:10 05 November 2015
1
South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, P. R. China and 2Scientific Observing and Experimental Station of South China Sea Fishery Resources and Environments, Ministry of Agriculture, Guangzhou, P. R. China Abstract
Keywords
This study presented the complete mitochondrial genome of the Torpedo scad Megalaspis cordyla, the only member of its genus, as well as its phylogenetic position in Carangidae. The genome is 16,566 bp containing the usual 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, and 1 control region. Gene organization is similar to that observed in most other vertebrates. Gene overlapping and separating were also observed in M. cordyla mitogenome. The overall base compositions of mitogenome was 28.83% A, 25.81% T, 15.93% G, and 29.43% C. Phylogenetic analyses using the concatenated sequence of the protein-coding genes of the reported Carangidae mitogenome showed similar results in the neighbour-joining and Bayesian inference trees. Three clades were formed as Subfamilies Caranginae, Seriolinae and Trachinotinae in Carangidae. M. cordyla was most closely related to the species in genus Caranx.
Carangidae, Megalaspis cordyla, mitochondrial genome
The torpedo scad, Megalaspis cordyla (Perciformes: Carangidae) is a species of schooling pelagic fish, which is distributed throughout the tropical and subtropical waters of the Indian and west Pacific Oceans (Froese & Pauly, 2011). It is of major importance to commercial fisheries in the central Indo-Pacific region and it is also the only member of the monotypic genus Megalaspis. Due to the lack of its genetic information, we determined the complete mitochondrial genome in the present study. Nine pairs of primers were designed for amplification of the mitochondrial fragments by PCR. After cloning, sequencing, and assembling, the complete mitochondrial genome sequence of M. cordyla was obtained for the first time. We expected the sequence could provide the basic data for studies on its population structure and fisheries management. We also examined its phylogenetic position with respect to 16 other species (with reported mitogenome) in Carangidae in order to further clarify their relationships. The gene structure and order of the complete mitochondrial genome of M. cordyla were identical to those typically obtained from other vertebrates (GenBank accession number KM522836). The total length was 16,566 bp, including 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and 1 non-coding control region. The overall base composition of the
Correspondence: Zuozhi Chen, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, P. R. China. Tel: +86 20 89108327. Fax: +86 20 84451442. E-mail: [email protected]
History Received 11 September 2014 Revised 19 September 2014 Accepted 26 September 2014 Published online 16 October 2014
heavy strand was 28.83% A, 25.81% T, 15.93% G, and 29.43% C with a slight AT bias of 54.64%. Gene overlapping and separating were also observed in M. cordyla mitogenome, which is a common characteristic found in other vertebrate mitochondrial genomes. There were 9 regions of gene overlaps totaling 23 bp (varying from 1 to 7 bp) and 12 intergenic spacer regions totaling 66 bp (varying from 1 to 37 bp). Most of the 13 protein-coding genes started with a typical ATG codon, except for COI and ATPase 6 which started with GTG and ATA, respectively. The usual TAA or TAG termination codons were found for most of the protein-coding genes. However, the other 3 genes (COII, ND4 and Cyt b) had an incomplete termination codon (T–). D-loop region was located between tRNAPro and tRNAPhe with 863 bp in length. The additional non-coding region was 37 bp in length and located between tRNAAsn and tRNACys genes. It was considered to be the origin of L-strand replication (Horai et al., 1995). Phylogenetic position for genus Megalaspis in Carangidae was determined by neighbour-joining (NJ; Saitou & Nei, 1987; Tamura et al., 2013) and Bayesian inference (BI, Ronquist & Huelsenbeck, 2003) analyses using the concatenated sequence of 13 protein-coding genes (without stop codons) extracted from the reported Carangidae mitogenomes, under the best-fit GTR + I + G model generated in Modeltest 3.07 (Posada & Crandall, 1998). The similar topology of both the NJ tree and the BI tree (Figure 1) showed that three clades could be divided as subfamilies Caranginae, Seriolinae and Trachinotinae in Carangidae based on the current dataset. Within subfamily Caranginae, genus Megalaspis was most closely related to Caranx, and they formed a clade sister to Alepes. The assemblage (Megalaspis, Caranx); Alepes) was a sister group to (Alectis, Carangoides).
Downloaded by [University of California, San Diego] at 16:10 05 November 2015
2
M. Li et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Topology of Neighbor-joining tree and Bayesian inference tree based on the concatenated sequence of 13 protein-coding genes extracted from the reported Carangidae mitogenomes, with Larimichthys crocea as an outgroup. Numbers at nodes correspond to Bootstrap proportions (left) from NJ analysis and Bayesian posterior probabilities (right) from BI analysis.
Declaration of interest This work was funded by the Financial Fund of the Ministry of Agriculture (No. NFZX2013), the Special Scientific Research Funds for Central Non-profit Institutes, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (No. 2013TS05) and the Financial Fund of Ministry of Science & Technology (No. 2013BAD13B06). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Froese R, Pauly D. editors. (2011). FishBase. World Wide Web electronic publication. Available at: www.fishbase.org, version (Accessed June 2014).
Horai S, Hayasaka K, Kondo R, Tsugane K, Takahata N. (1995). Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc Natl Acad Sci 92: 532–6. Posada D, Crandall KA. (1998). Modeltest: Testing the model of DNA substitution. Bioinformatics 14:817–18. Ronquist F, Huelsenbeck JF. (2003). MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–4. Saitou N, Nei M. (1987). The neighbour-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–25. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol 30:2725–9.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Mitochondrial genome of the Torpedo scad Megalaspis cordyla (Perciformes: Carangidae): genome characterization and phylogenetic consideration Min Li, Yufang Li & Zuozhi Chen To cite this article: Min Li, Yufang Li & Zuozhi Chen (2014): Mitochondrial genome of the Torpedo scad Megalaspis cordyla (Perciformes: Carangidae): genome characterization and phylogenetic consideration, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.971258
Published online: 16 Oct 2014.
Submit your article to this journal
Article views: 10
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: 05 November 2015, At: 16:10
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.971258
MITOGENOME ANNOUNCEMENT
Mitochondrial genome of the Torpedo scad Megalaspis cordyla (Perciformes: Carangidae): genome characterization and phylogenetic consideration Min Li1,2, Yufang Li1,2, and Zuozhi Chen1 Downloaded by [University of California, San Diego] at 16:10 05 November 2015
1
South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, P. R. China and 2Scientific Observing and Experimental Station of South China Sea Fishery Resources and Environments, Ministry of Agriculture, Guangzhou, P. R. China Abstract
Keywords
This study presented the complete mitochondrial genome of the Torpedo scad Megalaspis cordyla, the only member of its genus, as well as its phylogenetic position in Carangidae. The genome is 16,566 bp containing the usual 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, and 1 control region. Gene organization is similar to that observed in most other vertebrates. Gene overlapping and separating were also observed in M. cordyla mitogenome. The overall base compositions of mitogenome was 28.83% A, 25.81% T, 15.93% G, and 29.43% C. Phylogenetic analyses using the concatenated sequence of the protein-coding genes of the reported Carangidae mitogenome showed similar results in the neighbour-joining and Bayesian inference trees. Three clades were formed as Subfamilies Caranginae, Seriolinae and Trachinotinae in Carangidae. M. cordyla was most closely related to the species in genus Caranx.
Carangidae, Megalaspis cordyla, mitochondrial genome
The torpedo scad, Megalaspis cordyla (Perciformes: Carangidae) is a species of schooling pelagic fish, which is distributed throughout the tropical and subtropical waters of the Indian and west Pacific Oceans (Froese & Pauly, 2011). It is of major importance to commercial fisheries in the central Indo-Pacific region and it is also the only member of the monotypic genus Megalaspis. Due to the lack of its genetic information, we determined the complete mitochondrial genome in the present study. Nine pairs of primers were designed for amplification of the mitochondrial fragments by PCR. After cloning, sequencing, and assembling, the complete mitochondrial genome sequence of M. cordyla was obtained for the first time. We expected the sequence could provide the basic data for studies on its population structure and fisheries management. We also examined its phylogenetic position with respect to 16 other species (with reported mitogenome) in Carangidae in order to further clarify their relationships. The gene structure and order of the complete mitochondrial genome of M. cordyla were identical to those typically obtained from other vertebrates (GenBank accession number KM522836). The total length was 16,566 bp, including 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and 1 non-coding control region. The overall base composition of the
Correspondence: Zuozhi Chen, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou, P. R. China. Tel: +86 20 89108327. Fax: +86 20 84451442. E-mail: [email protected]
History Received 11 September 2014 Revised 19 September 2014 Accepted 26 September 2014 Published online 16 October 2014
heavy strand was 28.83% A, 25.81% T, 15.93% G, and 29.43% C with a slight AT bias of 54.64%. Gene overlapping and separating were also observed in M. cordyla mitogenome, which is a common characteristic found in other vertebrate mitochondrial genomes. There were 9 regions of gene overlaps totaling 23 bp (varying from 1 to 7 bp) and 12 intergenic spacer regions totaling 66 bp (varying from 1 to 37 bp). Most of the 13 protein-coding genes started with a typical ATG codon, except for COI and ATPase 6 which started with GTG and ATA, respectively. The usual TAA or TAG termination codons were found for most of the protein-coding genes. However, the other 3 genes (COII, ND4 and Cyt b) had an incomplete termination codon (T–). D-loop region was located between tRNAPro and tRNAPhe with 863 bp in length. The additional non-coding region was 37 bp in length and located between tRNAAsn and tRNACys genes. It was considered to be the origin of L-strand replication (Horai et al., 1995). Phylogenetic position for genus Megalaspis in Carangidae was determined by neighbour-joining (NJ; Saitou & Nei, 1987; Tamura et al., 2013) and Bayesian inference (BI, Ronquist & Huelsenbeck, 2003) analyses using the concatenated sequence of 13 protein-coding genes (without stop codons) extracted from the reported Carangidae mitogenomes, under the best-fit GTR + I + G model generated in Modeltest 3.07 (Posada & Crandall, 1998). The similar topology of both the NJ tree and the BI tree (Figure 1) showed that three clades could be divided as subfamilies Caranginae, Seriolinae and Trachinotinae in Carangidae based on the current dataset. Within subfamily Caranginae, genus Megalaspis was most closely related to Caranx, and they formed a clade sister to Alepes. The assemblage (Megalaspis, Caranx); Alepes) was a sister group to (Alectis, Carangoides).
Downloaded by [University of California, San Diego] at 16:10 05 November 2015
2
M. Li et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Topology of Neighbor-joining tree and Bayesian inference tree based on the concatenated sequence of 13 protein-coding genes extracted from the reported Carangidae mitogenomes, with Larimichthys crocea as an outgroup. Numbers at nodes correspond to Bootstrap proportions (left) from NJ analysis and Bayesian posterior probabilities (right) from BI analysis.
Declaration of interest This work was funded by the Financial Fund of the Ministry of Agriculture (No. NFZX2013), the Special Scientific Research Funds for Central Non-profit Institutes, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (No. 2013TS05) and the Financial Fund of Ministry of Science & Technology (No. 2013BAD13B06). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Froese R, Pauly D. editors. (2011). FishBase. World Wide Web electronic publication. Available at: www.fishbase.org, version (Accessed June 2014).
Horai S, Hayasaka K, Kondo R, Tsugane K, Takahata N. (1995). Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc Natl Acad Sci 92: 532–6. Posada D, Crandall KA. (1998). Modeltest: Testing the model of DNA substitution. Bioinformatics 14:817–18. Ronquist F, Huelsenbeck JF. (2003). MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572–4. Saitou N, Nei M. (1987). The neighbour-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–25. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evol 30:2725–9.
