http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.895994
MITOGENOME ANNOUNCEMENT
Characterization of the mitochondrial genome of the Malabar trevally Carangoides malabaricus and related phylogenetic analyses Min Li1,2, Zirong Huang1, and Zuozhi Chen1 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
Mitochondrial DNA Downloaded from informahealthcare.com by Dalhousie University on 12/29/14 For personal use only.
1
Abstract
Keywords
The Malabar trevally Carangoides malabaricus is a widely distributed inshore fish species and commercially important in some tropical regions. This study presented the complete mitochondrial genome of C. malabaricus as well as its phylogenetic position in Carangidae. The entire sequence was 16,561 bp in length, including the typical structure of 13 proteincoding genes, 22 tRNA genes, 2 rRNA genes, 1 control regions and 1 L-strand replication origin. The arrangement of the genes was in line with other teleosts. The genome was composed of 29.6% C, 27.8% A, 26.2% T and 16.4% G, showing an obvious anti G bias. Phylogenetic analyses using the concatenated sequence of the protein-coding genes showed similar results in the Neighbour-Joining and Bayesian inference trees. Three clades were formed as Subfamilies Caranginae, Seriolinae and Trachinotinae in Carangidae based on the current dataset. C. malabaricus was most closely related to the species in the same genus.
Carangoides malabaricus, Carangidae, mitochondrial genome
The Malabar trevally Carangoides malabaricus (Perciformes: Carangidae) is an inshore marine fish distributed throughout the Indian and west Pacific Oceans from South Africa in the west to Japan and Australia in the east (Froese & Pauly, 2013). It is a highly demanded and one of the most important fish commercially harvested in tropical regions. Due to the lack of its genetic information, we determined the complete mitochondrial genome in the present study with the expectation to provide the basic data for studies on its population structure and fisheries management. We also examined its phylogenetic position with respect to 12 other species (with reported mitogenome) in Carangidae in order to further clarify their relationships. The entire mitogenome of C. malabaricus was 16,561 bp in length and comprised 22 transfer RNA genes (tRNA), 13 proteincoding genes, 2 ribosomal RNA genes (12S rRNA and 16S rRNA), 1 control region (D-loop) and 1 origin of light strand replication (OL). The complete genome was characterized and deposited in GenBank database with the accession number
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 27 January 2014 Revised 11 February 2014 Accepted 16 February 2014 Published online 11 March 2014
KJ174514. The arrangement of the multiple genes was in line with other teleosts. With the exception of NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes (Gln, Ala, Asn, Cys, Try, Ser (UCN), Glu and Pro), all other genes were encoded on the heavy strand. The total base composition of C. malabaricus mitogenome was C (29.6%)4A (27.8%)4T (26.2%)4G (16.4%), showing an obvious bias against G commonly observed in fish mitogenome. Most protein-coding genes initiated with ATG except for COX1, which began with GTG. Three types of stop codon were used in open reading frames: TAA (COX1, COX3, ATP6, ATP8, ND4L and ND5), TAG (ND1, ND2, ND3 and ND6) and incomplete stop codons T (COX2, ND4 and CYTB). Based on the concatenated sequence of 13 protein-coding genes (without stop codons) extracted from the reported Carangidae mitogenomes, phylogenetic trees were constructed by employing Neighbour-Joining (NJ; Saitou & Nei, 1987; Tamura et al., 2013) and Bayesian inference (BI; Ronquist & Huelsenbeck, 2003) analyses, under the best-fit GTR + I + G model generated in Modeltest 3.07 (Posada & Crandall, 1998). The similar topology of both the BI tree and the NJ tree (Figure 1) showed that C. malabaricus was most closely related to Carangoides armatus, which belonged to the same genus. Based on the current dataset, three clades could be divided as subfamilies Caranginae, Seriolinae and Trachinotinae in Carangidae. Within subfamilies Caranginae, Genera Caranx and Alepes formed a clade, which was the sister-group of genus Carangoides. Genus Trachurus had a sister relationship to Decapterus, and they formed a clade which was sister to genus Selar. Subfamily Trachinotini, as a sister-group to the clade of Caranginae and Seriolinae, had a basal position in the tree.
2
M. Li et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Dalhousie University on 12/29/14 For personal use only.
Figure 1. Topology of neighbour-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 analysisand Bayesian posterior probabilities (right) from BI analysis.
Declaration of interest
References
This work was funded by the planned Science & Technology Project of Guangdong Province (No. 2011B031100001), the Special Scientific Research Funds for Central Non-profit Institutes, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (No. 2012YD03), the Financial Fund of the Ministry of Agriculture (No. NFZX2013), the Financial Fund of Ministry of Science & Technology (No. 2013BAD13B06) and the National Natural Science Foundation of China (No. 31100362). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
Froese R, Pauly D, editors. (2013). FishBase. World Wide Web electronic publication. Available at: www.fishbase.org, version (Accessed December 2013). 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.
MITOGENOME ANNOUNCEMENT
Characterization of the mitochondrial genome of the Malabar trevally Carangoides malabaricus and related phylogenetic analyses Min Li1,2, Zirong Huang1, and Zuozhi Chen1 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
Mitochondrial DNA Downloaded from informahealthcare.com by Dalhousie University on 12/29/14 For personal use only.
1
Abstract
Keywords
The Malabar trevally Carangoides malabaricus is a widely distributed inshore fish species and commercially important in some tropical regions. This study presented the complete mitochondrial genome of C. malabaricus as well as its phylogenetic position in Carangidae. The entire sequence was 16,561 bp in length, including the typical structure of 13 proteincoding genes, 22 tRNA genes, 2 rRNA genes, 1 control regions and 1 L-strand replication origin. The arrangement of the genes was in line with other teleosts. The genome was composed of 29.6% C, 27.8% A, 26.2% T and 16.4% G, showing an obvious anti G bias. Phylogenetic analyses using the concatenated sequence of the protein-coding genes showed similar results in the Neighbour-Joining and Bayesian inference trees. Three clades were formed as Subfamilies Caranginae, Seriolinae and Trachinotinae in Carangidae based on the current dataset. C. malabaricus was most closely related to the species in the same genus.
Carangoides malabaricus, Carangidae, mitochondrial genome
The Malabar trevally Carangoides malabaricus (Perciformes: Carangidae) is an inshore marine fish distributed throughout the Indian and west Pacific Oceans from South Africa in the west to Japan and Australia in the east (Froese & Pauly, 2013). It is a highly demanded and one of the most important fish commercially harvested in tropical regions. Due to the lack of its genetic information, we determined the complete mitochondrial genome in the present study with the expectation to provide the basic data for studies on its population structure and fisheries management. We also examined its phylogenetic position with respect to 12 other species (with reported mitogenome) in Carangidae in order to further clarify their relationships. The entire mitogenome of C. malabaricus was 16,561 bp in length and comprised 22 transfer RNA genes (tRNA), 13 proteincoding genes, 2 ribosomal RNA genes (12S rRNA and 16S rRNA), 1 control region (D-loop) and 1 origin of light strand replication (OL). The complete genome was characterized and deposited in GenBank database with the accession number
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 27 January 2014 Revised 11 February 2014 Accepted 16 February 2014 Published online 11 March 2014
KJ174514. The arrangement of the multiple genes was in line with other teleosts. With the exception of NADH dehydrogenase subunit 6 (ND6) and eight tRNA genes (Gln, Ala, Asn, Cys, Try, Ser (UCN), Glu and Pro), all other genes were encoded on the heavy strand. The total base composition of C. malabaricus mitogenome was C (29.6%)4A (27.8%)4T (26.2%)4G (16.4%), showing an obvious bias against G commonly observed in fish mitogenome. Most protein-coding genes initiated with ATG except for COX1, which began with GTG. Three types of stop codon were used in open reading frames: TAA (COX1, COX3, ATP6, ATP8, ND4L and ND5), TAG (ND1, ND2, ND3 and ND6) and incomplete stop codons T (COX2, ND4 and CYTB). Based on the concatenated sequence of 13 protein-coding genes (without stop codons) extracted from the reported Carangidae mitogenomes, phylogenetic trees were constructed by employing Neighbour-Joining (NJ; Saitou & Nei, 1987; Tamura et al., 2013) and Bayesian inference (BI; Ronquist & Huelsenbeck, 2003) analyses, under the best-fit GTR + I + G model generated in Modeltest 3.07 (Posada & Crandall, 1998). The similar topology of both the BI tree and the NJ tree (Figure 1) showed that C. malabaricus was most closely related to Carangoides armatus, which belonged to the same genus. Based on the current dataset, three clades could be divided as subfamilies Caranginae, Seriolinae and Trachinotinae in Carangidae. Within subfamilies Caranginae, Genera Caranx and Alepes formed a clade, which was the sister-group of genus Carangoides. Genus Trachurus had a sister relationship to Decapterus, and they formed a clade which was sister to genus Selar. Subfamily Trachinotini, as a sister-group to the clade of Caranginae and Seriolinae, had a basal position in the tree.
2
M. Li et al.
Mitochondrial DNA, Early Online: 1–2
Mitochondrial DNA Downloaded from informahealthcare.com by Dalhousie University on 12/29/14 For personal use only.
Figure 1. Topology of neighbour-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 analysisand Bayesian posterior probabilities (right) from BI analysis.
Declaration of interest
References
This work was funded by the planned Science & Technology Project of Guangdong Province (No. 2011B031100001), the Special Scientific Research Funds for Central Non-profit Institutes, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences (No. 2012YD03), the Financial Fund of the Ministry of Agriculture (No. NFZX2013), the Financial Fund of Ministry of Science & Technology (No. 2013BAD13B06) and the National Natural Science Foundation of China (No. 31100362). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
Froese R, Pauly D, editors. (2013). FishBase. World Wide Web electronic publication. Available at: www.fishbase.org, version (Accessed December 2013). 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.
