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 DNA sequencing of Vieja synspila, a cichlid fish Bin Xu, Jianzhong Gao, Xuelong Wang, Zaizhong Chen & Chenghui Wang To cite this article: Bin Xu, Jianzhong Gao, Xuelong Wang, Zaizhong Chen & Chenghui Wang (2014): Complete mitochondrial DNA sequencing of Vieja synspila, a cichlid fish, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.908378
Published online: 12 Jun 2014.
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Date: 05 November 2015, At: 19:06
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.908378
SHORT COMMUNICATION
Complete mitochondrial DNA sequencing of Vieja synspila, a cichlid fish Bin Xu, Jianzhong Gao, Xuelong Wang, Zaizhong Chen, and Chenghui Wang
Downloaded by [University of California, San Diego] at 19:06 05 November 2015
Key Laboratory of Freshwater Fishery Germplasm Resources, Ministry of Agriculture of P.R. China, Shanghai University Knowledge Service Platform, Shanghai Ocean University Aquatic Animal Breeding Center (ZF1206), Shanghai, P.R. China Abstract
Keywords
The Redhead cichlid (Vieja synspila) is an important aquarium fish and a useful phylogenetic organism of the Cichlidae family. In this study, we sequenced the mitochondrial genome of the Redhead cichlid for the first time. The mitogenome (16,543 bp) had the typical mitochondrial characteristics of other cichlid fish, including 13 protein-coding, 22 tRNA, two rRNA genes and one putative control region. This sequence will be helpful in studying the phylogenetic relationships between cichlid fish.
Cichlida, mitogenome, Redhead cichlid
Cichlid fish are an important fish species in biology because of their extremely diverse morphology, behavior, and ecology (He et al., 2011). Cichlid fish are relatively large and colorful aquarium species (Nelson, 1994). Cichlid fish such as Vieja synspila, which are present in Mesoamerica, i.e. the region from southern Mexico to Panama (Concheiro Pe´rez et al., 2007), have been extensively cultured around the world. However, the taxonomic classification of the Vieja genus has been poorly performed due to variations in fish morphology (McMahan et al., 2010). Some scholars have proposed a number of different classifications, which resulted in confusion about the classification of the species (McMahan et al., 2010). The mitochondrial genome allows taxonomic classifications. Therefore, we sequenced the mitochondrial genome of V. synspila, a representative species in the Vieja genus within the Cichlidae family. In this study, V. synspila fishes were obtained from the aquarium at Shanghai Ocean University. The primers were designed according to the partial mtDNA sequences of 16sRNA (DQ119180) (Chakrabarty, 2006), COI (GU817283) (Unpublished), ND4 (GU737108) (Lopez-Fernandez et al., 2010), and Cytb (FJ668648) (McMahan et al., 2010) of V. synspila deposited in GenBank. PCR amplification and sequencing of the products were performed according to the method described by He et al. (2011) with slight modifications. The mitochondrial DNA of V. synspila was 16,543 bp in length; its sequence has been deposited in GenBank (accession number: KF879808). Similar to other cichlid fish, the mtDNA of V. synspila consisted of 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region (Table 1). In the 13 protein-coding genes, ATG was the start codon; however, in COI, GTG was the start codon. The stop codon, TAA, was present in COI, ATP8, ATP6, ND1, ND4L, ND6, and Cytb; TAG was present
Correspondence: Z. Z. Chen, Shanghai University Knowledge Service Platform, Shanghai Ocean University, 999 Huchenghuan Road, 201306 Shanghai, P.R. China. Tel: +86 21 61900412. E-mail: [email protected]
History Received 25 February 2014 Revised 16 March 2014 Accepted 22 March 2014 Published online 6 June 2014
Table 1. Characteristics of the mitochondrial genomes of Vieja synspila. Position
Phe
tRNA 12sRNA tRNAVal 16sRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COI tRNASer(UCN) tRNAAsp COII tRNALys ATP8 ATP6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro CR
Start
Stop
Size (bp)
1 70 1015 1087 2777 2851 3828 3897 3967 4037 5083 5156 5226 5333 5399 5470 7054 7128 7206 7897 7972 8130 8813 9597 9669 10,018 10,087 10,377 11,758 11,827 11,899 11,972 13,807 14,329 14,402 15,546 15,617 15,687
69 1014 1086 2776 2850 3825 3897 3967 4036 5082 5154 5224 5298 5398 5468 7032 7124 7200 7896 7970 8139 8813 9597 9668 10,019 10,086 10,383 11,757 11,826 11,894 11,971 13,810 14,328 14,397 15,538 15,617 15,686 16,543
69 945 72 1690 74 975 70 71 70 1046 72 69 73 66 70 1563 71 73 691 74 168 684 785 72 351 69 297 1381 69 68 73 1839 522 69 1137 72 70 857
Codon Start
Stop
ATG
TAA
ATG
TA–
GTG
TAA
ATG
T– –
ATG ATG ATG
TAA TAA TA–
ATG
TAG
ATG ATG
TAA T– –
ATG ATG
TAG TAA
ATG
TAA
Intergenic region
Strand
0 0 0 0 0 2 1 1 0 0 1 1 34 0 1 21 3 5 0 1 0 1 1 0 2 0 7 0 0 4 0 4 0 4 7 1 0
H H H H H H H L H H H L L L L H L H H H H H H H H H H H H H H H L L H H L H
H and L indicate genes transcribed on the heavy and light strand, respectively.
2
B. Xu et al.
in ND3 and ND5; an incomplete stop codon ‘‘TA–’’ was found in COIII and ND2, and ‘‘T– –’’ was found in COII and ND4. The 12 s and 16 s rRNA genes were 945 and 1690 bp in length, respectively. The size of the 22 tRNA ranged from 66 bp to 74 bp. The control region, which was 857 bp, was located between tRNAPro and tRNAPhe. The base composition consisted of A ¼ 27.8%, C ¼ 31.7%, G ¼ 15.8%, and T ¼ 24.8%, which is characteristic of mitochondrial genomes of other bony fish (Cheng et al., 2010; Wang et al., 2008).
Acknowledgements The authors would like to thank Professor Shaojun Liu and his colleagues in Hunan Normal University of China for their constructive comments. We thank Elixigen Corporation (Huntington Beach, California, USA) for helping in proofreading and editing the English of final manuscript.
Downloaded by [University of California, San Diego] at 19:06 05 November 2015
Declaration of interest This work was supported by a grant from the Shanghai University Knowledge Service Platform, Shanghai Ocean University Aquatic Animal Breeding Center (ZF1206). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Chakrabarty P. (2006). Systematics and historical biogeography of Greater Antillean Cichlidae. Mol Phylogenet Evol 39:619–27.
Mitochondrial DNA, Early Online: 1–2
Cheng Y, Xu T, Shi G, Wang R. (2010). Complete mitochondrial genome of the miiuy croaker Miichthys miiuy (Perciformes, Sciaenidae) with phylogenetic consideration. Mar Genomics 3:201–9. ˇ ´ıcˇan O, Ortı´ G, Bermingham E, Doadrio I, Concheiro Pe´rez GA, R Zardoya R. (2007). Phylogeny and biogeography of 91 species of heroine cichlids (Teleostei: Cichlidae) based on sequences of the cytochrome b gene. Mol Phylogenet Evol 43:91–110. He A, Luo Y, Yang H, Liu L, Li S, Wang C. (2011). Complete mitochondrial DNA sequences of the Nile tilapia (Oreochromis niloticus) and Blue tilapia (Oreochromis aureus): Genome characterization and phylogeny applications. Mol Biol Rep 38:2015–21. He AY, Luo YJ, Yang H, Liu LP, Li SF, Wang CH. (2011). Complete mitochondrial DNA sequences of the Nile tilapia (Oreochromis niloticus) and Blue tilapia (Oreochromis aureus): Genome characterization and phylogeny applications. Mol Biol Rep 38:2015–21. Lopez-Fernandez H, Winemiller KO, Honeycutt RL. (2010). Multilocus phylogeny and rapid radiations in Neotropical cichlid fishes (Perciformes: Cichlidae: Cichlinae). Mol Phylogenet Evol 55: 1070–86. McMahan CD, Geheber AD, Piller KR. (2010). Molecular systematics of the enigmatic Middle American genus Vieja (Teleostei: Cichlidae). Mol Phylogenet Evol 57:1293–300. Nelson JS. (1994). Fishes of the world. 2nd ed. New York: John Wiley, 390 pp. Wang C, Chen Q, Lu G, Xu J, Yang Q, Li S. (2008). Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella, Teleostei): Insight into its phylogenic position within Cyprinidae. Gene 424:96–101.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
Complete mitochondrial DNA sequencing of Vieja synspila, a cichlid fish Bin Xu, Jianzhong Gao, Xuelong Wang, Zaizhong Chen & Chenghui Wang To cite this article: Bin Xu, Jianzhong Gao, Xuelong Wang, Zaizhong Chen & Chenghui Wang (2014): Complete mitochondrial DNA sequencing of Vieja synspila, a cichlid fish, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.908378
Published online: 12 Jun 2014.
Submit your article to this journal
Article views: 13
View related articles
View Crossmark data
Citing articles: 2 View citing articles
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: 19:06
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.908378
SHORT COMMUNICATION
Complete mitochondrial DNA sequencing of Vieja synspila, a cichlid fish Bin Xu, Jianzhong Gao, Xuelong Wang, Zaizhong Chen, and Chenghui Wang
Downloaded by [University of California, San Diego] at 19:06 05 November 2015
Key Laboratory of Freshwater Fishery Germplasm Resources, Ministry of Agriculture of P.R. China, Shanghai University Knowledge Service Platform, Shanghai Ocean University Aquatic Animal Breeding Center (ZF1206), Shanghai, P.R. China Abstract
Keywords
The Redhead cichlid (Vieja synspila) is an important aquarium fish and a useful phylogenetic organism of the Cichlidae family. In this study, we sequenced the mitochondrial genome of the Redhead cichlid for the first time. The mitogenome (16,543 bp) had the typical mitochondrial characteristics of other cichlid fish, including 13 protein-coding, 22 tRNA, two rRNA genes and one putative control region. This sequence will be helpful in studying the phylogenetic relationships between cichlid fish.
Cichlida, mitogenome, Redhead cichlid
Cichlid fish are an important fish species in biology because of their extremely diverse morphology, behavior, and ecology (He et al., 2011). Cichlid fish are relatively large and colorful aquarium species (Nelson, 1994). Cichlid fish such as Vieja synspila, which are present in Mesoamerica, i.e. the region from southern Mexico to Panama (Concheiro Pe´rez et al., 2007), have been extensively cultured around the world. However, the taxonomic classification of the Vieja genus has been poorly performed due to variations in fish morphology (McMahan et al., 2010). Some scholars have proposed a number of different classifications, which resulted in confusion about the classification of the species (McMahan et al., 2010). The mitochondrial genome allows taxonomic classifications. Therefore, we sequenced the mitochondrial genome of V. synspila, a representative species in the Vieja genus within the Cichlidae family. In this study, V. synspila fishes were obtained from the aquarium at Shanghai Ocean University. The primers were designed according to the partial mtDNA sequences of 16sRNA (DQ119180) (Chakrabarty, 2006), COI (GU817283) (Unpublished), ND4 (GU737108) (Lopez-Fernandez et al., 2010), and Cytb (FJ668648) (McMahan et al., 2010) of V. synspila deposited in GenBank. PCR amplification and sequencing of the products were performed according to the method described by He et al. (2011) with slight modifications. The mitochondrial DNA of V. synspila was 16,543 bp in length; its sequence has been deposited in GenBank (accession number: KF879808). Similar to other cichlid fish, the mtDNA of V. synspila consisted of 13 protein-coding genes, two rRNA genes, 22 tRNA genes, and one control region (Table 1). In the 13 protein-coding genes, ATG was the start codon; however, in COI, GTG was the start codon. The stop codon, TAA, was present in COI, ATP8, ATP6, ND1, ND4L, ND6, and Cytb; TAG was present
Correspondence: Z. Z. Chen, Shanghai University Knowledge Service Platform, Shanghai Ocean University, 999 Huchenghuan Road, 201306 Shanghai, P.R. China. Tel: +86 21 61900412. E-mail: [email protected]
History Received 25 February 2014 Revised 16 March 2014 Accepted 22 March 2014 Published online 6 June 2014
Table 1. Characteristics of the mitochondrial genomes of Vieja synspila. Position
Phe
tRNA 12sRNA tRNAVal 16sRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COI tRNASer(UCN) tRNAAsp COII tRNALys ATP8 ATP6 COIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer(AGY) tRNALeu(CUN) ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro CR
Start
Stop
Size (bp)
1 70 1015 1087 2777 2851 3828 3897 3967 4037 5083 5156 5226 5333 5399 5470 7054 7128 7206 7897 7972 8130 8813 9597 9669 10,018 10,087 10,377 11,758 11,827 11,899 11,972 13,807 14,329 14,402 15,546 15,617 15,687
69 1014 1086 2776 2850 3825 3897 3967 4036 5082 5154 5224 5298 5398 5468 7032 7124 7200 7896 7970 8139 8813 9597 9668 10,019 10,086 10,383 11,757 11,826 11,894 11,971 13,810 14,328 14,397 15,538 15,617 15,686 16,543
69 945 72 1690 74 975 70 71 70 1046 72 69 73 66 70 1563 71 73 691 74 168 684 785 72 351 69 297 1381 69 68 73 1839 522 69 1137 72 70 857
Codon Start
Stop
ATG
TAA
ATG
TA–
GTG
TAA
ATG
T– –
ATG ATG ATG
TAA TAA TA–
ATG
TAG
ATG ATG
TAA T– –
ATG ATG
TAG TAA
ATG
TAA
Intergenic region
Strand
0 0 0 0 0 2 1 1 0 0 1 1 34 0 1 21 3 5 0 1 0 1 1 0 2 0 7 0 0 4 0 4 0 4 7 1 0
H H H H H H H L H H H L L L L H L H H H H H H H H H H H H H H H L L H H L H
H and L indicate genes transcribed on the heavy and light strand, respectively.
2
B. Xu et al.
in ND3 and ND5; an incomplete stop codon ‘‘TA–’’ was found in COIII and ND2, and ‘‘T– –’’ was found in COII and ND4. The 12 s and 16 s rRNA genes were 945 and 1690 bp in length, respectively. The size of the 22 tRNA ranged from 66 bp to 74 bp. The control region, which was 857 bp, was located between tRNAPro and tRNAPhe. The base composition consisted of A ¼ 27.8%, C ¼ 31.7%, G ¼ 15.8%, and T ¼ 24.8%, which is characteristic of mitochondrial genomes of other bony fish (Cheng et al., 2010; Wang et al., 2008).
Acknowledgements The authors would like to thank Professor Shaojun Liu and his colleagues in Hunan Normal University of China for their constructive comments. We thank Elixigen Corporation (Huntington Beach, California, USA) for helping in proofreading and editing the English of final manuscript.
Downloaded by [University of California, San Diego] at 19:06 05 November 2015
Declaration of interest This work was supported by a grant from the Shanghai University Knowledge Service Platform, Shanghai Ocean University Aquatic Animal Breeding Center (ZF1206). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Chakrabarty P. (2006). Systematics and historical biogeography of Greater Antillean Cichlidae. Mol Phylogenet Evol 39:619–27.
Mitochondrial DNA, Early Online: 1–2
Cheng Y, Xu T, Shi G, Wang R. (2010). Complete mitochondrial genome of the miiuy croaker Miichthys miiuy (Perciformes, Sciaenidae) with phylogenetic consideration. Mar Genomics 3:201–9. ˇ ´ıcˇan O, Ortı´ G, Bermingham E, Doadrio I, Concheiro Pe´rez GA, R Zardoya R. (2007). Phylogeny and biogeography of 91 species of heroine cichlids (Teleostei: Cichlidae) based on sequences of the cytochrome b gene. Mol Phylogenet Evol 43:91–110. He A, Luo Y, Yang H, Liu L, Li S, Wang C. (2011). Complete mitochondrial DNA sequences of the Nile tilapia (Oreochromis niloticus) and Blue tilapia (Oreochromis aureus): Genome characterization and phylogeny applications. Mol Biol Rep 38:2015–21. He AY, Luo YJ, Yang H, Liu LP, Li SF, Wang CH. (2011). Complete mitochondrial DNA sequences of the Nile tilapia (Oreochromis niloticus) and Blue tilapia (Oreochromis aureus): Genome characterization and phylogeny applications. Mol Biol Rep 38:2015–21. Lopez-Fernandez H, Winemiller KO, Honeycutt RL. (2010). Multilocus phylogeny and rapid radiations in Neotropical cichlid fishes (Perciformes: Cichlidae: Cichlinae). Mol Phylogenet Evol 55: 1070–86. McMahan CD, Geheber AD, Piller KR. (2010). Molecular systematics of the enigmatic Middle American genus Vieja (Teleostei: Cichlidae). Mol Phylogenet Evol 57:1293–300. Nelson JS. (1994). Fishes of the world. 2nd ed. New York: John Wiley, 390 pp. Wang C, Chen Q, Lu G, Xu J, Yang Q, Li S. (2008). Complete mitochondrial genome of the grass carp (Ctenopharyngodon idella, Teleostei): Insight into its phylogenic position within Cyprinidae. Gene 424:96–101.
