http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.987252
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the midas cichlid (Amphilophus citrinellus) Bin Xu1,2, Jianzhong Gao1,2, Zaizhong Chen1,2, Lei Wang1,2, Zhongpu Li1,2, Qi Zhou1,2, and Chenghui Wang1,2 Mitochondrial DNA Downloaded from informahealthcare.com by Chinese University of Hong Kong on 02/14/15 For personal use only.
1
Key Laboratory of Freshwater Fishery Germplasm Resources, Ministry of Agriculture, Shanghai, P.R. China and 2Shanghai University Knowledge Service Platform, Shanghai Ocean University Aquatic Animal Breeding Center (ZF1206), Shanghai, P.R. China Abstract
Keywords
The midas cichlid (Amphilophus citrinellus) is an important aquarium fish that has served as a model organism for studying sympatric speciation. In this study, we sequenced the complete mitochondrial genome of the midas cichlid. We report that the cichlid’s mitochondrial genome is a circular DNA double strand of 16,521 bp length, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. The overall-base compositions of the H-strand are as follows: A, 28.56%; C, 30.69%; G, 15.11%; T, 25.64%. This study provides important genomic data to further the research of the genetic evolution of cichlids.
Cichlidae, midas cichlid, mitochondrial genome
Fishes of the family Cichlidae are useful model organisms for studying evolutionary ecology as they exhibit extensive adaptive radiation and phenotypic plasticity (Klingenberg et al., 2003). The midas cichlid, Amphilophus citrinellus (Gu¨nther, 1864), is distributed in Central America and is well-known worldwide for its impressive coloration. In evolutionary research, A. citrinellus is used as a model organism to study sympatric speciation, particularly in the crater lakes of Nicaragua where species are isolated via color and trophic polymorphisms (Elmer KR et al., 2009; Meyer, 1990). The majority of these studies have used morphological variation as a tool to examine speciation, with very few utilizing the power of genomic data, such as mitochondrial DNA (Barluenga & Meyer, 2010). This is due to the absence of sequence data for the complete mitochondrial genome of A. citrinellus. In this study, we sequenced the complete mitochondrial genome of A. citrinellusi, using a previously established method of PCR amplification and sequencing (He et al., 2011). We obtained a caudal fin from A. citrinellus from the Shanghai Ocean University. We designed five primer pairs according to the complete mitogenome sequences of the Redhead cichlid (Vieja synspila; KF879808) and other sequenced genes from A. citrinellus (16 s RNA: GU737199; COI: DQ119198; ND4: HM050088; Cyt b: AY843348).
History Received 26 October 2014 Accepted 10 November 2014 Published online 9 December 2014
Our work revealed that the mitochondrial genome of A. citrinellus is 16,521 bp in length and contains 13 proteincoding genes, 2 rRNA genes, 22 tRNA genes and a single control region (GeneBank: KJ562277). As in other vertebrates, most of the mitochondrial genes of A. citrinellus are encoded on the H-strand, except for the ND6 gene and eight tRNA genes (Gln, Ala, Asn, Cys, Tyr, Ser (UCN), Glu and Pro) that are encoded on the L-strand (Table 1). We report that 12 proteincoding genes use ATG as a start codon, while COI uses GTG as a start codon. Open reading frames of A. citrinellus terminated with TAA (ND1, ND2, COI, ATP8, ATP6, ND4L, Cytb), TAG (ND3, ND5, ND6), TA (COIII), T (COII, ND4). The A. citrinellus mitochondrial genome overlapped by a total of 29 bp in 10 different locations from 1 to 10 bp. We also discovered 12 non-coding regions with a total length of 74 bp. The 12S gene (946 bp) and the 16S rRNA gene (1687 bp) are located between the tRNAPhe and the tRNALeu (UUR) gene, and are separated by the tRNAVal gene. The control region (849 bp) is located between the tRNAPro gene and the tRNAPhe gene and has a high A + T content (60.77%). The overall base compositions of the H-strand are as follows: A, 28.56%; C, 30.69%; G, 15.11%; T, 25.64%. The overall content of A + T in the mitochondrial was similar to the value reported for other bony fishes (54.20%; Cheng et al., 2010).
Correspondence: Zaizhong Chen, Shanghai Ocean University, 999 Huchenghuan Road, 201306 Shanghai, P.R. China. Tel: +86 21 61900412. E-mail: [email protected]
2
B. Xu et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characteristics of the mitochondrial genome of the Midas cichlid, A. citrinellus.
Mitochondrial DNA Downloaded from informahealthcare.com by Chinese University of Hong Kong on 02/14/15 For personal use only.
Gene tRNAPhe 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 D-loop
Start position number
Stop position number
Size (bp)
1 70 1016 1088 2775 2849 3826 3895 3965 4034 5080 5153 5223 5332 5387 5468 7038 7112 7190 7881 7956 8114 8797 9581 9653 10,002 10,071 10,361 11,742 11,811 11,882 11,955 13,790 14,312 14,385 15,531 15,602 15,673
69 1015 1087 2774 2848 3823 3895 3965 4033 5080 5151 5221 5295 5396 5466 7030 7108 7184 7880 7954 8123 8797 9581 9652 10,003 10,070 10,367 11,741 11,810 11,877 11,954 13,793 14,311 14,380 15,521 15,602 15,672 16,521
69 946 72 1687 74 975 70 71 70 1047 72 69 73 65 70 1563 71 73 691 74 168 684 785 72 351 69 297 1381 69 67 73 1839 522 69 1137 72 71 849
Acknowledgements The authors would like to thank Professor Shaojun Liu and his colleagues in Hunan Normal University of China for their constructive comments.
Declaration of interest The authors report no conflict of interest. The authors alone are responsible for the content and writing of the paper.
References Barluenga M, Meyer A. (2010). Phylogeography, colonization and population history of the midas cichlid species complex (Amphilophus spp.) in the Nicaraguan crater lakes. BMC Evol Biol 10:326.
Start codon
Stop codon
ATG
TAA
ATG
TAA
GTG
TAA
ATG
T– –
ATG ATG ATG
TAA TAA TA–
ATG
TAG
ATG ATG
TAA T– –
ATG ATG
TAG TAG
ATG
TAA
Intergenic nucleotide 0 0 0 0 0 2 1 1 0 1 1 1 36 0 1 7 3 5 0 1 10 1 1 0 2 0 7 0 0 4 0 4 0 4 9 1 0
Strand 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
Cheng YZ, Xu TJ, Shi G, Wang RX. (2010). Complete mitochondrial genome of the miiuy croaker Miichthys miiuy (Perciformes, Sciaenidae) with phylogenetic consideration. Mar Genom 3:201–9. Elmer KR, Lehtonen TK, Meyer A. (2009). Color assortative mating contributes to sympatric divergence of neotropical cichlid fish. Evolution 63:2750–57. 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. Klingenberg CP, Barluenga M, Meyer A. (2003). Body shape variation in cichlid fishes of the Amphilophus citrinellus species complex. Biol J Linnean Soc 80:397–408. Meyer A. (1990). Ecological and evolutionary consequences of the trophic polymorphism in Cichlasoma citrinellum (Pisces Cichlidae). Biol J Linnean Soc 39:279–99.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the midas cichlid (Amphilophus citrinellus) Bin Xu1,2, Jianzhong Gao1,2, Zaizhong Chen1,2, Lei Wang1,2, Zhongpu Li1,2, Qi Zhou1,2, and Chenghui Wang1,2 Mitochondrial DNA Downloaded from informahealthcare.com by Chinese University of Hong Kong on 02/14/15 For personal use only.
1
Key Laboratory of Freshwater Fishery Germplasm Resources, Ministry of Agriculture, Shanghai, P.R. China and 2Shanghai University Knowledge Service Platform, Shanghai Ocean University Aquatic Animal Breeding Center (ZF1206), Shanghai, P.R. China Abstract
Keywords
The midas cichlid (Amphilophus citrinellus) is an important aquarium fish that has served as a model organism for studying sympatric speciation. In this study, we sequenced the complete mitochondrial genome of the midas cichlid. We report that the cichlid’s mitochondrial genome is a circular DNA double strand of 16,521 bp length, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 control region. The overall-base compositions of the H-strand are as follows: A, 28.56%; C, 30.69%; G, 15.11%; T, 25.64%. This study provides important genomic data to further the research of the genetic evolution of cichlids.
Cichlidae, midas cichlid, mitochondrial genome
Fishes of the family Cichlidae are useful model organisms for studying evolutionary ecology as they exhibit extensive adaptive radiation and phenotypic plasticity (Klingenberg et al., 2003). The midas cichlid, Amphilophus citrinellus (Gu¨nther, 1864), is distributed in Central America and is well-known worldwide for its impressive coloration. In evolutionary research, A. citrinellus is used as a model organism to study sympatric speciation, particularly in the crater lakes of Nicaragua where species are isolated via color and trophic polymorphisms (Elmer KR et al., 2009; Meyer, 1990). The majority of these studies have used morphological variation as a tool to examine speciation, with very few utilizing the power of genomic data, such as mitochondrial DNA (Barluenga & Meyer, 2010). This is due to the absence of sequence data for the complete mitochondrial genome of A. citrinellus. In this study, we sequenced the complete mitochondrial genome of A. citrinellusi, using a previously established method of PCR amplification and sequencing (He et al., 2011). We obtained a caudal fin from A. citrinellus from the Shanghai Ocean University. We designed five primer pairs according to the complete mitogenome sequences of the Redhead cichlid (Vieja synspila; KF879808) and other sequenced genes from A. citrinellus (16 s RNA: GU737199; COI: DQ119198; ND4: HM050088; Cyt b: AY843348).
History Received 26 October 2014 Accepted 10 November 2014 Published online 9 December 2014
Our work revealed that the mitochondrial genome of A. citrinellus is 16,521 bp in length and contains 13 proteincoding genes, 2 rRNA genes, 22 tRNA genes and a single control region (GeneBank: KJ562277). As in other vertebrates, most of the mitochondrial genes of A. citrinellus are encoded on the H-strand, except for the ND6 gene and eight tRNA genes (Gln, Ala, Asn, Cys, Tyr, Ser (UCN), Glu and Pro) that are encoded on the L-strand (Table 1). We report that 12 proteincoding genes use ATG as a start codon, while COI uses GTG as a start codon. Open reading frames of A. citrinellus terminated with TAA (ND1, ND2, COI, ATP8, ATP6, ND4L, Cytb), TAG (ND3, ND5, ND6), TA (COIII), T (COII, ND4). The A. citrinellus mitochondrial genome overlapped by a total of 29 bp in 10 different locations from 1 to 10 bp. We also discovered 12 non-coding regions with a total length of 74 bp. The 12S gene (946 bp) and the 16S rRNA gene (1687 bp) are located between the tRNAPhe and the tRNALeu (UUR) gene, and are separated by the tRNAVal gene. The control region (849 bp) is located between the tRNAPro gene and the tRNAPhe gene and has a high A + T content (60.77%). The overall base compositions of the H-strand are as follows: A, 28.56%; C, 30.69%; G, 15.11%; T, 25.64%. The overall content of A + T in the mitochondrial was similar to the value reported for other bony fishes (54.20%; Cheng et al., 2010).
Correspondence: Zaizhong Chen, Shanghai Ocean University, 999 Huchenghuan Road, 201306 Shanghai, P.R. China. Tel: +86 21 61900412. E-mail: [email protected]
2
B. Xu et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characteristics of the mitochondrial genome of the Midas cichlid, A. citrinellus.
Mitochondrial DNA Downloaded from informahealthcare.com by Chinese University of Hong Kong on 02/14/15 For personal use only.
Gene tRNAPhe 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 D-loop
Start position number
Stop position number
Size (bp)
1 70 1016 1088 2775 2849 3826 3895 3965 4034 5080 5153 5223 5332 5387 5468 7038 7112 7190 7881 7956 8114 8797 9581 9653 10,002 10,071 10,361 11,742 11,811 11,882 11,955 13,790 14,312 14,385 15,531 15,602 15,673
69 1015 1087 2774 2848 3823 3895 3965 4033 5080 5151 5221 5295 5396 5466 7030 7108 7184 7880 7954 8123 8797 9581 9652 10,003 10,070 10,367 11,741 11,810 11,877 11,954 13,793 14,311 14,380 15,521 15,602 15,672 16,521
69 946 72 1687 74 975 70 71 70 1047 72 69 73 65 70 1563 71 73 691 74 168 684 785 72 351 69 297 1381 69 67 73 1839 522 69 1137 72 71 849
Acknowledgements The authors would like to thank Professor Shaojun Liu and his colleagues in Hunan Normal University of China for their constructive comments.
Declaration of interest The authors report no conflict of interest. The authors alone are responsible for the content and writing of the paper.
References Barluenga M, Meyer A. (2010). Phylogeography, colonization and population history of the midas cichlid species complex (Amphilophus spp.) in the Nicaraguan crater lakes. BMC Evol Biol 10:326.
Start codon
Stop codon
ATG
TAA
ATG
TAA
GTG
TAA
ATG
T– –
ATG ATG ATG
TAA TAA TA–
ATG
TAG
ATG ATG
TAA T– –
ATG ATG
TAG TAG
ATG
TAA
Intergenic nucleotide 0 0 0 0 0 2 1 1 0 1 1 1 36 0 1 7 3 5 0 1 10 1 1 0 2 0 7 0 0 4 0 4 0 4 9 1 0
Strand 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
Cheng YZ, Xu TJ, Shi G, Wang RX. (2010). Complete mitochondrial genome of the miiuy croaker Miichthys miiuy (Perciformes, Sciaenidae) with phylogenetic consideration. Mar Genom 3:201–9. Elmer KR, Lehtonen TK, Meyer A. (2009). Color assortative mating contributes to sympatric divergence of neotropical cichlid fish. Evolution 63:2750–57. 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. Klingenberg CP, Barluenga M, Meyer A. (2003). Body shape variation in cichlid fishes of the Amphilophus citrinellus species complex. Biol J Linnean Soc 80:397–408. Meyer A. (1990). Ecological and evolutionary consequences of the trophic polymorphism in Cichlasoma citrinellum (Pisces Cichlidae). Biol J Linnean Soc 39:279–99.
