http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.919467

MITOGENOME ANNOUNCEMENT

Complete mitochondrial genome of the Red devil cichlid (Amphilophus citrinellus) Hong-Mei Song1, Chao Liu1, Yi Liu1, Min-Xia Wei2, Jian-ren Luo1, and Yin-chang Hu1 1

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Key Lab of Tropical and Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, PR China and 2College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, PR China Abstract

Keywords

In this study, the complete mitochondrial genome sequence of Amphilophus citrinellus was firstly sequenced and determined. The total genome is 16,522 bp in length with an A + T content of 54.19%, and contained 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes and two main non-coding regions. The gene composition and order is similar to that of most other vertebrates, as is base composition and codon usage. These data will provide useful molecular information for phylogenetic relationships within the family Cichlidae species.

Amphilophus citrinellus, Cichlidae, mitochondrial genome

Mitochondrial DNA is becoming increasingly important for evolutionary, genetic diversity studies and identification of species. Cichlid fishes are powerful model systems to test predictions of speciation and adaptive radiation theory for decades (Prosdocimi et al., 2012), since this family of fish comprises both the fastest rates of evolution (Genner & Turner, 2005) and the most divers adaptive radiations (Barluenga & Meyer, 2010; Salzburger, 2009). To our knowledge, some complete mitogenome of Cichlidae fish were reported including Petrochromis trewavasae, Tropheus moorii (Fischer et al., 2013), Paratilapia pollen (GenBank: AP009508.1), Astronotus ocellatus (GenBank: AP009127.1), Oreochromis niloticus (GenBank: GU370126.1), O. aureus (GenBank: GU370125.1) and so on. But, no complete mitochondrial genome sequence of Amphilophus genus in the Cichlidae family was available. In this study, we reported the first complete mitogenome of Amphilophus citrinellus (GenBank accession number KJ081546) using PCR method. The mitogenome of A. citrinellus is a typical circular DNA molecule of 16,522 bp in length with a standard set of 13 proteincoding genes (PCGs), 22 tRNAs, 2 rRNAs and a non-coding control region (D-loop) (Table 1). The gene order and gene content are similar to that of other vertebrates. Except for the eight tRNA and ND6 genes, all other mitochondrial genes are encoded on the H-strand. The nucleotide composition of complete mitogenome is 28.6% (A), 25.6% (T), 30.7% (C), and 15.1% (G),

History Received 10 April 2014 Accepted 26 April 2014 Published online 3 June 2014

respectively. The A + T content (54.2%) is slightly more than that of P. trewavasae (54.0%) and T. moorii (53.7%). Seven gene junctions with the length of overlapping sequence ranging from 1 to 10 bp are found with the largest overlap (10 bp) involving the ATP8 and ATP6 gene. The total length of the 13 PCGs is 11,435 bp, with the average A + T content (52.9%). Among 13 PCGs, the lowest A + T content is 46.8% in ND4L, while the highest is 56.5% in ND3. Eleven PCGs start with an ATG codon, except for COX1 (GTG) and ND6 (CTA) (Table 1). Eight PCGs (ND1, COX1, ATP6, ATP8, ND4L, ND5, ND6 and CYTB) have the TAA or TAG termination codon, and the other five genes (COX2, COX3, ND2, ND3 and ND4) have T or TA incomplete stop codon. The length of two subunits of rRNA (12S and 16S) are 946 and 1687 bp, respectively, with an overall A + T content of 52.6%. The 22 tRNA genes range in length from 61 bp (tRNACys) to 74 bp (tRNALys). The A. citrinellus mitochondrial genome has 11 intergenic spacers in a total of 69 bp with length varying from 1 to 40 bp. The longest intergenic spacer in the mitochondrial genome locates between tRNAAsn and tRNACys. Amphilophus citrinellus contains a non-coding region of 849 bp, which have two central conserved sequence block (CSB-F and CSB-E) occur at positions 280–297 and 500–513 bp, and three conserved sequence blocks (CSB1, CSB2 and CSB3) occur at positions 637–662, 718–734 and 763–782 bp.

Correspondence: Yin-chang Hu, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou City 510380, Guangdong Province, People’s Republic of China. Tel: +86 2081616088. Fax: +86 2081616162 (work). E-mail: [email protected]

2

H.-M. Song et al.

Mitochondrial DNA, Early Online: 1–2

Table 1. Complete mitochondrial genomes of A. citrinellus.

Gene

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Phe

tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu(UUR) ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COX1 tRNASer(UCN) tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer (AGY) tRNALeu (CUN) ND5 ND6 tRNAGlu CYTB tRNAThr tRNAPro D-loop

Strand

Position

Size

INC*

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

1–69 70–1015 1016–1087 1088–2774 2775–2848 2849–3823 3826–3895 3895–3965 3965–4033 4034–5079 5080–5151 5153–5221 5223–5295 5336–5396 5397–5466 5468–7030 7038–7109 7113–7185 7191–7881 7882–7955 7957–8124 8115–8798 8798–9581 9582–9653 9654–10,002 10,003–10,071 10,072–10,368 10,362–11,742 11,743–11,811 11,812–11878 11,883–11,955 11,956–13,794 13,791–14,312 14,313–14,381 14,386–15,522 15,532–15,603 15,603–15,673 15,674–16,522

69 946 72 1687 74 975 70 71 69 1046 72 69 73 61 70 1563 72 73 691 74 168 684 784 72 349 69 297 1381 69 67 73 1839 522 69 1137 72 71 849

0 0 0 0 0 2 1 1 0 0 1 1 40 0 1 7 3 5 0 1 10 1 0 0 0 0 7 0 0 4 0 4 0 4 1 0 0

Base composition (%)

Codon Start–Stop

A

G

T

C

A+T

ATG–TAA

26.3

12.5

26.7

34.6

52.9

ATG–TA

26.7

11.0

24.0

38.2

50.7

GTG–TAA

25.3

17.0

29.2

28.5

54.5

ATG–T

28.9

15.8

26.9

28.4

55.9

ATG–TAA ATG–TAA ATG–T

30.4 26.3 27.7

11.9 12.4 15.8

21.4 27.5 25.6

36.3 33.8 30.9

51.8 53.8 53.3

ATG–T

25.2

12.6

31.2

31.0

56.5

ATG–TAA ATG–TA

20.5 26.6

14.8 13.0

26.3 27.0

38.4 33.4

46.8 53.6

ATG–TAG CTA–TAG

28.4 38.1

11.7 10.5

27.4 14.8

32.5 36.6

55.8 52.9

ATG–TAA

25.8

14.4

23.4

36.5

49.1

31.2

14.4

29. 6

24.9

60.8

ND1–ND6, NADH dehydrogenase subunits 1–6; COX1–COX3, cytochrome c oxidase subunits 1–3; ATP8 and ATP6, ATPase subunits 6 and 8; CYTB, cytochrome b. H and L correspond to the H and L strand, respectively. *Numbers correspond to the nucleotides separating adjacent genes. Negative numbers indicate overlapping nucleotides.

Declaration of interest This study is supported by program of National Science Infrastructure Platform and Guangdong Science-technology Project (2011B060400023). The authors report no conflicts of interests. The authors alone are responsible for doing the research and writing 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. Fischer C, Koblmu¨ller S, Gu¨lly C, Schlo¨tterer C, Sturmbauer C, Thallinger GG. (2013). Complete mitochondrial DNA sequences of

the Threadfin Cichlid (Petrochromis trewavasae) and the Blunthead Cichlid (Tropheus moorii) and patterns of mitochondrial genome evolution in Cichlid fishes. PLoS One 8:e67048. Genner MJ, Turner GF. (2005). The mbuna Cichlids of Lake Malawi: A model for rapid speciation and adaptive radiation. Fish Fish 6:1–34. Prosdocimi F, Carvalho DC, Almeida RN, Beheregaray LB. (2012). The complete mitochondrial genome of two recently derived species of the fish genus Nannoperca (Perciformes, Percichthyidae). Mol Biol Rep 39:2767–72. Salzburger W. (2009). The interaction of sexually and naturally selected traits in the adaptive radiations of cichlid fishes. Mol Ecol 18:169–85.

Complete mitochondrial genome of the Red devil cichlid (Amphilophus citrinellus).

In this study, the complete mitochondrial genome sequence of Amphilophus citrinellus was firstly sequenced and determined. The total genome is 16,522 ...
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