http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.958720
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the spinner shark Carcharhinus brevipinna Xiao Chen1,2, Dan Xiang2, Xin Peng2, Weiming Ai1,2, and Hao Chen1 Department of Marine Science, Wenzhou Medical University, Wenzhou, P.R. China and 2Zhejiang Mariculture Research Institute, Wenzhou, Zhejiang, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by Ryerson University on 12/01/14 For personal use only.
1
Abstract
Keywords
The mitochondrial genome of the spinner shark (Carcharhinus brevipinna) was determined in this study. It was 16,706 bp in length with the typical genomic organization and gene order as most vertebrates. Whole nucleotide base composition was 31.3% A, 25.3% C, 13.2% G and 30.1% T. Among the protein-coding genes, there are three overlapping reading-frames on the same strand, while one of it on the opposite strand. Two start codons (ATG and GTG) and three stop codons (AGG, TAG and TAA/T) were used in 13 protein-coding genes. The 22 tRNA ranged from 67 (tRNA-Cys and tRNA-Ser2) to 75 bp (tRNA-Leu1) in length. Only the tRNA-Ser2 could not fold into the typical clover-leaf structure, which lost the dihydrouridine (DHU) arm and replaced by a simple loop. The control region was 1064 bp in length and showed a higher AT content (66.8%) than the average value of whole mitogenome (61.4%).
Carcharhinus brevipinna, Carcharhiniformes, mitogenome
The spinner shark (Carcharhinus brevipinna) belongs to the family Carcharhinidae. The name ‘‘spinner’’ is due to its feeding activity that spinning leaps to pursue the preys at high speed. The common length of C. brevipinna is 250 cm TL (Sommer et al., 1996), and its max length attains to 300 cm TL (Sanches, 1991). Carcharhinus brevipinna is distributed in tropical, subtropical and warm temperate near shore waters worldwide, except the eastern Pacific Ocean (Burgess, 2009). The variation in its tooth shape and coloration with age and between geographical regions caused much taxonomic confusion (Compagno, 1984). The phylogenetic position of C. brevipinna is still unclear in subsequent studies (Dosay-Akbulut, 2008; Naylor, 1992). Here we present the
History Received 20 August 2014 Accepted 23 August 2014 Published online 30 September 2014
mitogenome of C. brevipinna (GenBank accession No. KM244770), hoping it could contribute to the phylogenetic study of Carcharhinidae. One specimen of C. brevipinna was collected from Ranong, Thailand. The experimental protocols and data analysis methods followed Chen et al. (2013). The complete size of the whole mitogenome in C. brevipinna was 16,706 bp. It had a typical genomic organization and gene order (13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region; Table 1) as most vertebrates. Nucleotide base composition of C. brevipinna was 31.3% A, 25.3% C, 13.2% G and 30.1% T. The AT content (61.4%) was higher than the GC content (38.5%) and the
Table 1. Organization of the mitogenome in C. brevipinna. Gene tRNA-Phe 12S rRNA tRNA-Val 16S rRNA tRNA-Leu1 (UAA) ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn OL
Strand
Position
Size (bp)
H H H H H H H L H H H L L –
1–69 70–1025 1026–1097 1098–2767 2768–2842 2843–3817 3818–3887 3889–3960 3960–4028 4029–5075 5074–5144 5146–5214 5215–5287 5288–5322
69 956 72 1670 75 975 70 72 69 1047 71 69 73 35
Start codon
Stop codon
ATG
TAA
ATG
TAG
Intergenic spacer 0 0 0 0 0 0 1 1 0 2 1 0 0 0 (continued )
Correspondence: X. Chen, Wenzhou Medical University, Wenzhou 325005, P.R. China. Tel: +86 577 86689773. Fax: +86 577 86689780. E-mail: [email protected]
2
X. Chen et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Mitochondrial DNA Downloaded from informahealthcare.com by Ryerson University on 12/01/14 For personal use only.
Gene tRNA-Cys tRNA-Tyr COI tRNA-Ser1 (UGA) tRNA-Asp COII tRNA-Lys ATP8 ATP6 COIII tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser2 (GCU) tRNA-Leu2 (UAG) ND5 ND6 tRNA-Glu Cyt b tRNA-Thr tRNA-Pro Control region
Strand
Position
Size (bp)
L L H L H H H H H H H H H H H H H H H L L H H L –
5323–5389 5391–5459 5461–7017 7018–7088 7092–7161 7169–7859 7860–7933 7935–8102 8093–8776 8776–9561 9564–9633 9634–9984 9983–10,052 10,053–10,349 10,343–11,723 11,724–11,792 11,793–11,859 11,860–11,931 11,932–13,761 13,757–14,278 14,279–14,348 14,351–15,496 15,496–15,567 15,570–15,638 15,639–16,706
67 69 1550 71 70 691 74 168 684 786 70 351 70 297 1381 69 67 72 1830 501 70 1146 72 69 1068
bias against G on the L-strand was consistent with observations in vertebrates. Among the protein-coding genes, there were three overlapping reading-frames on the same strand. The ATP6 and ATP8 genes shared 10 nucleotides, the ATP6 and COIII genes shared one nucleotide, while ND4 and ND4L genes shared 7 nucleotides. Furthermore, ND5 and ND6 shared 5 nucleotides on the opposite strand. All 13 protein-coding genes except for COI gene started with initiation codon ATG, whereas COI gene started with initiation codon GTG. The ND6 gene stopped by the AGG codon, the remaining genes used the TAG and TAA or incomplete T as the terminal codon. The length of 12S and 16S rRNA genes was 956 and 1670 bp, respectively. These two rRNA genes were located between tRNAPhe and tRNA-Leu1 and were separated by tRNA-Val. The 22 tRNA ranged from 67 (tRNA-Cys and tRNA-Ser2) to 75 bp (tRNA-Leu1) in length; 11 tRNAs formed three conserved clusters (IQM, WANCY and HSL). All tRNA genes had a typical clover-leaf structure, except tRNA-Ser2 which lost the dihydrouridine (DHU) arm and replaced by a simple loop. A 35 bp inserted sequence was identified as the origin of L-strand replication (OL) between tRNA-Asn and tRNA-Cys genes. It formed a hairpin structure with 9 bp stem and 12 bp loop. The control region was 1064 bp in length, located between tRNA-Pro and tRNA-Phe. The base composition of control region was 31.7% A, 19.5% C, 13.7% G and 35.1% T. It presented a higher AT content (66.8%) than the average value for the whole mitogenome (61.4%). The high AT content is due to the abundant poly A and poly T.
Start codon
Stop codon
GTG
TAA
ATG
T– –
ATG ATG ATG
TAA TAA TAA
ATG
TAG
ATG ATG
TAA T– –
ATG ATG
TAA AGG
ATG
TAG
Intergenic spacer 1 1 0 3 7 0 1 10 1 2 0 2 0 7 0 0 0 0 5 0 2 1 2 0
Declaration of interest This study was supported by the National Natural Sciences Foundation of China (41006080) and Zhejiang Province Important Science & Technology Key Projects (2012C13005). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Burgess, GH. (2009). Carcharhinus brevipinna. The IUCN Red List of Threatened Species. Version 2014.2. Available at: www.iucnredlist.org (Accessed 7 August 2014) Chen X, Ai W, Ye L, Wang X, Lin C, Yang S. (2013). The complete mitochondrial genome of the grey bamboo shark (Chiloscyllium griseum) (Orectolobiformes: Hemiscylliidae): genomic characterization and phylogenetic application. Acta Oceanol Sin 32:59–65. Compagno LJV. (1984). Sharks of the world: An annotated and illustrated catalogue of shark species known to date. Rome: Food and Agricultural Organization. p 466–8. Dosay-Akbulut M. (2008). The phylogenetic relationship within the genus Carcharhinus. Comptes Rendus Biologies 331:500–9. Naylor, GJP. (1992). The phylogenetic relationships among requiem and hammerhead sharks: inferring phylogeny when thousands of equally most parsimonious trees result. Cladistics 8:295–318. Sanches JG. (1991). Cata´logo dos principais peixes marinhos da Repu´blica de Guine´-Bissau. Publicac¸o˜es avulsas do I.N.I.P. No. 16. p 429. Sommer C, Schneider W, Poutiers JM. (1996). FAO species identification field guide for fishery purposes. The living marine resources of Somalia. Rome: FAO. p 376.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the spinner shark Carcharhinus brevipinna Xiao Chen1,2, Dan Xiang2, Xin Peng2, Weiming Ai1,2, and Hao Chen1 Department of Marine Science, Wenzhou Medical University, Wenzhou, P.R. China and 2Zhejiang Mariculture Research Institute, Wenzhou, Zhejiang, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by Ryerson University on 12/01/14 For personal use only.
1
Abstract
Keywords
The mitochondrial genome of the spinner shark (Carcharhinus brevipinna) was determined in this study. It was 16,706 bp in length with the typical genomic organization and gene order as most vertebrates. Whole nucleotide base composition was 31.3% A, 25.3% C, 13.2% G and 30.1% T. Among the protein-coding genes, there are three overlapping reading-frames on the same strand, while one of it on the opposite strand. Two start codons (ATG and GTG) and three stop codons (AGG, TAG and TAA/T) were used in 13 protein-coding genes. The 22 tRNA ranged from 67 (tRNA-Cys and tRNA-Ser2) to 75 bp (tRNA-Leu1) in length. Only the tRNA-Ser2 could not fold into the typical clover-leaf structure, which lost the dihydrouridine (DHU) arm and replaced by a simple loop. The control region was 1064 bp in length and showed a higher AT content (66.8%) than the average value of whole mitogenome (61.4%).
Carcharhinus brevipinna, Carcharhiniformes, mitogenome
The spinner shark (Carcharhinus brevipinna) belongs to the family Carcharhinidae. The name ‘‘spinner’’ is due to its feeding activity that spinning leaps to pursue the preys at high speed. The common length of C. brevipinna is 250 cm TL (Sommer et al., 1996), and its max length attains to 300 cm TL (Sanches, 1991). Carcharhinus brevipinna is distributed in tropical, subtropical and warm temperate near shore waters worldwide, except the eastern Pacific Ocean (Burgess, 2009). The variation in its tooth shape and coloration with age and between geographical regions caused much taxonomic confusion (Compagno, 1984). The phylogenetic position of C. brevipinna is still unclear in subsequent studies (Dosay-Akbulut, 2008; Naylor, 1992). Here we present the
History Received 20 August 2014 Accepted 23 August 2014 Published online 30 September 2014
mitogenome of C. brevipinna (GenBank accession No. KM244770), hoping it could contribute to the phylogenetic study of Carcharhinidae. One specimen of C. brevipinna was collected from Ranong, Thailand. The experimental protocols and data analysis methods followed Chen et al. (2013). The complete size of the whole mitogenome in C. brevipinna was 16,706 bp. It had a typical genomic organization and gene order (13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region; Table 1) as most vertebrates. Nucleotide base composition of C. brevipinna was 31.3% A, 25.3% C, 13.2% G and 30.1% T. The AT content (61.4%) was higher than the GC content (38.5%) and the
Table 1. Organization of the mitogenome in C. brevipinna. Gene tRNA-Phe 12S rRNA tRNA-Val 16S rRNA tRNA-Leu1 (UAA) ND1 tRNA-Ile tRNA-Gln tRNA-Met ND2 tRNA-Trp tRNA-Ala tRNA-Asn OL
Strand
Position
Size (bp)
H H H H H H H L H H H L L –
1–69 70–1025 1026–1097 1098–2767 2768–2842 2843–3817 3818–3887 3889–3960 3960–4028 4029–5075 5074–5144 5146–5214 5215–5287 5288–5322
69 956 72 1670 75 975 70 72 69 1047 71 69 73 35
Start codon
Stop codon
ATG
TAA
ATG
TAG
Intergenic spacer 0 0 0 0 0 0 1 1 0 2 1 0 0 0 (continued )
Correspondence: X. Chen, Wenzhou Medical University, Wenzhou 325005, P.R. China. Tel: +86 577 86689773. Fax: +86 577 86689780. E-mail: [email protected]
2
X. Chen et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Mitochondrial DNA Downloaded from informahealthcare.com by Ryerson University on 12/01/14 For personal use only.
Gene tRNA-Cys tRNA-Tyr COI tRNA-Ser1 (UGA) tRNA-Asp COII tRNA-Lys ATP8 ATP6 COIII tRNA-Gly ND3 tRNA-Arg ND4L ND4 tRNA-His tRNA-Ser2 (GCU) tRNA-Leu2 (UAG) ND5 ND6 tRNA-Glu Cyt b tRNA-Thr tRNA-Pro Control region
Strand
Position
Size (bp)
L L H L H H H H H H H H H H H H H H H L L H H L –
5323–5389 5391–5459 5461–7017 7018–7088 7092–7161 7169–7859 7860–7933 7935–8102 8093–8776 8776–9561 9564–9633 9634–9984 9983–10,052 10,053–10,349 10,343–11,723 11,724–11,792 11,793–11,859 11,860–11,931 11,932–13,761 13,757–14,278 14,279–14,348 14,351–15,496 15,496–15,567 15,570–15,638 15,639–16,706
67 69 1550 71 70 691 74 168 684 786 70 351 70 297 1381 69 67 72 1830 501 70 1146 72 69 1068
bias against G on the L-strand was consistent with observations in vertebrates. Among the protein-coding genes, there were three overlapping reading-frames on the same strand. The ATP6 and ATP8 genes shared 10 nucleotides, the ATP6 and COIII genes shared one nucleotide, while ND4 and ND4L genes shared 7 nucleotides. Furthermore, ND5 and ND6 shared 5 nucleotides on the opposite strand. All 13 protein-coding genes except for COI gene started with initiation codon ATG, whereas COI gene started with initiation codon GTG. The ND6 gene stopped by the AGG codon, the remaining genes used the TAG and TAA or incomplete T as the terminal codon. The length of 12S and 16S rRNA genes was 956 and 1670 bp, respectively. These two rRNA genes were located between tRNAPhe and tRNA-Leu1 and were separated by tRNA-Val. The 22 tRNA ranged from 67 (tRNA-Cys and tRNA-Ser2) to 75 bp (tRNA-Leu1) in length; 11 tRNAs formed three conserved clusters (IQM, WANCY and HSL). All tRNA genes had a typical clover-leaf structure, except tRNA-Ser2 which lost the dihydrouridine (DHU) arm and replaced by a simple loop. A 35 bp inserted sequence was identified as the origin of L-strand replication (OL) between tRNA-Asn and tRNA-Cys genes. It formed a hairpin structure with 9 bp stem and 12 bp loop. The control region was 1064 bp in length, located between tRNA-Pro and tRNA-Phe. The base composition of control region was 31.7% A, 19.5% C, 13.7% G and 35.1% T. It presented a higher AT content (66.8%) than the average value for the whole mitogenome (61.4%). The high AT content is due to the abundant poly A and poly T.
Start codon
Stop codon
GTG
TAA
ATG
T– –
ATG ATG ATG
TAA TAA TAA
ATG
TAG
ATG ATG
TAA T– –
ATG ATG
TAA AGG
ATG
TAG
Intergenic spacer 1 1 0 3 7 0 1 10 1 2 0 2 0 7 0 0 0 0 5 0 2 1 2 0
Declaration of interest This study was supported by the National Natural Sciences Foundation of China (41006080) and Zhejiang Province Important Science & Technology Key Projects (2012C13005). The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Burgess, GH. (2009). Carcharhinus brevipinna. The IUCN Red List of Threatened Species. Version 2014.2. Available at: www.iucnredlist.org (Accessed 7 August 2014) Chen X, Ai W, Ye L, Wang X, Lin C, Yang S. (2013). The complete mitochondrial genome of the grey bamboo shark (Chiloscyllium griseum) (Orectolobiformes: Hemiscylliidae): genomic characterization and phylogenetic application. Acta Oceanol Sin 32:59–65. Compagno LJV. (1984). Sharks of the world: An annotated and illustrated catalogue of shark species known to date. Rome: Food and Agricultural Organization. p 466–8. Dosay-Akbulut M. (2008). The phylogenetic relationship within the genus Carcharhinus. Comptes Rendus Biologies 331:500–9. Naylor, GJP. (1992). The phylogenetic relationships among requiem and hammerhead sharks: inferring phylogeny when thousands of equally most parsimonious trees result. Cladistics 8:295–318. Sanches JG. (1991). Cata´logo dos principais peixes marinhos da Repu´blica de Guine´-Bissau. Publicac¸o˜es avulsas do I.N.I.P. No. 16. p 429. Sommer C, Schneider W, Poutiers JM. (1996). FAO species identification field guide for fishery purposes. The living marine resources of Somalia. Rome: FAO. p 376.
