http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.958705
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome sequence of Platypharodon extremus (Cypriniformes: Cyprinidae) Chunhua Li1,2, Wen Xiong1, Yifeng Chen1, and Dekui He1 1
Mitochondrial DNA Downloaded from informahealthcare.com by Rutgers University on 08/29/15 For personal use only.
Laboratory of Biological Invasion and Adaptive Evolution, Institute of Hydrobiology, Chinese Academy of Sciences, Wuchang District, Wuhan, Hubei Province, P.R. China and 2University of Chinese Academy of Sciences, Beijing, P.R. China Abstract
Keywords
Platypharodon extremus Herzenstein, 1891 (Cyprinidae: Schizothoracinae), is a monotypic genus species only found in the Qinghai–Tibet plateau of China. Due to human disturbance and related environmental change since the 1950s, the population of P. extremus declined rapidly. As a result, it was listed in the China Red Data Book of Endangered Animal and the China’s Protected Species Priority List. There exist very limited researches done on P. extremus. The poor understanding of this species limits the effective protection on this species. Here, we determined the complete mitochondrial DNA sequence of P. extremus. The results show that the mitogenome is 16,651 bp in length, which includes 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions: control region (D–loop) and origin of light-strand replication (OL). These baseline mitogenomic data provided by this study will facilitate the studies on P. extremus in genetics, developmental biology and conservation biology in the future.
Endangered species, mitogenomic, Platypharodon extremus, Schizothoracinae
Platypharodon extremus Herzenstein, 1891 (Cyprinidae: Schizothoracinae) is a monotypic genus species only found in the upper reaches of Yellow River at an altitude over 3000 m (Chen & Cao, 2000). Basic biological characteristics of P. extremus like dietary specialization, growing slowly, and late sexual maturation, limit its recruitment capacity and population growth. Due to overfishing, water conservation project construction, water pollution, and biological invasion since late 1950s (Yue, 1998), the population of P. extremus had declined rapidly. This species gradually retreated to headwaters with sparse resource in the Yellow River (Su et al., 2012; Yue & Chen, 1998). Although P. extremus had been listed in the China Red Data Book of Endangered Animal, Pisces (Yue & Chen, 1998) and the China’s Protected Species Priority List, there are extremely few researches focusing on P. extremus, the lack of knowledge on mitochondrial genome substantially hinders the stock evaluation and further conservation genetic studies for this endangered species. In this study, we designed 13 pairs of primers for polymerase chain reaction amplification based on original DNA sequences of cyprinid fish mitochondrial genomes, and by the way of assembling and alignment, we deposited the complete
Correspondence: D. He, Laboratory of Biological Invasion and Adaptive Evolution, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province 430072, P.R. China. Tel: +86 27 68780808. E-mail: [email protected]
History Received 13 August 2014 Accepted 23 August 2014 Published online 17 September 2014
mitochondrial DNA sequence of P. extremus in GenBank database with accession number KM2886956. Overall, the length of P. extremus mitochondrial genome is 16,651 bp. The arrangement, composition and codon usage of genes were consistent with the most of teleost fish. The mitochondrial is consisted by 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions: one control region (D–loop) and one origin of light-strand replication (OL) (Table 1). Except for a protein-coding gene (ND6) and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser, Glu and Pro) genes, most of the genes are encoded on the heavy strand (H-strand). The overall nucleotide base composition is 28.66% for A, 27.35% for T, 25.94% for C, 18.05% for G, with a high A + T content (56.01%), showing an obvious anti-G bias typical in teleost fishes (Tzeng et al., 1992). As shown in Table 1, of the initiation nucleotides in 13 proteincoding genes, except for COXI which starts with GTG, all others begin with the regular initiation codon TAG. In contrast, the termination codons of 13 protein-coding genes are varied. Two typical types of complete stop codons are shared by 10 proteincoding genes: TAG for four genes and TAA for six genes. The remaining three protein-coding genes COXII, ND4 and Cytb have incomplete stop codons: T (Table 1). There are 10 overlaps and 13 blank spaces exist in mitochondrial genome of P. extremus (Table 1). Four overlaps were found among the 13 protein-coding genes, as shown in ATP8-ATP6, ATP6-COXIII, ND-ND4L and ND5-ND6. The overlaps of the ATP genes appear to be common in most vertebrate mitochondrial genomes, with size ranging from 7 bp to 10 bp (Table 1). Only two overlaps are found among the 22 tRNA genes, i.e. tRNAIle-tRNAGln, tRNACys-tRNATyr.
2
C. Li et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characteristics of the mitochondrial genome of P. extremus. Position Locus
Mitochondrial DNA Downloaded from informahealthcare.com by Rutgers University on 08/29/15 For personal use only.
Phe
tRNA 12SrRNA tRNAVal 16SrRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn Rep origin tRNACys tRNATyr COX I tRNASer tRNAAsp COX II tRNALys ATP8 ATP6 COXIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro Control Region
Codon
Abbreviation
From
To
Size nucleotide (bp)
F 12S V 16S L nd1 I Q M nd2 W A N OL C Y cox1 S D cox2 K atp8 atp6 cox3 G nd3 R nd4L nd4 H S L nd5 nd6 E cytb T P CR
1 70 1028 1100 2782 2859 3837 3907 3980 4049 5094 5166 5236 5309 5342 5407 5479 7030 7104 7189 7880 7957 8115 8798 9583 9655 10,004 10,074 10,364 11,745 11,814 11,884 11,960 13,780 14,302 14,375 15,516 15,643 15,713
69 1027 1099 2781 2857 3833 3908 3977 4048 5095 5164 5234 5308 5344 5407 5477 7029 7100 7175 7879 7955 8121 8798 9583 9654 10,005 10,073 10,370 11,744 11,813 11,882 11,956 13,783 14,301 14,370 15,515 15,587 15,712 16,651
69 958 72 1682 76 975 72 71 69 1047 71 69 73 36 66 71 1551 71 72 691 76 165 684 786 72 351 70 297 1381 69 69 73 1824 522 69 1141 72 70 939
The remaining four overlaps are in genes ND2-tRNATrp, COXIIItRNAGly, COXIII-ATP6 and ND3-tRNAArg.
Acknowledgements The authors thank Chunlong Liu and Yangyang Liang for their assistance in sample collection.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. The research was supported by the National Nature Science Foundation of China (41030208, 31071900).
Start
Stop
Amino acid
Anti-codon
Intergentic nucleotide
Strand
GAA
0 0 0 0 1 3 2 2 0 2 1 1 0 3 1 1 0 3 13 0 1 7 1 1 0 2 0 7 0 0 1 3 4 0 4 0 55 0
H H H H H H H L H H H L L
TAC TAA ATG
TAG
324 GAT TTG CAT
ATG
TAG
348 TCA TGC GTT GCA GTA
GTG
TAA
516 TGA GTC
ATG
T– –
230
ATG ATG ATG
TAG TAA TAA
54 227 261
ATG
TAG
116
ATG ATG
TAA T– –
98 460
TTT
TCC TCG GTG GCT TAG ATG ATG
TAA TAA
607 173
ATG
T– –
380
TTC TGT TGG
L L H L H H H H H H H H H H H H H H H L L H H L
References Chen YF, Cao WX. (2000). Schizothoracinae. Schizothoracinae. In: Yue PQ, editor. Fauna Sinica, Osteichthyes, Cypriniformes III. Beijing: Science Press. p 386–7. Su JH, Zhang YP, Lou ZY, Liu HZ, Jiao WL, Wei YM. (2012). Population genetic Structure of endangered species Platypharodon extremus (Schizothoracinae, Cyprinidae) in Yellow River, China. Acta Zootaxonomica Sinica 37:29–35. Tzeng CS, Hui CF, Shen SC, Huang PC. (1992). The complete nucleotide sequence of the Crossostoma lacustre mitochondrial genome: Conservation and variations among vertebrates. Nucleic Acids Res 20:4853–8. Yue PQ, Chen YY. (1998). China Red Data Book of Endangered Animal. Beijing: Science Press.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome sequence of Platypharodon extremus (Cypriniformes: Cyprinidae) Chunhua Li1,2, Wen Xiong1, Yifeng Chen1, and Dekui He1 1
Mitochondrial DNA Downloaded from informahealthcare.com by Rutgers University on 08/29/15 For personal use only.
Laboratory of Biological Invasion and Adaptive Evolution, Institute of Hydrobiology, Chinese Academy of Sciences, Wuchang District, Wuhan, Hubei Province, P.R. China and 2University of Chinese Academy of Sciences, Beijing, P.R. China Abstract
Keywords
Platypharodon extremus Herzenstein, 1891 (Cyprinidae: Schizothoracinae), is a monotypic genus species only found in the Qinghai–Tibet plateau of China. Due to human disturbance and related environmental change since the 1950s, the population of P. extremus declined rapidly. As a result, it was listed in the China Red Data Book of Endangered Animal and the China’s Protected Species Priority List. There exist very limited researches done on P. extremus. The poor understanding of this species limits the effective protection on this species. Here, we determined the complete mitochondrial DNA sequence of P. extremus. The results show that the mitogenome is 16,651 bp in length, which includes 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions: control region (D–loop) and origin of light-strand replication (OL). These baseline mitogenomic data provided by this study will facilitate the studies on P. extremus in genetics, developmental biology and conservation biology in the future.
Endangered species, mitogenomic, Platypharodon extremus, Schizothoracinae
Platypharodon extremus Herzenstein, 1891 (Cyprinidae: Schizothoracinae) is a monotypic genus species only found in the upper reaches of Yellow River at an altitude over 3000 m (Chen & Cao, 2000). Basic biological characteristics of P. extremus like dietary specialization, growing slowly, and late sexual maturation, limit its recruitment capacity and population growth. Due to overfishing, water conservation project construction, water pollution, and biological invasion since late 1950s (Yue, 1998), the population of P. extremus had declined rapidly. This species gradually retreated to headwaters with sparse resource in the Yellow River (Su et al., 2012; Yue & Chen, 1998). Although P. extremus had been listed in the China Red Data Book of Endangered Animal, Pisces (Yue & Chen, 1998) and the China’s Protected Species Priority List, there are extremely few researches focusing on P. extremus, the lack of knowledge on mitochondrial genome substantially hinders the stock evaluation and further conservation genetic studies for this endangered species. In this study, we designed 13 pairs of primers for polymerase chain reaction amplification based on original DNA sequences of cyprinid fish mitochondrial genomes, and by the way of assembling and alignment, we deposited the complete
Correspondence: D. He, Laboratory of Biological Invasion and Adaptive Evolution, Institute of Hydrobiology, Chinese Academy of Sciences, No. 7 Donghu South Road, Wuchang District, Wuhan, Hubei Province 430072, P.R. China. Tel: +86 27 68780808. E-mail: [email protected]
History Received 13 August 2014 Accepted 23 August 2014 Published online 17 September 2014
mitochondrial DNA sequence of P. extremus in GenBank database with accession number KM2886956. Overall, the length of P. extremus mitochondrial genome is 16,651 bp. The arrangement, composition and codon usage of genes were consistent with the most of teleost fish. The mitochondrial is consisted by 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two non-coding regions: one control region (D–loop) and one origin of light-strand replication (OL) (Table 1). Except for a protein-coding gene (ND6) and eight tRNA (Gln, Ala, Asn, Cys, Tyr, Ser, Glu and Pro) genes, most of the genes are encoded on the heavy strand (H-strand). The overall nucleotide base composition is 28.66% for A, 27.35% for T, 25.94% for C, 18.05% for G, with a high A + T content (56.01%), showing an obvious anti-G bias typical in teleost fishes (Tzeng et al., 1992). As shown in Table 1, of the initiation nucleotides in 13 proteincoding genes, except for COXI which starts with GTG, all others begin with the regular initiation codon TAG. In contrast, the termination codons of 13 protein-coding genes are varied. Two typical types of complete stop codons are shared by 10 proteincoding genes: TAG for four genes and TAA for six genes. The remaining three protein-coding genes COXII, ND4 and Cytb have incomplete stop codons: T (Table 1). There are 10 overlaps and 13 blank spaces exist in mitochondrial genome of P. extremus (Table 1). Four overlaps were found among the 13 protein-coding genes, as shown in ATP8-ATP6, ATP6-COXIII, ND-ND4L and ND5-ND6. The overlaps of the ATP genes appear to be common in most vertebrate mitochondrial genomes, with size ranging from 7 bp to 10 bp (Table 1). Only two overlaps are found among the 22 tRNA genes, i.e. tRNAIle-tRNAGln, tRNACys-tRNATyr.
2
C. Li et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Characteristics of the mitochondrial genome of P. extremus. Position Locus
Mitochondrial DNA Downloaded from informahealthcare.com by Rutgers University on 08/29/15 For personal use only.
Phe
tRNA 12SrRNA tRNAVal 16SrRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn Rep origin tRNACys tRNATyr COX I tRNASer tRNAAsp COX II tRNALys ATP8 ATP6 COXIII tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu Cyt b tRNAThr tRNAPro Control Region
Codon
Abbreviation
From
To
Size nucleotide (bp)
F 12S V 16S L nd1 I Q M nd2 W A N OL C Y cox1 S D cox2 K atp8 atp6 cox3 G nd3 R nd4L nd4 H S L nd5 nd6 E cytb T P CR
1 70 1028 1100 2782 2859 3837 3907 3980 4049 5094 5166 5236 5309 5342 5407 5479 7030 7104 7189 7880 7957 8115 8798 9583 9655 10,004 10,074 10,364 11,745 11,814 11,884 11,960 13,780 14,302 14,375 15,516 15,643 15,713
69 1027 1099 2781 2857 3833 3908 3977 4048 5095 5164 5234 5308 5344 5407 5477 7029 7100 7175 7879 7955 8121 8798 9583 9654 10,005 10,073 10,370 11,744 11,813 11,882 11,956 13,783 14,301 14,370 15,515 15,587 15,712 16,651
69 958 72 1682 76 975 72 71 69 1047 71 69 73 36 66 71 1551 71 72 691 76 165 684 786 72 351 70 297 1381 69 69 73 1824 522 69 1141 72 70 939
The remaining four overlaps are in genes ND2-tRNATrp, COXIIItRNAGly, COXIII-ATP6 and ND3-tRNAArg.
Acknowledgements The authors thank Chunlong Liu and Yangyang Liang for their assistance in sample collection.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper. The research was supported by the National Nature Science Foundation of China (41030208, 31071900).
Start
Stop
Amino acid
Anti-codon
Intergentic nucleotide
Strand
GAA
0 0 0 0 1 3 2 2 0 2 1 1 0 3 1 1 0 3 13 0 1 7 1 1 0 2 0 7 0 0 1 3 4 0 4 0 55 0
H H H H H H H L H H H L L
TAC TAA ATG
TAG
324 GAT TTG CAT
ATG
TAG
348 TCA TGC GTT GCA GTA
GTG
TAA
516 TGA GTC
ATG
T– –
230
ATG ATG ATG
TAG TAA TAA
54 227 261
ATG
TAG
116
ATG ATG
TAA T– –
98 460
TTT
TCC TCG GTG GCT TAG ATG ATG
TAA TAA
607 173
ATG
T– –
380
TTC TGT TGG
L L H L H H H H H H H H H H H H H H H L L H H L
References Chen YF, Cao WX. (2000). Schizothoracinae. Schizothoracinae. In: Yue PQ, editor. Fauna Sinica, Osteichthyes, Cypriniformes III. Beijing: Science Press. p 386–7. Su JH, Zhang YP, Lou ZY, Liu HZ, Jiao WL, Wei YM. (2012). Population genetic Structure of endangered species Platypharodon extremus (Schizothoracinae, Cyprinidae) in Yellow River, China. Acta Zootaxonomica Sinica 37:29–35. Tzeng CS, Hui CF, Shen SC, Huang PC. (1992). The complete nucleotide sequence of the Crossostoma lacustre mitochondrial genome: Conservation and variations among vertebrates. Nucleic Acids Res 20:4853–8. Yue PQ, Chen YY. (1998). China Red Data Book of Endangered Animal. Beijing: Science Press.
