http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.905851
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome sequence of northeastern red deer (Cervus elaphus xanthopygus)
Mitochondrial DNA Downloaded from informahealthcare.com by The University of Manchester on 11/20/14 For personal use only.
Yuanchen Shao, Weilin Su, Huamiao Liu, Daiming Zha, Ranran Zhang, and Xiumei Xing State Key Laboratory of Special Economic Animal Molecular Biology, Institute of Special Wild Economic Animal and Plant Science, Chinese Academy Agricultural Sciences, Jilin, P.R. China Abstract
Keywords
The complete mitochondrial genome of the northeastern red deer, Cervus elaphus xanthopygus, was determined by accurate polymerase chain reaction. The entire genome is 16,416 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region, all of which are arranged in a typical vertebrate manner. The overall base composition of the northeastern red deer’s mitochondrial genome is 33.3% of A, 24.3% of C, 28.9% of T and 13.5% of G. A termination-associated sequence and several conserved central sequence block domains were discovered within the control region.
Cervus elaphus xanthopygus, mitogenome, red deer
Northeastern red deer is originally widespread throughout the Changbai mountain, Wondersun mountain and Xingan ridge in the northeastern China (Chen et al., 1997; Sheng & Ohtaishi, 1993). The species has been extirpated from much of its historical range due largely to hunting and habitat degradation, and is now only found in small fragmented populations in China (Stevens & Boness, 2003). It is classified as Endangered species by IUCN and is included in China red Data Book of Endangered Animal (Wang, 1998). Mitochondrial DNA (mtDNA) is an important genetic marker for studying animal origin and evolution (Shen et al., 2010; Stonking & Soodyall, 1996). In this study, we determined and analyzed the complete mtDNA sequences of the northeastern red deer to facilitate the identification of their origins. The mtDNA was extracted from the blood samples of the red deer, amplified with polymerase chain reaction and sequenced. Sequence analysis was carried out according to previously
History Received 9 March 2014 Accepted 15 March 2014 Published online 4 April 2014
described method (He et al., 2009). Fourteen primers were used to amplify the contiguous and overlapping segments. The complete mtDNA sequence has been deposited into the GenBank (Accession No. GU457434/NC-013836.1). The complete mtDNA of the red deer is 16,416 bp in length. It contains 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes and a noncoding region (D-loop). Most mitochondrial genes are encoded on the H strand, except the ND6 gene and eight tRNA genes. A common 35 bp space sequence and a common 35 bp overlapping sequence were discovered in the total 37 genes (Table 1). The nucleotide composition of the H strand sika deer mtDNA is 33.3% of A, 13.5% of G, 28.9% of T, and 24.3% of C. The total length of the 13 protein-coding genes is 11,406 bp. All protein-coding genes start with ATG, except the ND2, ND3, ND4L and ND5 genes, all of which start with ATA. TAA is the common stop codon, while ND2, Cytb and COX3 stop with TAG,
Table 1. Localization of the protein-coding genes of Cervus elaphus’s mitochondrial genome. Name Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp
Site 1–69 70–1024 1025–1091 1091–2663 2664–2738 2741–3697 3697–3765 3763–3834 3837–3905 3906–4949 4948–5015
Start codon
ATG
ATA
Stop codon
Length (bp)
Anti-codon GAA
TAA
69 955 67 1573 75 957 69 72 69 1044 68
TAG
Overlap
1 TAA GAT TTG CAT
1 3 2
TGG
Strand H H H H H H H L H H H (continued )
Correspondence: X. M. Xing, Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Jilin 132109, P.R. China. Tel: 132 58846941. Fax: 86 431 81919800. E-mail: [email protected]
2
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Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Name
Mitochondrial DNA Downloaded from informahealthcare.com by The University of Manchester on 11/20/14 For personal use only.
Ala
tRNA tRNAAsn tRNACys tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu CYTB tRNAThr tRNAPro D-loop
Site 5018–5085 5087–5159 5192–5259 5260–5328 5330–6874 6872–6940 6948–7015 7017–7700 7704–7772 7774–7974 7935–8615 8615–9399 9399–9467 9468–9813 9815–9883 9884–10,180 10,174–11,551 11,552–11,620 11,621–11,680 11,682–11,737 11,738–13,558 13,542–14,069 14,070–14,138 14,143–15,282 15,286–15,355 15,355–15,420 15,423–16,416
Start codon
Stop codon
ATG
TAA
ATG
TAA
ATG ATG ATG
TAA TAA TA
ATA
T– –
RTG ATG
TAA T– –
ATA ATG
TAA TAA
ATG
AGA
Length (bp)
Anti-codon
Overlap
Strand
68 73 68 69 1545 69 68 684 69 201 681 785 69 346 69 297 1378 69 60 56 1821 527 69 1140 70 66 994
TGC GTT GCA GTA
73
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
3 TGA GTC TTT 40 1 TCC
32
TCG 7 GTG TAG TTC TGT TGG
1 8
H and L denote heavy and light strands, respectively.
AGA and TA, respectively. The ND3 and ND4 genes both stop with a single T (Boore, 1999). The size of the 22 tRNA genes ranges from 56 to 75 bp. All tRNA genes have the potential of forming the cloverleaf secondary structure, except tRNASer(AGY) that does not have the ‘‘DHU’’ arm. The lengths of the 12S rRNA and 16 S rRNA are 955 and 1573 bp, respectively, and they are located between tRNAPhe and tRNALeu(UUR) but separated by tRNAVal. The nucleotide composition of both rRNAs is very similar to that of the 12 rRNA of the barking deer. The non-coding region is 994 bp in length and located between tRNApro and tRNAphe. Because of tandem repeats, different populations have different change. The conserved sequence blocks CSB-1, CSB-2 and CSB-3, the central conserved sequence block, and the termination-associated sequences TAS1TAS4 were also revealed in this study, which may be used to determine whether the numbers of repeated units indicate the origins of different populations or subspecies. In summary, the complete mtDNA sequence will provide a useful tool for generating the data that are needed to study and evaluate the genetic relationship among different subspecies.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
We would also like to thank National 863 Program of China (No. 2011AA100603), Science and Technology Commission, Jilin (No. 20126–2514) for this research.
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Chen HP, Wu JP, Zhang MH, editors. (1997). Heilong Jiang provincial red deer. Harbin, China: Northeast Forestry University Press. He LW, Dai B, Zeng B, Zhang XY, Chen BP, Yue BS, Li J. (2009). The complete mitochondrial genome of the Sichuan Hill Partridge (Arborophila rufipectus) and a phylogenetic analysis with related species. Gene 435:23–8. Shen YY, Liang L, Sun YB, Yue BS, Yang XJ, Murphy RW, Zhang YP. (2010). A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae. BMC Evol Biol 10:132–41. Sheng H, Ohtaishi L. (1993). The status of deer in China, biology and management. Amsterdam: Elsevier BV. Steven MA, Boness DJ. (2003). Influences of habitat features and human disturbance on use of breeding sites by a declining population of southern fur seal (Arctocephalus australis). J Zool 260: 145–52. Stoneking M, Soodyall H. (1996). Human evolution and the mitochondrial genome. Curr Opin Genet Dev 6:731–6. Wang S, editor. (1998). China red data book of endangered animals (In Chinese with English summary). Beijing: Science Press.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome sequence of northeastern red deer (Cervus elaphus xanthopygus)
Mitochondrial DNA Downloaded from informahealthcare.com by The University of Manchester on 11/20/14 For personal use only.
Yuanchen Shao, Weilin Su, Huamiao Liu, Daiming Zha, Ranran Zhang, and Xiumei Xing State Key Laboratory of Special Economic Animal Molecular Biology, Institute of Special Wild Economic Animal and Plant Science, Chinese Academy Agricultural Sciences, Jilin, P.R. China Abstract
Keywords
The complete mitochondrial genome of the northeastern red deer, Cervus elaphus xanthopygus, was determined by accurate polymerase chain reaction. The entire genome is 16,416 bp in length and contains 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and 1 control region, all of which are arranged in a typical vertebrate manner. The overall base composition of the northeastern red deer’s mitochondrial genome is 33.3% of A, 24.3% of C, 28.9% of T and 13.5% of G. A termination-associated sequence and several conserved central sequence block domains were discovered within the control region.
Cervus elaphus xanthopygus, mitogenome, red deer
Northeastern red deer is originally widespread throughout the Changbai mountain, Wondersun mountain and Xingan ridge in the northeastern China (Chen et al., 1997; Sheng & Ohtaishi, 1993). The species has been extirpated from much of its historical range due largely to hunting and habitat degradation, and is now only found in small fragmented populations in China (Stevens & Boness, 2003). It is classified as Endangered species by IUCN and is included in China red Data Book of Endangered Animal (Wang, 1998). Mitochondrial DNA (mtDNA) is an important genetic marker for studying animal origin and evolution (Shen et al., 2010; Stonking & Soodyall, 1996). In this study, we determined and analyzed the complete mtDNA sequences of the northeastern red deer to facilitate the identification of their origins. The mtDNA was extracted from the blood samples of the red deer, amplified with polymerase chain reaction and sequenced. Sequence analysis was carried out according to previously
History Received 9 March 2014 Accepted 15 March 2014 Published online 4 April 2014
described method (He et al., 2009). Fourteen primers were used to amplify the contiguous and overlapping segments. The complete mtDNA sequence has been deposited into the GenBank (Accession No. GU457434/NC-013836.1). The complete mtDNA of the red deer is 16,416 bp in length. It contains 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, 13 protein-coding genes and a noncoding region (D-loop). Most mitochondrial genes are encoded on the H strand, except the ND6 gene and eight tRNA genes. A common 35 bp space sequence and a common 35 bp overlapping sequence were discovered in the total 37 genes (Table 1). The nucleotide composition of the H strand sika deer mtDNA is 33.3% of A, 13.5% of G, 28.9% of T, and 24.3% of C. The total length of the 13 protein-coding genes is 11,406 bp. All protein-coding genes start with ATG, except the ND2, ND3, ND4L and ND5 genes, all of which start with ATA. TAA is the common stop codon, while ND2, Cytb and COX3 stop with TAG,
Table 1. Localization of the protein-coding genes of Cervus elaphus’s mitochondrial genome. Name Phe
tRNA 12S rRNA tRNAVal 16S rRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp
Site 1–69 70–1024 1025–1091 1091–2663 2664–2738 2741–3697 3697–3765 3763–3834 3837–3905 3906–4949 4948–5015
Start codon
ATG
ATA
Stop codon
Length (bp)
Anti-codon GAA
TAA
69 955 67 1573 75 957 69 72 69 1044 68
TAG
Overlap
1 TAA GAT TTG CAT
1 3 2
TGG
Strand H H H H H H H L H H H (continued )
Correspondence: X. M. Xing, Institute of Special Wild Economic Animal and Plant Science, Chinese Academy of Agricultural Sciences, Jilin 132109, P.R. China. Tel: 132 58846941. Fax: 86 431 81919800. E-mail: [email protected]
2
Y. Shao et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued
Name
Mitochondrial DNA Downloaded from informahealthcare.com by The University of Manchester on 11/20/14 For personal use only.
Ala
tRNA tRNAAsn tRNACys tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 ND6 tRNAGlu CYTB tRNAThr tRNAPro D-loop
Site 5018–5085 5087–5159 5192–5259 5260–5328 5330–6874 6872–6940 6948–7015 7017–7700 7704–7772 7774–7974 7935–8615 8615–9399 9399–9467 9468–9813 9815–9883 9884–10,180 10,174–11,551 11,552–11,620 11,621–11,680 11,682–11,737 11,738–13,558 13,542–14,069 14,070–14,138 14,143–15,282 15,286–15,355 15,355–15,420 15,423–16,416
Start codon
Stop codon
ATG
TAA
ATG
TAA
ATG ATG ATG
TAA TAA TA
ATA
T– –
RTG ATG
TAA T– –
ATA ATG
TAA TAA
ATG
AGA
Length (bp)
Anti-codon
Overlap
Strand
68 73 68 69 1545 69 68 684 69 201 681 785 69 346 69 297 1378 69 60 56 1821 527 69 1140 70 66 994
TGC GTT GCA GTA
73
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
3 TGA GTC TTT 40 1 TCC
32
TCG 7 GTG TAG TTC TGT TGG
1 8
H and L denote heavy and light strands, respectively.
AGA and TA, respectively. The ND3 and ND4 genes both stop with a single T (Boore, 1999). The size of the 22 tRNA genes ranges from 56 to 75 bp. All tRNA genes have the potential of forming the cloverleaf secondary structure, except tRNASer(AGY) that does not have the ‘‘DHU’’ arm. The lengths of the 12S rRNA and 16 S rRNA are 955 and 1573 bp, respectively, and they are located between tRNAPhe and tRNALeu(UUR) but separated by tRNAVal. The nucleotide composition of both rRNAs is very similar to that of the 12 rRNA of the barking deer. The non-coding region is 994 bp in length and located between tRNApro and tRNAphe. Because of tandem repeats, different populations have different change. The conserved sequence blocks CSB-1, CSB-2 and CSB-3, the central conserved sequence block, and the termination-associated sequences TAS1TAS4 were also revealed in this study, which may be used to determine whether the numbers of repeated units indicate the origins of different populations or subspecies. In summary, the complete mtDNA sequence will provide a useful tool for generating the data that are needed to study and evaluate the genetic relationship among different subspecies.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
We would also like to thank National 863 Program of China (No. 2011AA100603), Science and Technology Commission, Jilin (No. 20126–2514) for this research.
References Boore JL. (1999). Animal mitochondrial genomes. Nucleic Acids Res 27: 1767–80. Chen HP, Wu JP, Zhang MH, editors. (1997). Heilong Jiang provincial red deer. Harbin, China: Northeast Forestry University Press. He LW, Dai B, Zeng B, Zhang XY, Chen BP, Yue BS, Li J. (2009). The complete mitochondrial genome of the Sichuan Hill Partridge (Arborophila rufipectus) and a phylogenetic analysis with related species. Gene 435:23–8. Shen YY, Liang L, Sun YB, Yue BS, Yang XJ, Murphy RW, Zhang YP. (2010). A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae. BMC Evol Biol 10:132–41. Sheng H, Ohtaishi L. (1993). The status of deer in China, biology and management. Amsterdam: Elsevier BV. Steven MA, Boness DJ. (2003). Influences of habitat features and human disturbance on use of breeding sites by a declining population of southern fur seal (Arctocephalus australis). J Zool 260: 145–52. Stoneking M, Soodyall H. (1996). Human evolution and the mitochondrial genome. Curr Opin Genet Dev 6:731–6. Wang S, editor. (1998). China red data book of endangered animals (In Chinese with English summary). Beijing: Science Press.
