http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1018200
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of a wild Alashan Red Deer (Cervus elaphus alxaicus) Zhensheng Liu1,2, Jifei Wang1, Yujiao Sun1, Zhijun Hou1, and Liwei Teng1,2 College of Wildlife Resources, Northeast Forestry University, Harbin, P.R. China and 2Key Laboratory of Wildlife Conservation, China State Forestry Administration, Harbin, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/07/15 For personal use only.
1
Abstract
Keywords
The complete mitochondrial genome of a wild red deer from Helan Mountain, China was sequenced and annotated newly. The total length of the mitochondrial genome is 16,428 bp, with a base composition of 33.3% A, 28.8% T, 24.4% C and 13.5% G, and it contains 12S rRNA gene, 16S rRNA gene, 22 tRNA genes, 13 protein-coding genes and 1 control region.
Alashan red deer, Cervus elaphus alxaicus, complete mitochondrial genome History Received 23 November 2014 Revised 19 January 2015 Accepted 24 January 2015 Published online 19 February 2015
Red deer is also known as Cervus elaphus belongs to Artiodactyla, Cervidae. They inhabit most of Europe, the Caucasus Mountains region, Asia Minor, Iran, parts of western Asia, and central Asia (Gyllenstein et al., 1983; Knap & Avsic-Zupanc, 2013). Red deer is ruminant, one of the largest deer species. Among the 24 subspecies in the world, 57 subspecies distributed in China, and most are specialty subspecies in China (Jia et al., 2011; Mahmut et al., 2002; Wu et al., 2005). There are a number of red deer in China, but due to excessive hunting and habitat loss, the population has drastically declined (Mahmut et al., 2002). Now, the red deer was listed in International Union for Conservation of Nature (IUCN) Red List and China National II level protected animals (Comizzoli et al., 2001). The Helan Mountain region is one of centralized areas of red deer geographical population. The Helan Mountains are surrounded by Yinchuan City, deserts and Yellow River. The population density of Alashan red deer is only related to the number of births and deaths without immigration and emigration in
the large scale (Jiang et al., 2014). Alashan red deer only distribute in the middle of Helan Mountain, which is the only surviving effective population of this subspecies. In our study, the body of the wild red deer was found dead in December 2013 at Helan Mountain, Ningxia Hui Autonomous Region, China. Our experiment materials were taken from muscle tissue from the hind legs. In this study, the complete mitochondrial genome of a wild red deer was sequenced using muscle tissue. Mitochondria/Cytosol Isolation Kit (P060097) was used to extract mitochondrial DNA and 14 pairs of primers were used for polymerase chain reaction (PCR)-amplifying the mitochondrial genome. MEGA5.03 software was used for sequence splicing and analyses. The total length of the genome was 16,428 bp, with a base composition of 33.3% A, 28.8% T, 24.4% C, and 13.5% G. The mitogenome contains 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, 13 protein-coding genes and 1 control region (Table 1). This mitochondrial genome sequence was submitted to the GenBank with the accession number KP172593.
Table 1. Annotation of the Alashan red deer. Gene
Start position Phe
tRNA 12S rRNA tRNAVal 16S RNA tRNALeu ND1 tRNAIle tRNAGln
1 70 1025 1091 2664 2741 3697 3763
Stop position 69 1024 1091 2663 2738 3696 3765 3834
Length (bp)
Anticodon
69 955 67 1573 75 956 69 72
GAA
Start condon
Stop codon
TAC TAA ATG GAT TTG
TAA
Strand + + + + + + +
(continued )
Correspondence: Liwei Teng, College of Wildlife Resources, Northeast Forestry University, Harbin, China. E-mail: [email protected]
2
Z. Liu et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Gene
Start position
Stop position
Length (bp)
Anticodon
3837 3906 4948 5018 5088 5193 5261 5331 6873 6949 7018 7705 7775 7936 8616 9400 9469 9816 9885 10,175 11,553 11,622 11,683 11,753 13,557 14,085 14,158 15,301 15,370 15,438
3905 4947 5015 5086 5160 5260 5329 6875 6941 7016 7701 7773 7975 8616 9399 9468 9814 9884 10,181 11,552 11,621 11,681 11,752 13,573 14,084 14,153 15,297 15,370 15,435 16,428
69 1042 68 69 73 68 69 1545 69 68 684 69 201 681 784 69 346 69 297 1378 69 60 70 1821 528 69 1140 70 66 991
CAT
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/07/15 For personal use only.
Met
tRNA ND2 tRNATrp tRNAAla 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 CR
Except ND6, all the protein-coding genes were in the heavy chain. ATP8 was the shortest one which was 201 bp and ND5 was the longest one which was 1821 bp. The length of 22 tRNA genes from 60 to 75, and the length of 12s rRNA and 16S rRNA were separately 955 bp and 1573 bp. The protein-coding genes of Nd2, Nd3, and Nd5 used the start codon ATA, and the remaining protein-coding genes initiated with ATG. Except for Nd2 (TAG stop codon) and Cyt b (AGA stop codon), the remaining eight protein-coding genes terminated with TAA same to some other mammalian species such as sika deer (Shao et al., 2014). Analysis of the control region, we found that a high mutation and a tandem repeat sequence and heterogeneity exists between the same species like tiger (Sun et al., 2014).
Acknowledgements The authors are grateful to Zhijun Hou for the help of portion data Analysis.
Declaration of interest This research was supported by ‘‘the Fundamental Research Funds for the Central Universities (2572014CA03, DL13EA01)’’, and the National Nature Science Foundation of China (31372221, 30970371).
References Comizzoli P, Mermillod P, Cognie Y, Chai N, Legendre X, Mauge R. (2001). Successful in vitro production of embryos in the red deer
Start condon
Stop codon
Strand
ATA
TAG
+ + +
ATG
TAA
+
ATG
TAA
ATG ATG ATG
TAA TAA TA
ATA
T–
ATG ATG
TAA T–
ATA ATG
TAA TAA
ATG
AGA
TCA TGC GTT GCA GTA TGA GTC TTT
TCC TCG GTG GCT TAG
+ + + + + + + + + + + + + + +
TTC TGT TGG
+ + +
(Cervus elaphus) and the sika deer (Cervus nippon). Theriogenology 55:649–59. Gyllenstein U, Ryman N, Reuterwall C, Dratch P. (1983). Genetic differentiation in four European subspecies of red deer (Cervus elaphus L.). Heredity (Edinb) 51:561–80. Jia B, Li RY, Zhao ZS, Yan GQ, Xi JF, Blair HT, Li DQ, et al. (2011). Analysis of genetic diversity and phylogenetic relationship of red deer subspecies in XinJiang, China. Anim Sci J 82: 517–22. Jiang LC, Gou LK, Zhang X, Zhao QM, Tan S, Peng R, Wei YQ, Zou FD. (2014). Complete mitochondrial genome of a new subspecies of the blue sheep, Pseudois nayaur (Cetartiodactyla: Caprinae) from Helan Mountain in China. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.855759. Knap N, Avsic-Zupanc T. (2013). Correlation of TBE incidence with red deer and roe deer abundance in Slovenia. PLoS One 8:e66380. Mahmut H, Masuda R, Onuma M, Takahashi M, Nagata J, Suzuki M, Ohtaishi N. (2002). Molecular phylogeography of the red deer (Cervus elaphus) populations in Xinjiang of China: Comparison with other Asian, European, and North American populations. Zool Sci 19: 485–95. Shao Y, Zha D, Xing X, Su W, Liu H, Zhang R. (2014). Complete mitochondrial genome sequence of northeastern sika deer (Cervus nippon hortulorum). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.900671. Sun Y, Lu T, Sun Z, Guan W, Liu Z, Teng L, Wang S, Ma Y. (2014). Complete mitochondrial genome of a wild Siberian tiger. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/ 19401736.2013.840597. Wu H, Wan QH, Fang SG, Zhang SY. (2005). Application of mitochondrial DNA sequence analysis in the forensic identification of Chinese sika deer subspecies. Forensic Sci Int 148: 101–5.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of a wild Alashan Red Deer (Cervus elaphus alxaicus) Zhensheng Liu1,2, Jifei Wang1, Yujiao Sun1, Zhijun Hou1, and Liwei Teng1,2 College of Wildlife Resources, Northeast Forestry University, Harbin, P.R. China and 2Key Laboratory of Wildlife Conservation, China State Forestry Administration, Harbin, P.R. China
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/07/15 For personal use only.
1
Abstract
Keywords
The complete mitochondrial genome of a wild red deer from Helan Mountain, China was sequenced and annotated newly. The total length of the mitochondrial genome is 16,428 bp, with a base composition of 33.3% A, 28.8% T, 24.4% C and 13.5% G, and it contains 12S rRNA gene, 16S rRNA gene, 22 tRNA genes, 13 protein-coding genes and 1 control region.
Alashan red deer, Cervus elaphus alxaicus, complete mitochondrial genome History Received 23 November 2014 Revised 19 January 2015 Accepted 24 January 2015 Published online 19 February 2015
Red deer is also known as Cervus elaphus belongs to Artiodactyla, Cervidae. They inhabit most of Europe, the Caucasus Mountains region, Asia Minor, Iran, parts of western Asia, and central Asia (Gyllenstein et al., 1983; Knap & Avsic-Zupanc, 2013). Red deer is ruminant, one of the largest deer species. Among the 24 subspecies in the world, 57 subspecies distributed in China, and most are specialty subspecies in China (Jia et al., 2011; Mahmut et al., 2002; Wu et al., 2005). There are a number of red deer in China, but due to excessive hunting and habitat loss, the population has drastically declined (Mahmut et al., 2002). Now, the red deer was listed in International Union for Conservation of Nature (IUCN) Red List and China National II level protected animals (Comizzoli et al., 2001). The Helan Mountain region is one of centralized areas of red deer geographical population. The Helan Mountains are surrounded by Yinchuan City, deserts and Yellow River. The population density of Alashan red deer is only related to the number of births and deaths without immigration and emigration in
the large scale (Jiang et al., 2014). Alashan red deer only distribute in the middle of Helan Mountain, which is the only surviving effective population of this subspecies. In our study, the body of the wild red deer was found dead in December 2013 at Helan Mountain, Ningxia Hui Autonomous Region, China. Our experiment materials were taken from muscle tissue from the hind legs. In this study, the complete mitochondrial genome of a wild red deer was sequenced using muscle tissue. Mitochondria/Cytosol Isolation Kit (P060097) was used to extract mitochondrial DNA and 14 pairs of primers were used for polymerase chain reaction (PCR)-amplifying the mitochondrial genome. MEGA5.03 software was used for sequence splicing and analyses. The total length of the genome was 16,428 bp, with a base composition of 33.3% A, 28.8% T, 24.4% C, and 13.5% G. The mitogenome contains 2 rRNA genes (12S rRNA and 16S rRNA), 22 tRNA genes, 13 protein-coding genes and 1 control region (Table 1). This mitochondrial genome sequence was submitted to the GenBank with the accession number KP172593.
Table 1. Annotation of the Alashan red deer. Gene
Start position Phe
tRNA 12S rRNA tRNAVal 16S RNA tRNALeu ND1 tRNAIle tRNAGln
1 70 1025 1091 2664 2741 3697 3763
Stop position 69 1024 1091 2663 2738 3696 3765 3834
Length (bp)
Anticodon
69 955 67 1573 75 956 69 72
GAA
Start condon
Stop codon
TAC TAA ATG GAT TTG
TAA
Strand + + + + + + +
(continued )
Correspondence: Liwei Teng, College of Wildlife Resources, Northeast Forestry University, Harbin, China. E-mail: [email protected]
2
Z. Liu et al.
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Gene
Start position
Stop position
Length (bp)
Anticodon
3837 3906 4948 5018 5088 5193 5261 5331 6873 6949 7018 7705 7775 7936 8616 9400 9469 9816 9885 10,175 11,553 11,622 11,683 11,753 13,557 14,085 14,158 15,301 15,370 15,438
3905 4947 5015 5086 5160 5260 5329 6875 6941 7016 7701 7773 7975 8616 9399 9468 9814 9884 10,181 11,552 11,621 11,681 11,752 13,573 14,084 14,153 15,297 15,370 15,435 16,428
69 1042 68 69 73 68 69 1545 69 68 684 69 201 681 784 69 346 69 297 1378 69 60 70 1821 528 69 1140 70 66 991
CAT
Mitochondrial DNA Downloaded from informahealthcare.com by Kainan University on 04/07/15 For personal use only.
Met
tRNA ND2 tRNATrp tRNAAla 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 CR
Except ND6, all the protein-coding genes were in the heavy chain. ATP8 was the shortest one which was 201 bp and ND5 was the longest one which was 1821 bp. The length of 22 tRNA genes from 60 to 75, and the length of 12s rRNA and 16S rRNA were separately 955 bp and 1573 bp. The protein-coding genes of Nd2, Nd3, and Nd5 used the start codon ATA, and the remaining protein-coding genes initiated with ATG. Except for Nd2 (TAG stop codon) and Cyt b (AGA stop codon), the remaining eight protein-coding genes terminated with TAA same to some other mammalian species such as sika deer (Shao et al., 2014). Analysis of the control region, we found that a high mutation and a tandem repeat sequence and heterogeneity exists between the same species like tiger (Sun et al., 2014).
Acknowledgements The authors are grateful to Zhijun Hou for the help of portion data Analysis.
Declaration of interest This research was supported by ‘‘the Fundamental Research Funds for the Central Universities (2572014CA03, DL13EA01)’’, and the National Nature Science Foundation of China (31372221, 30970371).
References Comizzoli P, Mermillod P, Cognie Y, Chai N, Legendre X, Mauge R. (2001). Successful in vitro production of embryos in the red deer
Start condon
Stop codon
Strand
ATA
TAG
+ + +
ATG
TAA
+
ATG
TAA
ATG ATG ATG
TAA TAA TA
ATA
T–
ATG ATG
TAA T–
ATA ATG
TAA TAA
ATG
AGA
TCA TGC GTT GCA GTA TGA GTC TTT
TCC TCG GTG GCT TAG
+ + + + + + + + + + + + + + +
TTC TGT TGG
+ + +
(Cervus elaphus) and the sika deer (Cervus nippon). Theriogenology 55:649–59. Gyllenstein U, Ryman N, Reuterwall C, Dratch P. (1983). Genetic differentiation in four European subspecies of red deer (Cervus elaphus L.). Heredity (Edinb) 51:561–80. Jia B, Li RY, Zhao ZS, Yan GQ, Xi JF, Blair HT, Li DQ, et al. (2011). Analysis of genetic diversity and phylogenetic relationship of red deer subspecies in XinJiang, China. Anim Sci J 82: 517–22. Jiang LC, Gou LK, Zhang X, Zhao QM, Tan S, Peng R, Wei YQ, Zou FD. (2014). Complete mitochondrial genome of a new subspecies of the blue sheep, Pseudois nayaur (Cetartiodactyla: Caprinae) from Helan Mountain in China. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2013.855759. Knap N, Avsic-Zupanc T. (2013). Correlation of TBE incidence with red deer and roe deer abundance in Slovenia. PLoS One 8:e66380. Mahmut H, Masuda R, Onuma M, Takahashi M, Nagata J, Suzuki M, Ohtaishi N. (2002). Molecular phylogeography of the red deer (Cervus elaphus) populations in Xinjiang of China: Comparison with other Asian, European, and North American populations. Zool Sci 19: 485–95. Shao Y, Zha D, Xing X, Su W, Liu H, Zhang R. (2014). Complete mitochondrial genome sequence of northeastern sika deer (Cervus nippon hortulorum). Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/19401736.2014.900671. Sun Y, Lu T, Sun Z, Guan W, Liu Z, Teng L, Wang S, Ma Y. (2014). Complete mitochondrial genome of a wild Siberian tiger. Mitochondrial DNA. [Epub ahead of print]. doi: 10.3109/ 19401736.2013.840597. Wu H, Wan QH, Fang SG, Zhang SY. (2005). Application of mitochondrial DNA sequence analysis in the forensic identification of Chinese sika deer subspecies. Forensic Sci Int 148: 101–5.
