http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2013.873930
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of a German Shepherd (Canis lupus familiaris breed German Shepherd) provides insights into genome-wide sequence variations Qing-Hui Jia1, Hong-Bin Liu2, Xiao-Long Gu3, Jie-Feng Li4, and Yan-Long Liu1
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 02/10/15 For personal use only.
1
Key Laboratory of Preventive Veterinary Medicine in Hebei Province, Hebei Normal University of Science and Technology, Qinhuangdao, China, Department of pharmacy, Hebei North University, Zhangjiakou, China, 3Department of Animal Science and Technology, Hebei North University, Zhangjiakou, China, and 4Department of Animal Science, Institute of Animal Science of Hebei, Baoding, China
2
Abstract
Keywords
In this work, we report the complete mitochondrial genome sequence of a German shepherd. The total length of the mitogenome was 16,727 bp. It contained the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a non-coding control region (D-loop region). The arrangement of these genes was the same as that found in other dogs. All the protein initial codons were ATG, except for ND2, ND3 and ND5 starting with ATA. Sequence comparison indicates that D-loop region harbors most sequence variations.
Genome, German shepherd, mitochondrion
The German Shepherd (Canis lupus familiaris breed German Shepherd), a breed of dog that originally named in 1899, was domesticated for utility, intelligence, and to be a multipurpose servant of human beings (Goldbecker & Hart, 1967). Their capacity, temperament, structural efficiency and other natural skills were quite excellent than other dogs, which is among the most common dog breeds trained by the military, law enforcement and service/assistance programs. In addition, it is also an extremely popular companion dog breed for human (Moody et al., 2006; Tsai et al., 2012). In this study, the complete mitochondrial genome of a German Shepherd (an individual comes from Germany) was reported. This mitochondrial genome sequence was submitted to the GenBank with the accession number KF907307. The total length of the mitogenome is 16,727 bp, and the base composition was 31.7% A, 28.7% T, 25.5% C and 14.1% G and an obvious A–T (60.4%)-rich feature. The arrangement of the multiple genes is in line with other canine animals (Bjo¨rnerfeldt et al., 2006; Webb & Allard, 2009; Zhang & Chen, 2010; Zhang et al., 2013). It comprises two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). Besides the ND2,
History Received 6 December 2013 Accepted 7 December 2013 Published online 17 January 2014
ND3 and ND5 genes initiating with ATA, the rest of the protein coding genes employed ATG as their start codon. All the mitogenome genes were encoded on the H strand except for ND6, and eight tRNA genes. These genes had four types of termination codon, including TAG for ND2, CytB for AGA, eight genes for TAA, and an incomplete termination codon T– – for COX3, ND3 and ND4. The 12S rRNA and 16S rRNA separated by the tRNAVal are 954 bp and 1580 bp in length, respectively, and the result was the same as in other dogs. The control region is 1270 bp in length, located between the tRNAPhe gene and the tRNAPro gene. Comparing mtDNA sequence of this German Shepherd with other individual/breeds (Bjo¨rnerfeldt et al., 2006; Webb & Allard, 2009; Zhang & Chen, 2010; Zhang et al., 2013) indicated genome-wide sequence variations (Figure 1). In general, sequence comparison indicated the D-loop region harbors the most sequence variations in the whole genome, and other regions shown nearly equal sequence variations, which was consistent with previous studies (Imes et al., 2012; Webb & Allard, 2009). Meanwhile, we also showed that our sequenced German Shepherd has a sequence insertion in the D-loop region relative to two other German Shepherd sequences (Figure 1).
Correspondence: Qing-Hui Jia, Key Laboratory of Preventive Veterinary Medicine in Hebei Province, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China. E-mail: [email protected]
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 02/10/15 For personal use only.
2
Q.-H. Jia et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Genome-wide sequence variation among four dog mitochondrial genome sequences. The four sequences (in line with the figure) are the German Shepherd reported this time, two German Shepherd previous reported (EU408277; DQ480489), and Canis lupus (NC_008092) was served as a reference. The identity plots show sequence identity among these mitochondrial genome sequences. Genome regions are color-coded as coding and non-coding regions. tRNA genes are not shown in this figure.
Acknowledgements The authors would like to thank the anonymous reviews of the paper for critical reading of the paper.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Bjo¨rnerfeldt S, Webster MT, Vila` C. (2006). Relaxation of selective constraint on dog mitochondrial DNA following domestication. Genome Res 16:990–4. Goldbecker WM, Hart EH. (1967). This is the German Shepherd. Jersey City: TFH Publications Inc. Imes DL, Wictum EJ, Allard MW, Sacks BN. (2012). Identification of single nucleotide polymorphisms within the mtDNA genome of the
domestic dog to discriminate individuals with common HVI haplotypes. Forensic Sci Int Genet 6:630–9. Moody JA, Clark LA, Murphy KE. (2006) Working dogs: History and applications. In: Ostrander EA, Giger U, Lindblad-Toh K, editors. The dog and its genome. Woodbury: Cold Spring Harbor Laboratory Press. p 1–18. Tsai KL, Noorai RE, Starr-Moss AN, Quignon P, Rinz CJ, Ostrander EA, Steiner JM, et al. (2012). Genome-wide association studies for multiple diseases of the German Shepherd Dog. Mamm Genome 23:203–11. Webb KM, Allard MW. (2009). Mitochondrial genome DNA analysis of the domestic dog: Identifying informative SNPs outside of the control region. J Forensic Sci 54:275–88. Zhang H, Chen L. (2010). The complete mitochondrial genome of the raccoon dog. Mitochondrial DNA 21:59–61. Zhang H, Zhang J, Zhao C, Chen L, Sha W, Liu G. (2013). Complete mitochondrial genome of Canis lupus campestris. Mitochondrial DNA 24:1–2. doi: 10.3109/19401736.2013.823186.
MITOGENOME ANNOUNCEMENT
Complete mitochondrial genome of a German Shepherd (Canis lupus familiaris breed German Shepherd) provides insights into genome-wide sequence variations Qing-Hui Jia1, Hong-Bin Liu2, Xiao-Long Gu3, Jie-Feng Li4, and Yan-Long Liu1
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 02/10/15 For personal use only.
1
Key Laboratory of Preventive Veterinary Medicine in Hebei Province, Hebei Normal University of Science and Technology, Qinhuangdao, China, Department of pharmacy, Hebei North University, Zhangjiakou, China, 3Department of Animal Science and Technology, Hebei North University, Zhangjiakou, China, and 4Department of Animal Science, Institute of Animal Science of Hebei, Baoding, China
2
Abstract
Keywords
In this work, we report the complete mitochondrial genome sequence of a German shepherd. The total length of the mitogenome was 16,727 bp. It contained the typical structure of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a non-coding control region (D-loop region). The arrangement of these genes was the same as that found in other dogs. All the protein initial codons were ATG, except for ND2, ND3 and ND5 starting with ATA. Sequence comparison indicates that D-loop region harbors most sequence variations.
Genome, German shepherd, mitochondrion
The German Shepherd (Canis lupus familiaris breed German Shepherd), a breed of dog that originally named in 1899, was domesticated for utility, intelligence, and to be a multipurpose servant of human beings (Goldbecker & Hart, 1967). Their capacity, temperament, structural efficiency and other natural skills were quite excellent than other dogs, which is among the most common dog breeds trained by the military, law enforcement and service/assistance programs. In addition, it is also an extremely popular companion dog breed for human (Moody et al., 2006; Tsai et al., 2012). In this study, the complete mitochondrial genome of a German Shepherd (an individual comes from Germany) was reported. This mitochondrial genome sequence was submitted to the GenBank with the accession number KF907307. The total length of the mitogenome is 16,727 bp, and the base composition was 31.7% A, 28.7% T, 25.5% C and 14.1% G and an obvious A–T (60.4%)-rich feature. The arrangement of the multiple genes is in line with other canine animals (Bjo¨rnerfeldt et al., 2006; Webb & Allard, 2009; Zhang & Chen, 2010; Zhang et al., 2013). It comprises two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). Besides the ND2,
History Received 6 December 2013 Accepted 7 December 2013 Published online 17 January 2014
ND3 and ND5 genes initiating with ATA, the rest of the protein coding genes employed ATG as their start codon. All the mitogenome genes were encoded on the H strand except for ND6, and eight tRNA genes. These genes had four types of termination codon, including TAG for ND2, CytB for AGA, eight genes for TAA, and an incomplete termination codon T– – for COX3, ND3 and ND4. The 12S rRNA and 16S rRNA separated by the tRNAVal are 954 bp and 1580 bp in length, respectively, and the result was the same as in other dogs. The control region is 1270 bp in length, located between the tRNAPhe gene and the tRNAPro gene. Comparing mtDNA sequence of this German Shepherd with other individual/breeds (Bjo¨rnerfeldt et al., 2006; Webb & Allard, 2009; Zhang & Chen, 2010; Zhang et al., 2013) indicated genome-wide sequence variations (Figure 1). In general, sequence comparison indicated the D-loop region harbors the most sequence variations in the whole genome, and other regions shown nearly equal sequence variations, which was consistent with previous studies (Imes et al., 2012; Webb & Allard, 2009). Meanwhile, we also showed that our sequenced German Shepherd has a sequence insertion in the D-loop region relative to two other German Shepherd sequences (Figure 1).
Correspondence: Qing-Hui Jia, Key Laboratory of Preventive Veterinary Medicine in Hebei Province, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China. E-mail: [email protected]
Mitochondrial DNA Downloaded from informahealthcare.com by McMaster University on 02/10/15 For personal use only.
2
Q.-H. Jia et al.
Mitochondrial DNA, Early Online: 1–2
Figure 1. Genome-wide sequence variation among four dog mitochondrial genome sequences. The four sequences (in line with the figure) are the German Shepherd reported this time, two German Shepherd previous reported (EU408277; DQ480489), and Canis lupus (NC_008092) was served as a reference. The identity plots show sequence identity among these mitochondrial genome sequences. Genome regions are color-coded as coding and non-coding regions. tRNA genes are not shown in this figure.
Acknowledgements The authors would like to thank the anonymous reviews of the paper for critical reading of the paper.
Declaration of interest The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
References Bjo¨rnerfeldt S, Webster MT, Vila` C. (2006). Relaxation of selective constraint on dog mitochondrial DNA following domestication. Genome Res 16:990–4. Goldbecker WM, Hart EH. (1967). This is the German Shepherd. Jersey City: TFH Publications Inc. Imes DL, Wictum EJ, Allard MW, Sacks BN. (2012). Identification of single nucleotide polymorphisms within the mtDNA genome of the
domestic dog to discriminate individuals with common HVI haplotypes. Forensic Sci Int Genet 6:630–9. Moody JA, Clark LA, Murphy KE. (2006) Working dogs: History and applications. In: Ostrander EA, Giger U, Lindblad-Toh K, editors. The dog and its genome. Woodbury: Cold Spring Harbor Laboratory Press. p 1–18. Tsai KL, Noorai RE, Starr-Moss AN, Quignon P, Rinz CJ, Ostrander EA, Steiner JM, et al. (2012). Genome-wide association studies for multiple diseases of the German Shepherd Dog. Mamm Genome 23:203–11. Webb KM, Allard MW. (2009). Mitochondrial genome DNA analysis of the domestic dog: Identifying informative SNPs outside of the control region. J Forensic Sci 54:275–88. Zhang H, Chen L. (2010). The complete mitochondrial genome of the raccoon dog. Mitochondrial DNA 21:59–61. Zhang H, Zhang J, Zhao C, Chen L, Sha W, Liu G. (2013). Complete mitochondrial genome of Canis lupus campestris. Mitochondrial DNA 24:1–2. doi: 10.3109/19401736.2013.823186.
