http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1007322
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the Jacobin pigeon (Columba livia breed Jacobin) Wen-Xiao He1 and Jin-Feng Jia2 Mitochondrial DNA Downloaded from informahealthcare.com by Nanyang Technological University on 03/04/15 For personal use only.
1
Artillery Training Base of General Staff, Xuanhua, PR China and 2School of Economics and Management, Hebei North University, Zhangjiakou, PR China Abstract
Keywords
The Jacobin is a breed of fancy pigeon developed over many years of selective breeding that originated in Asia. In the present work, we report the complete mitochondrial genome sequence of Jacobin pigeon for the first time. The total length of the mitogenome was 17,245 bp with the base composition of 30.18% for A, 23.98% for T, 31.88% for C, and 13.96% for G and an A-T (54.17 %)-rich feature was detected. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region. The arrangement of all genes was identical to the typical mitochondrial genomes of pigeon. The complete mitochondrial genome sequence of Jacobin pigeon would serve as an important data set of the germplasm resources for further study.
Genome, Jacobin pigeon (Columba livia), mitochondrion
The Jacobin is a breed of fancy pigeon developed over many years of selective breeding that originated in Asia (Levi, 1977). Jacobins, along with other varieties of domesticated pigeons, are all descendants from the Rock Pigeon (Columba livia), which is a member of the bird family Columbidae (Levi, 1965). It is in the Asian feather and voice pigeon show group. The breed is known for its feathered hood over its head. Now, their genomic sequence of a number of Rock Pigeon breeds was available (Shapiro et al., 2013), while their mitochondrial genome sequences were lagged behind. Here, we reported a Jacobin
History Received 29 December 2014 Accepted 30 December 2014 Published online 18 February 2015
pigeon mitochondrial genome for the first time. The complete mitochondrial genome is 17,245 bp in size (GenBank accession number KP319029, it is not due to release date) containing 37 genes coding for 13 typical protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region (D-loop region) (Table 1). The overall characteristics including mitochondrial genome organization and gene arrangement pattern are identical to those of other birds (Kan et al., 2010, 2013; Khan & Arif, 2013). Except for the ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The overall
Table 1. List of genes encoded by Jacobin Pigeon mitochondrial genome. Position Gene
From Phe
tRNA 12SrRNA tRNAVal 16SrRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn
1 70 1044 1155 2710 2796 3779 3855 3925 3994 5034 5106 5177
Base composition (%) To 69 1031 1116 2665 2783 3761 3849 3925 3993 5034 5104 5174 5249
Size (bp)
A
C
G
T
69 962 73 1511 74 966 71 71 69 1041 71 69 73
30.4 31.3 32.9 33.5 24.3 26.0 32.4 36.6 27.5 31.7 35.2 30.4 30.1
34.8 27.2 24.7 25.2 27.0 34.3 21.1 21.1 30.4 34.2 23.9 24.6 32.9
21.7 20.4 19.2 19.3 24.3 12.9 19.7 11.3 20.3 10.2 18.3 18.8 17.8
13.0 21.1 23.3 22.0 24.3 26.8 26.8 31.0 21.7 23.9 22.5 26.1 19.2
Start codon
Stop codon
ATG
AGA
ATG
TA–
Strand H H H H H H H L H H H L L (continued )
Correspondence: Wen-Xiao He, Artillery Training Base of General Staff, Xuanhua 075000, PR China. Tel/Fax: +86 313 3366535. E-mail: [email protected]
2
W.-X. He & J.-F. Jia
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Position Gene
Mitochondrial DNA Downloaded from informahealthcare.com by Nanyang Technological University on 03/04/15 For personal use only.
Cys
tRNA tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 Cyt b tRNAThr tRNAPro ND6 tRNAGlu D-loop
Base composition (%)
From
To
Size (bp)
A
C
G
T
5252 5318 5391 6933 7009 7080 7765 7837 7995 8678 9462 9531 9884 9954 10,244 11,622 11,692 11,756 11,828 13,654 14,797 14,872 14,987 15,512 15,583
5318 5389 6941 7006 7077 7763 7835 8004 8678 9461 9530 9882 9952 10,250 11,621 11,690 11,755 11,827 13,642 14,796 14,865 14,941 15,508 15,582 17,245
67 72 1551 74 69 684 71 168 684 784 69 352 69 297 1378 69 64 72 1815 1143 69 70 522 71 1663
31.3 34.7 26.1 31.1 33.3 30.4 28.2 32.5 28.5 26.8 33.3 27.0 34.8 27.6 30.5 31.9 29.7 30.6 31.2 27.4 30.4 35.7 42.1 26.8 30.7
25.4 27.8 32.1 29.7 23.2 30.8 22.5 38.3 35.1 33.3 26.1 34.1 24.6 33.3 35.8 24.6 28.1 19.4 34.3 35.7 20.3 25.7 37.7 32.4 28.3
17.9 15.3 16.2 16.2 15.9 14.6 22.5 4.5 9.8 15.1 15.9 12.2 13.0 14.5 10.7 15.9 20.3 22.2 11.3 12.2 18.8 12.9 9.2 19.7 13.4
25.4 22.2 25.6 23.0 27.5 24.1 26.8 24.7 26.6 24.9 24.6 26.7 27.5 24.6 23.0 27.5 21.9 27.8 23.1 24.7 30.4 25.7 10.9 21.1 27.7
base composition of the mitochondrial genome is 30.18% A, 31.88% C, 13.96% G, and 23.98% T with an A-T content of 54.17%. Among the 13 protein-coding genes, 9 genes including ND2, COX2, ATP8, ATP6, COX3, ND4L, ND4, Cyt b and ND6 start with common initiation ATG, the remaining COX1 and ND5 uses unusual initiation codon GTG, and ND1 uses ATA, ND3 utilized ATT. Three complete and general termination codons are used in 10 protein-coding genes (ND1, COX1, COX2, ATP8, ATP6, ND3, ND4L, ND5, Cyt b and ND6) and the remaining COX3 and ND4 have an incomplete termination codon ‘‘T’’, ND2 have an incomplete termination codon ‘‘TA’’. The 12S rRNA and 16S rRNA separated by the tRNAval are 962 and 1511 bp in length, respectively (Table 1). The control region of the Jacobin pigeon mtDNA is 1663 bp long. We expect that this genome sequence can serve as an important data set of the germplasm resources or evolutionary study (Khan & Arif, 2013).
Declaration of interest This work was supported by the Natural Science Foundation of Hebei Province, China (Grant number: C2015405016), Natural Science
Start codon
Stop codon
GTG
AGG
ATG
TAA
ATG ATG ATG
TAA TAA T––
ATT
TAA
ATG ATG
TAA T––
GTG ATG
AGA TAA
ATG
TAG
Strand L L H L H H H H H H H H H H H H H H H H H L L H
L
Research Key Programs of Educational Department of Hebei Province (Grant number: ZD20131045) and Key Programs of Hebei North University (Grant number: ZD201306). The authors declare no conflicts of interest.
References Kan XZ, Li XF, Zhang LQ, Chen L, Qian CJ, Zhang XW, Wang L. (2010). Characterization of the complete mitochondrial genome of the Rock pigeon, Columba livia (Columbiformes: Columbidae). Genet Mol Res 9:1234–49. Kan XZ, Yuan J, Zhang L, Li X, Yu L, Chen L, Guo ZC, Yang JK. (2013). Complete mitochondrial genome of the Tristram’s Bunting, Emberiza tristrami (Aves: Passeriformes): The first representative of the family Emberizidae with six boxes in the central conserved domain II of control region. Mitochondrial DNA 24:648–50. Khan HA, Arif IA. (2013). COI barcodes and phylogeny of doves (Columbidae family). Mitochondrial DNA 24:689–96. Levi WM. (1965). Encyclopedia of pigeon breeds. Sumter (SC): Levi Publishing. Levi WM. (1977). The pigeon. Sumter (SC): Levi Publishing. Shapiro MD, Kronenberg Z, Li C, Domyan ET, Pan H, Campbell M, Tan H, et al. (2013). Genomic diversity and evolution of the head crest in the Rock Pigeon. Science 339:1063–7.
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the Jacobin pigeon (Columba livia breed Jacobin) Wen-Xiao He1 and Jin-Feng Jia2 Mitochondrial DNA Downloaded from informahealthcare.com by Nanyang Technological University on 03/04/15 For personal use only.
1
Artillery Training Base of General Staff, Xuanhua, PR China and 2School of Economics and Management, Hebei North University, Zhangjiakou, PR China Abstract
Keywords
The Jacobin is a breed of fancy pigeon developed over many years of selective breeding that originated in Asia. In the present work, we report the complete mitochondrial genome sequence of Jacobin pigeon for the first time. The total length of the mitogenome was 17,245 bp with the base composition of 30.18% for A, 23.98% for T, 31.88% for C, and 13.96% for G and an A-T (54.17 %)-rich feature was detected. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region. The arrangement of all genes was identical to the typical mitochondrial genomes of pigeon. The complete mitochondrial genome sequence of Jacobin pigeon would serve as an important data set of the germplasm resources for further study.
Genome, Jacobin pigeon (Columba livia), mitochondrion
The Jacobin is a breed of fancy pigeon developed over many years of selective breeding that originated in Asia (Levi, 1977). Jacobins, along with other varieties of domesticated pigeons, are all descendants from the Rock Pigeon (Columba livia), which is a member of the bird family Columbidae (Levi, 1965). It is in the Asian feather and voice pigeon show group. The breed is known for its feathered hood over its head. Now, their genomic sequence of a number of Rock Pigeon breeds was available (Shapiro et al., 2013), while their mitochondrial genome sequences were lagged behind. Here, we reported a Jacobin
History Received 29 December 2014 Accepted 30 December 2014 Published online 18 February 2015
pigeon mitochondrial genome for the first time. The complete mitochondrial genome is 17,245 bp in size (GenBank accession number KP319029, it is not due to release date) containing 37 genes coding for 13 typical protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a control region (D-loop region) (Table 1). The overall characteristics including mitochondrial genome organization and gene arrangement pattern are identical to those of other birds (Kan et al., 2010, 2013; Khan & Arif, 2013). Except for the ND6 and eight tRNA genes, all other mitochondrial genes are encoded on the heavy strand. The overall
Table 1. List of genes encoded by Jacobin Pigeon mitochondrial genome. Position Gene
From Phe
tRNA 12SrRNA tRNAVal 16SrRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn
1 70 1044 1155 2710 2796 3779 3855 3925 3994 5034 5106 5177
Base composition (%) To 69 1031 1116 2665 2783 3761 3849 3925 3993 5034 5104 5174 5249
Size (bp)
A
C
G
T
69 962 73 1511 74 966 71 71 69 1041 71 69 73
30.4 31.3 32.9 33.5 24.3 26.0 32.4 36.6 27.5 31.7 35.2 30.4 30.1
34.8 27.2 24.7 25.2 27.0 34.3 21.1 21.1 30.4 34.2 23.9 24.6 32.9
21.7 20.4 19.2 19.3 24.3 12.9 19.7 11.3 20.3 10.2 18.3 18.8 17.8
13.0 21.1 23.3 22.0 24.3 26.8 26.8 31.0 21.7 23.9 22.5 26.1 19.2
Start codon
Stop codon
ATG
AGA
ATG
TA–
Strand H H H H H H H L H H H L L (continued )
Correspondence: Wen-Xiao He, Artillery Training Base of General Staff, Xuanhua 075000, PR China. Tel/Fax: +86 313 3366535. E-mail: [email protected]
2
W.-X. He & J.-F. Jia
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Position Gene
Mitochondrial DNA Downloaded from informahealthcare.com by Nanyang Technological University on 03/04/15 For personal use only.
Cys
tRNA tRNATyr COX1 tRNASer tRNAAsp COX2 tRNALys ATP8 ATP6 COX3 tRNAGly ND3 tRNAArg ND4L ND4 tRNAHis tRNASer tRNALeu ND5 Cyt b tRNAThr tRNAPro ND6 tRNAGlu D-loop
Base composition (%)
From
To
Size (bp)
A
C
G
T
5252 5318 5391 6933 7009 7080 7765 7837 7995 8678 9462 9531 9884 9954 10,244 11,622 11,692 11,756 11,828 13,654 14,797 14,872 14,987 15,512 15,583
5318 5389 6941 7006 7077 7763 7835 8004 8678 9461 9530 9882 9952 10,250 11,621 11,690 11,755 11,827 13,642 14,796 14,865 14,941 15,508 15,582 17,245
67 72 1551 74 69 684 71 168 684 784 69 352 69 297 1378 69 64 72 1815 1143 69 70 522 71 1663
31.3 34.7 26.1 31.1 33.3 30.4 28.2 32.5 28.5 26.8 33.3 27.0 34.8 27.6 30.5 31.9 29.7 30.6 31.2 27.4 30.4 35.7 42.1 26.8 30.7
25.4 27.8 32.1 29.7 23.2 30.8 22.5 38.3 35.1 33.3 26.1 34.1 24.6 33.3 35.8 24.6 28.1 19.4 34.3 35.7 20.3 25.7 37.7 32.4 28.3
17.9 15.3 16.2 16.2 15.9 14.6 22.5 4.5 9.8 15.1 15.9 12.2 13.0 14.5 10.7 15.9 20.3 22.2 11.3 12.2 18.8 12.9 9.2 19.7 13.4
25.4 22.2 25.6 23.0 27.5 24.1 26.8 24.7 26.6 24.9 24.6 26.7 27.5 24.6 23.0 27.5 21.9 27.8 23.1 24.7 30.4 25.7 10.9 21.1 27.7
base composition of the mitochondrial genome is 30.18% A, 31.88% C, 13.96% G, and 23.98% T with an A-T content of 54.17%. Among the 13 protein-coding genes, 9 genes including ND2, COX2, ATP8, ATP6, COX3, ND4L, ND4, Cyt b and ND6 start with common initiation ATG, the remaining COX1 and ND5 uses unusual initiation codon GTG, and ND1 uses ATA, ND3 utilized ATT. Three complete and general termination codons are used in 10 protein-coding genes (ND1, COX1, COX2, ATP8, ATP6, ND3, ND4L, ND5, Cyt b and ND6) and the remaining COX3 and ND4 have an incomplete termination codon ‘‘T’’, ND2 have an incomplete termination codon ‘‘TA’’. The 12S rRNA and 16S rRNA separated by the tRNAval are 962 and 1511 bp in length, respectively (Table 1). The control region of the Jacobin pigeon mtDNA is 1663 bp long. We expect that this genome sequence can serve as an important data set of the germplasm resources or evolutionary study (Khan & Arif, 2013).
Declaration of interest This work was supported by the Natural Science Foundation of Hebei Province, China (Grant number: C2015405016), Natural Science
Start codon
Stop codon
GTG
AGG
ATG
TAA
ATG ATG ATG
TAA TAA T––
ATT
TAA
ATG ATG
TAA T––
GTG ATG
AGA TAA
ATG
TAG
Strand L L H L H H H H H H H H H H H H H H H H H L L H
L
Research Key Programs of Educational Department of Hebei Province (Grant number: ZD20131045) and Key Programs of Hebei North University (Grant number: ZD201306). The authors declare no conflicts of interest.
References Kan XZ, Li XF, Zhang LQ, Chen L, Qian CJ, Zhang XW, Wang L. (2010). Characterization of the complete mitochondrial genome of the Rock pigeon, Columba livia (Columbiformes: Columbidae). Genet Mol Res 9:1234–49. Kan XZ, Yuan J, Zhang L, Li X, Yu L, Chen L, Guo ZC, Yang JK. (2013). Complete mitochondrial genome of the Tristram’s Bunting, Emberiza tristrami (Aves: Passeriformes): The first representative of the family Emberizidae with six boxes in the central conserved domain II of control region. Mitochondrial DNA 24:648–50. Khan HA, Arif IA. (2013). COI barcodes and phylogeny of doves (Columbidae family). Mitochondrial DNA 24:689–96. Levi WM. (1965). Encyclopedia of pigeon breeds. Sumter (SC): Levi Publishing. Levi WM. (1977). The pigeon. Sumter (SC): Levi Publishing. Shapiro MD, Kronenberg Z, Li C, Domyan ET, Pan H, Campbell M, Tan H, et al. (2013). Genomic diversity and evolution of the head crest in the Rock Pigeon. Science 339:1063–7.
