http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2015.1007308
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the ice pigeon (Columba livia breed ice) Rui-Hua Zhang1 and Wen-Xiao He2 1
Mitochondrial DNA Downloaded from informahealthcare.com by University Library Utrecht on 03/13/15 For personal use only.
Key Laboratory of Preventive Veterinary Medicine, Department of Veterinary Medicine, Animal Science College, Hebei North University, Zhangjiakou, PR China and 2Artillery Training Base of General Staff, Xuanhua, PR China
Abstract
Keywords
The ice pigeon is a breed of fancy pigeon developed over many years of selective breeding. In the present work, we report the complete mitochondrial genome sequence of ice pigeon for the first time. The total length of the mitogenome was 17,236 bp with the base composition of 30.2% for A, 24.0% for T, 31.9% for C, and 13.9% for G and an A-T (54.2 %)-rich feature was detected. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The arrangement of all genes was identical to the typical mitochondrial genomes of pigeon. The complete mitochondrial genome sequence of ice pigeon would serve as an important data set of the germplasm resources for further study.
Genome, ice pigeon (Columba livia), mitochondrion
The Ice Pigeon is a breed of fancy pigeon developed over many years of selective breeding (Levi, 1977). Ice Pigeons, 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). The breed is known and named for its ‘‘ice-blue’’ color. Due to the feather dust responsible for the Ice Pigeon’s unique coloration, they may not be suitable for people with allergies. 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.
History Received 23 December 2014 Accepted 30 December 2014 Published online 27 February 2015
Here, we reported an ice pigeon mitochondrial genome for the first time. The complete mitochondrial genome is 17,236 bp in size (GenBakn accession number KP306517, it is not due to release date) containing 37 genes coding for 13 typical proteincoding 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
Table 1. List of genes encoded by ice Pigeon mitochondrial genome. Position Gene
From Phe
tRNA 12SrRNA tRNAVal 16SrRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COX1
1 70 1043 1116 2705 2791 3774 3850 3920 3989 5029 5101 5172 5247 5313 5386
Base composition (%) To 69 1042 1115 2703 2778 3756 3844 3920 3988 5028 5099 5169 5244 5313 5384 6936
Size (bp)
A
C
G
T
69 973 73 1588 74 966 71 71 69 1040 71 69 73 67 72 1551
30.4 31.7 31.5 33.7 24.3 26.0 33.8 36.6 29.0 31.8 33.8 33.3 31.5 28.4 37.5 26.1
34.8 27.3 27.4 25.4 27.0 34.1 22.5 21.1 30.4 34.1 25.4 29.0 28.8 29.9 26.4 32.0
21.7 19.9 20.5 18.8 24.3 13.0 18.3 9.9 17.4 10.1 18.3 14.5 17.8 17.9 13.9 16.2
13.0 21.1 20.5 22.1 24.3 26.9 25.4 32.4 23.2 23.9 22.5 23.2 21.9 23.9 22.2 25.7
Start codon
Stop codon
ATG
AGA
ATG
TA–
GTG
AGG
Strand H H H H H H H L H H H L L L L H (continued )
Correspondence: Rui-Hua Zhang, Key Laboratory of Preventive Veterinary Medicine, Department of Veterinary Medicine, Animal Science College, Hebei North University, Zhangjiakou 075131, PR China. Tel/Fax:+ 86 313 4029336. E-mail: [email protected]
2
R.-H. Zhang & W.-X. He
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Position Gene
Mitochondrial DNA Downloaded from informahealthcare.com by University Library Utrecht on 03/13/15 For personal use only.
Ser
tRNA 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
6928 7004 7075 7760 7832 7990 8673 9457 9526 9879 9949 10,239 11,617 11,686 11,751 11,823 13,649 14,792 14,867 14,982 15,507 15,578
7001 7072 7758 7830 7999 8673 9456 9525 9877 9947 10,245 11,616 11,685 11,751 11,822 13,637 14,791 14,860 14,936 15,503 15,577 17,236
74 69 684 71 168 684 784 69 352 69 297 1378 69 66 72 1815 1143 69 70 522 71 1659
28.4 31.9 30.4 28.2 31.0 28.5 26.8 30.4 27.0 31.9 27.6 30.4 36.2 31.8 31.9 31.1 26.9 33.3 30.0 42.0 25.4 30.8
27.0 24.6 30.7 25.4 36.3 35.1 33.3 27.5 34.1 24.6 33.3 35.8 23.2 27.3 15.3 34.5 35.9 21.7 27.1 37.7 32.4 28.5
18.9 15.9 14.6 22.5 7.1 9.9 15.1 17.4 12.2 13.0 14.5 10.7 13.0 18.2 20.8 11.4 12.6 15.9 14.3 9.4 21.1 13.3
25.7 27.5 24.3 23.9 25.6 26.5 24.9 24.6 26.7 30.4 24.6 23.1 27.5 22.7 31.9 23.0 24.6 29.0 28.6 10.9 21.1 27.4
the heavy strand. The overall base composition of the mitochondrial genome is 30.2% A, 31.9% C, 13.9% G, and 24.0% T with an A-T content of 54.2%. Among the 13 protein-coding genes, 9 genes including ND2, COX2, ATP8, ATP6, COX3, ND4L, ND4, Cytb 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 973 and 1588 bp in length, respectively (Table 1). The control region of the ice pigeon mtDNA is 1659 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
ATG
TAA
ATG ATG ATG
TAA TAA T– –
ATT
TAA
ATG ATG
TAA T– –
GTG ATG
AGA TAA
ATG
TAG
Strand 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).
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. Mitochond DNA 24:648–50. Khan HA, Arif IA. (2013). COI barcodes and phylogeny of doves (Columbidae family). Mitochond 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 ice pigeon (Columba livia breed ice) Rui-Hua Zhang1 and Wen-Xiao He2 1
Mitochondrial DNA Downloaded from informahealthcare.com by University Library Utrecht on 03/13/15 For personal use only.
Key Laboratory of Preventive Veterinary Medicine, Department of Veterinary Medicine, Animal Science College, Hebei North University, Zhangjiakou, PR China and 2Artillery Training Base of General Staff, Xuanhua, PR China
Abstract
Keywords
The ice pigeon is a breed of fancy pigeon developed over many years of selective breeding. In the present work, we report the complete mitochondrial genome sequence of ice pigeon for the first time. The total length of the mitogenome was 17,236 bp with the base composition of 30.2% for A, 24.0% for T, 31.9% for C, and 13.9% for G and an A-T (54.2 %)-rich feature was detected. It harbored 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The arrangement of all genes was identical to the typical mitochondrial genomes of pigeon. The complete mitochondrial genome sequence of ice pigeon would serve as an important data set of the germplasm resources for further study.
Genome, ice pigeon (Columba livia), mitochondrion
The Ice Pigeon is a breed of fancy pigeon developed over many years of selective breeding (Levi, 1977). Ice Pigeons, 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). The breed is known and named for its ‘‘ice-blue’’ color. Due to the feather dust responsible for the Ice Pigeon’s unique coloration, they may not be suitable for people with allergies. 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.
History Received 23 December 2014 Accepted 30 December 2014 Published online 27 February 2015
Here, we reported an ice pigeon mitochondrial genome for the first time. The complete mitochondrial genome is 17,236 bp in size (GenBakn accession number KP306517, it is not due to release date) containing 37 genes coding for 13 typical proteincoding 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
Table 1. List of genes encoded by ice Pigeon mitochondrial genome. Position Gene
From Phe
tRNA 12SrRNA tRNAVal 16SrRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys tRNATyr COX1
1 70 1043 1116 2705 2791 3774 3850 3920 3989 5029 5101 5172 5247 5313 5386
Base composition (%) To 69 1042 1115 2703 2778 3756 3844 3920 3988 5028 5099 5169 5244 5313 5384 6936
Size (bp)
A
C
G
T
69 973 73 1588 74 966 71 71 69 1040 71 69 73 67 72 1551
30.4 31.7 31.5 33.7 24.3 26.0 33.8 36.6 29.0 31.8 33.8 33.3 31.5 28.4 37.5 26.1
34.8 27.3 27.4 25.4 27.0 34.1 22.5 21.1 30.4 34.1 25.4 29.0 28.8 29.9 26.4 32.0
21.7 19.9 20.5 18.8 24.3 13.0 18.3 9.9 17.4 10.1 18.3 14.5 17.8 17.9 13.9 16.2
13.0 21.1 20.5 22.1 24.3 26.9 25.4 32.4 23.2 23.9 22.5 23.2 21.9 23.9 22.2 25.7
Start codon
Stop codon
ATG
AGA
ATG
TA–
GTG
AGG
Strand H H H H H H H L H H H L L L L H (continued )
Correspondence: Rui-Hua Zhang, Key Laboratory of Preventive Veterinary Medicine, Department of Veterinary Medicine, Animal Science College, Hebei North University, Zhangjiakou 075131, PR China. Tel/Fax:+ 86 313 4029336. E-mail: [email protected]
2
R.-H. Zhang & W.-X. He
Mitochondrial DNA, Early Online: 1–2
Table 1. Continued.
Position Gene
Mitochondrial DNA Downloaded from informahealthcare.com by University Library Utrecht on 03/13/15 For personal use only.
Ser
tRNA 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
6928 7004 7075 7760 7832 7990 8673 9457 9526 9879 9949 10,239 11,617 11,686 11,751 11,823 13,649 14,792 14,867 14,982 15,507 15,578
7001 7072 7758 7830 7999 8673 9456 9525 9877 9947 10,245 11,616 11,685 11,751 11,822 13,637 14,791 14,860 14,936 15,503 15,577 17,236
74 69 684 71 168 684 784 69 352 69 297 1378 69 66 72 1815 1143 69 70 522 71 1659
28.4 31.9 30.4 28.2 31.0 28.5 26.8 30.4 27.0 31.9 27.6 30.4 36.2 31.8 31.9 31.1 26.9 33.3 30.0 42.0 25.4 30.8
27.0 24.6 30.7 25.4 36.3 35.1 33.3 27.5 34.1 24.6 33.3 35.8 23.2 27.3 15.3 34.5 35.9 21.7 27.1 37.7 32.4 28.5
18.9 15.9 14.6 22.5 7.1 9.9 15.1 17.4 12.2 13.0 14.5 10.7 13.0 18.2 20.8 11.4 12.6 15.9 14.3 9.4 21.1 13.3
25.7 27.5 24.3 23.9 25.6 26.5 24.9 24.6 26.7 30.4 24.6 23.1 27.5 22.7 31.9 23.0 24.6 29.0 28.6 10.9 21.1 27.4
the heavy strand. The overall base composition of the mitochondrial genome is 30.2% A, 31.9% C, 13.9% G, and 24.0% T with an A-T content of 54.2%. Among the 13 protein-coding genes, 9 genes including ND2, COX2, ATP8, ATP6, COX3, ND4L, ND4, Cytb 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 973 and 1588 bp in length, respectively (Table 1). The control region of the ice pigeon mtDNA is 1659 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
ATG
TAA
ATG ATG ATG
TAA TAA T– –
ATT
TAA
ATG ATG
TAA T– –
GTG ATG
AGA TAA
ATG
TAG
Strand 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).
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. Mitochond DNA 24:648–50. Khan HA, Arif IA. (2013). COI barcodes and phylogeny of doves (Columbidae family). Mitochond 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.
