http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, 2015; 26(1): 162–163 ! 2015 Informa UK Ltd. DOI: 10.3109/19401736.2014.1003851
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of the Fancy Pigeon, Columba livia (Columbiformes: Columbidae) Rui-Hua Zhang, Ming-Ju Xu, Cun-Lian Wang, Tong Xu, Dong Wei, Bao-Jian Liu, and Guo-Hua Wang
Mitochondrial DNA Downloaded from informahealthcare.com by Yale Dermatologic Surgery on 05/14/15 For personal use only.
Department of Veterinary Medicine, Key Laboratory of Preventive Veterinary Medicine, Animal Science College, Hebei North University, Zhangjiakou, PR China Abstract
Keywords
The fancy pigeons are domesticated varieties of the rock pigeon developed over many years of selective breeding. In the present work, we report the complete mitochondrial genome sequence of fancy pigeon for the first time. The total length of the mitogenome was 17,233 bp with the base composition of 30.1% for A, 24.0% for T, 31.9% for C, and 14.0% 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 fancy pigeon would serve as an important data set of the germplasm resources for further study.
Fancy Pigeon (Columba livia), genome, mitochondrion
The fancy pigeons are domesticated varieties of the rock pigeon (Columba livia), which is a member of the bird family Columbidae. The rock pigeon includes the domestic pigeon, the feral pigeon, and the wild Rock pigeon. This species has been domesticated for several thousand years, giving rise to the domestic pigeon. Many domestic birds have escaped or have been released over the years, and have given rise to the feral pigeon. Feral pigeons are descendants of wild rock pigeons that have adapted to the urban habitat. 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 fancy pigeon mitochondrial genome for the first time. The complete mitochondrial genome is 17,233 bp in size (GenBank accession number KP168712, it is not due to the 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
History Received 24 November 2014 Accepted 5 December 2014 Published online 28 January 2015
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 base composition of the mitochondrial genome is 30.1% A, 31.9% C, 14.0% 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 1589 bp in length, respectively (Table 1). The control region of the fancy pigeon mtDNA is 1657 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).
Correspondence: Tong Xu, Animal Science College, Hebei North University, Zhangjiakou 075131, PR China. Tel/Fax: + 86 313 4029336. E-mail: [email protected]
Mitogenome of the Fancy Pigeon
DOI: 10.3109/19401736.2014.1003851
163
Table 1. List of genes encoded by fancy Pigeon mitochondrial genome. Position Gene
Mitochondrial DNA Downloaded from informahealthcare.com by Yale Dermatologic Surgery on 05/14/15 For personal use only.
Phe
tRNA 12SrRNA tRNAVal 16SrRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys 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
1 70 1043 1116 2705 2790 3773 3849 3919 3988 5028 5100 5171 5246 5312 5385 6927 7003 7074 7759 7831 7989 8672 9456 9525 9878 9948 10,238 11,616 11,685 11,750 11,822 13,648 14,791 14,862 14,981 15,506 15,577
69 1042 1115 2704 2778 3755 3843 3919 3987 5027 5098 5168 5243 5312 5383 6935 7000 7071 7757 7829 7998 8672 9455 9524 9876 9946 10,244 11,615 11,684 11,750 11,821 13,636 14,790 14,859 14,931 15,502 15,576 17,233
69 973 73 1589 74 966 71 71 69 1040 71 69 73 67 72 1551 74 69 684 71 168 684 784 69 352 69 297 1378 69 66 72 1815 1143 69 70 522 71 1657
30.0 31.6 32.9 33.7 24.3 30.0 32.4 38.0 30.0 31.6 33.8 31.9 30.1 29.9 36.1 26.0 30.0 34.8 30.3 29.6 32.1 28.7 26.7 31.9 27.0 31.9 27.6 30.3 34.8 30.3 33.3 31.1 26.9 31.9 32.9 42.0 25.4 30.8
34.8 27.5 24.7 25.7 25.7 33.0 22.5 22.5 30.4 34.0 25.4 26.1 31.5 28.4 26.4 32.0 28.4 21.7 30.6 23.9 38.7 35.2 33.4 24.6 34.1 23.2 33.3 35.8 23.2 27.3 18.1 34.4 36.0 21.7 27.1 37.7 31.0 28.4
23.2 19.8 19.2 18.9 24.3 13.0 19.7 10.0 18.8 10.3 18.3 15.9 17.8 17.9 15.3 16.2 17.6 15.9 14.6 21.1 5.4 9.7 15.1 17.4 12.2 15.9 14.5 10.7 14.5 19.7 19.4 11.4 12.6 17.4 14.3 9.4 21.1 13.4
13.0 21.1 23.3 21.6 25.7 27.0 25.4 29.6 21.7 24.0 22.5 26.1 24.7 23.9 22.2 25.7 24.3 27.5 24.6 25.4 23.8 26.5 24.9 26.1 26.7 30.0 24.6 23.3 27.5 22.7 29.2 23.1 24.4 29.0 25.7 10.9 22.5 27.4
Declaration of interest This work was supported by the Natural Science 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
Start codon
Stop codon
ATG
AGA
ATG
TA–
GTG
AGG
ATG
TAA
ATG ATG ATG
TAA TAA T– –
ATT
TAA
ATG ATG
TAA T– –
GTG ATG
AGA TAA
ATG
TAG
Strand H H H H H H H L H H H L L L L H L H H H H H H H H H H H H H H H H H L L L H
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. 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 Fancy Pigeon, Columba livia (Columbiformes: Columbidae) Rui-Hua Zhang, Ming-Ju Xu, Cun-Lian Wang, Tong Xu, Dong Wei, Bao-Jian Liu, and Guo-Hua Wang
Mitochondrial DNA Downloaded from informahealthcare.com by Yale Dermatologic Surgery on 05/14/15 For personal use only.
Department of Veterinary Medicine, Key Laboratory of Preventive Veterinary Medicine, Animal Science College, Hebei North University, Zhangjiakou, PR China Abstract
Keywords
The fancy pigeons are domesticated varieties of the rock pigeon developed over many years of selective breeding. In the present work, we report the complete mitochondrial genome sequence of fancy pigeon for the first time. The total length of the mitogenome was 17,233 bp with the base composition of 30.1% for A, 24.0% for T, 31.9% for C, and 14.0% 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 fancy pigeon would serve as an important data set of the germplasm resources for further study.
Fancy Pigeon (Columba livia), genome, mitochondrion
The fancy pigeons are domesticated varieties of the rock pigeon (Columba livia), which is a member of the bird family Columbidae. The rock pigeon includes the domestic pigeon, the feral pigeon, and the wild Rock pigeon. This species has been domesticated for several thousand years, giving rise to the domestic pigeon. Many domestic birds have escaped or have been released over the years, and have given rise to the feral pigeon. Feral pigeons are descendants of wild rock pigeons that have adapted to the urban habitat. 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 fancy pigeon mitochondrial genome for the first time. The complete mitochondrial genome is 17,233 bp in size (GenBank accession number KP168712, it is not due to the 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
History Received 24 November 2014 Accepted 5 December 2014 Published online 28 January 2015
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 base composition of the mitochondrial genome is 30.1% A, 31.9% C, 14.0% 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 1589 bp in length, respectively (Table 1). The control region of the fancy pigeon mtDNA is 1657 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).
Correspondence: Tong Xu, Animal Science College, Hebei North University, Zhangjiakou 075131, PR China. Tel/Fax: + 86 313 4029336. E-mail: [email protected]
Mitogenome of the Fancy Pigeon
DOI: 10.3109/19401736.2014.1003851
163
Table 1. List of genes encoded by fancy Pigeon mitochondrial genome. Position Gene
Mitochondrial DNA Downloaded from informahealthcare.com by Yale Dermatologic Surgery on 05/14/15 For personal use only.
Phe
tRNA 12SrRNA tRNAVal 16SrRNA tRNALeu ND1 tRNAIle tRNAGln tRNAMet ND2 tRNATrp tRNAAla tRNAAsn tRNACys 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
1 70 1043 1116 2705 2790 3773 3849 3919 3988 5028 5100 5171 5246 5312 5385 6927 7003 7074 7759 7831 7989 8672 9456 9525 9878 9948 10,238 11,616 11,685 11,750 11,822 13,648 14,791 14,862 14,981 15,506 15,577
69 1042 1115 2704 2778 3755 3843 3919 3987 5027 5098 5168 5243 5312 5383 6935 7000 7071 7757 7829 7998 8672 9455 9524 9876 9946 10,244 11,615 11,684 11,750 11,821 13,636 14,790 14,859 14,931 15,502 15,576 17,233
69 973 73 1589 74 966 71 71 69 1040 71 69 73 67 72 1551 74 69 684 71 168 684 784 69 352 69 297 1378 69 66 72 1815 1143 69 70 522 71 1657
30.0 31.6 32.9 33.7 24.3 30.0 32.4 38.0 30.0 31.6 33.8 31.9 30.1 29.9 36.1 26.0 30.0 34.8 30.3 29.6 32.1 28.7 26.7 31.9 27.0 31.9 27.6 30.3 34.8 30.3 33.3 31.1 26.9 31.9 32.9 42.0 25.4 30.8
34.8 27.5 24.7 25.7 25.7 33.0 22.5 22.5 30.4 34.0 25.4 26.1 31.5 28.4 26.4 32.0 28.4 21.7 30.6 23.9 38.7 35.2 33.4 24.6 34.1 23.2 33.3 35.8 23.2 27.3 18.1 34.4 36.0 21.7 27.1 37.7 31.0 28.4
23.2 19.8 19.2 18.9 24.3 13.0 19.7 10.0 18.8 10.3 18.3 15.9 17.8 17.9 15.3 16.2 17.6 15.9 14.6 21.1 5.4 9.7 15.1 17.4 12.2 15.9 14.5 10.7 14.5 19.7 19.4 11.4 12.6 17.4 14.3 9.4 21.1 13.4
13.0 21.1 23.3 21.6 25.7 27.0 25.4 29.6 21.7 24.0 22.5 26.1 24.7 23.9 22.2 25.7 24.3 27.5 24.6 25.4 23.8 26.5 24.9 26.1 26.7 30.0 24.6 23.3 27.5 22.7 29.2 23.1 24.4 29.0 25.7 10.9 22.5 27.4
Declaration of interest This work was supported by the Natural Science 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
Start codon
Stop codon
ATG
AGA
ATG
TA–
GTG
AGG
ATG
TAA
ATG ATG ATG
TAA TAA T– –
ATT
TAA
ATG ATG
TAA T– –
GTG ATG
AGA TAA
ATG
TAG
Strand H H H H H H H L H H H L L L L H L H H H H H H H H H H H H H H H H H L L L H
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. 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.
