Mitochondrial DNA The Journal of DNA Mapping, Sequencing, and Analysis
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Archangel pigeon Hua Wu, Bao-guang Liu, Gong-zheng Hu, Jian-hua Liu, Li Yuan & Yu-shan Pan To cite this article: Hua Wu, Bao-guang Liu, Gong-zheng Hu, Jian-hua Liu, Li Yuan & Yu-shan Pan (2014): The complete mitochondrial genome of Archangel pigeon, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.919479
Published online: 09 Jul 2014.
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Date: 06 November 2015, At: 22:45
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.919479
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Archangel pigeon Hua Wu1*, Bao-guang Liu1,2*, Gong-zheng Hu1, Jian-hua Liu1, Li Yuan1, and Yu-shan Pan1 College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, PR China and 2Department of Animal Husbandry and Veterinary, Tibetan Vocational and Technical College, Lhasa, Tibet, PR China
Downloaded by [NUS National University of Singapore] at 22:45 06 November 2015
1
Abstract
Keywords
The Archangel pigeon mitochondrial DNA has 17,235 bp and its structural organization is conserved compared to those of other birds. In this study, we report the basic characteristics of the Archangel mitochondrial genome, including structural organization and base composition of the rRNAs, tRNAs and protein-coding genes, as well as characteristics of tRNAs. These features are applicable for the study of phylogenetic relationships in pigeons.
Archangel pigeon, genome, mitochondrion
Pigeons were domesticated approximately 5000 years ago (Driscoll et al., 2009; Sossinka, 1982). They exhibited remarkable breed’s diversity, such as theatrical alterations in craniofacial formation, colors of plumage pigmentation, feather position and structure, vocalizations, flying capability, and several other characters (Levi, 1965; Price, 2002). The Archangel is a breed of fancy pigeon with remarkable metallic sheen of its feathers. The Archangel is a branch of descendants from the Rock Pigeon (Columba livia). Boasting the unusual appearance, it is always kept as an ornamental or fancy breed (Levi, 1965). Here, we reported Archangel pigeon mitochondrial genome for the first time. The complete mitochondrial DNA sequence of Archangel pigeon consisted of 17,235 bp and has been registered in GenBank with the accession number KJ722068. The structural organization of the complete mitogenome is shown in Table 1. It consisted two rRNAs, 22 tRNAs and 13 proteincoding genes with a control region and the overall characteristics including mitochondrial genome organization and gene arrangement pattern are identical to those of other birds (Kan et al., 2010; Khan & Arif, 2013). As expected, most coding genes as well as tRNAs and rRNAs are encoded on the H strand, although the ND6 gene and eight tRNA genes are encoded on the L strand. Of the 13 protein-coding genes of Archangel mtDNA. The genes in the Archangel mitogenome are in the same order as other vertebrates and no structural abnormalities were observed. The 12S and 16S ribosomal RNA genes contained 962 and 1507 bp, respectively. These genes are located between tRNAPhe and tRNALeu genes and are future separated by the gene tRNAVal. The start and stop codons of the 13 protein-coding genes in the Archangel mitogenome are
*These two authors contributed equally to this work. Correspondence: Hua Wu, College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou 450002, PR China. E-mail: [email protected]
History Received 19 April 2014 Accepted 26 April 2014 Published online 9 July 2014
Table 1. List of genes encoded by Archangel pigeon mitochondrial genome. Position Gene
From
To
Size (bp)
tRNAPhe 12S rRNA tRNAVal 16S rRNA 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
1 70 1043 1153 2701 2786 3769 3845 3915 3984 5024 5096 5167 5242 5308 5381 6923 6999 7070 7755 7827 7985 8668 9452 9521 9874 9944 10,234 11,612 11,683 11,746 11,818 13,644 14,787 14,862 14,980 15,502 15,573
69 1031 1114 2659 2774 3751 3839 3915 3983 5024 5094 5164 5239 5308 5379 6931 6996 7067 7753 7825 7994 8668 9451 9520 9872 9942 10,240 11,611 11,680 11,746 11,817 13,632 14,786 14,855 14,931 15,498 15,572 17,235
69 962 72 1507 74 966 71 71 69 1041 71 69 73 67 72 1551 74 69 684 71 168 684 784 69 351 69 297 1378 69 64 72 1815 1143 69 70 519 71 1663
Base composition (%) A
C
G
29.0 31.2 31.9 33.6 24.3 25.9 32.4 29.6 29.0 32.0 35.2 26.1 20.6 23.9 22.2 26.1 24.3 34.8 30.6 29.6 32.1 28.2 26.5 31.9 26.8 33.9 27.6 30.6 34.8 29.7 34.7 31.2 27.5 31.9 25.7 10.8 22.5 30.7
34.8 27.4 27.8 24.7 25.7 34.1 22.5 9.9 30.4 34.0 25.4 15.9 17.8 16.4 15.3 32.0 17.6 21.7 30.8 23.9 38.7 35.1 33.3 24.6 34.2 23.2 33.3 35.8 23.2 28.1 18.0 34.4 35.8 21.7 12.9 9.2 21.1 27.5
23.2 20.3 19.5 19.1 24.3 13.0 19.7 22.5 18.8 10.1 16.9 26.1 31.5 28.4 26.4 16.2 28.4 16.0 14.5 21.1 5.4 10.1 15.3 17.4 12.2 15.9 14.5 10.5 14.5 18.8 18.1 11.3 12.1 17.4 27.1 37.8 31.0 14.1
T
Start Stop codon codon Strand
13.0 21.1 20.8 22.6 25.7 27.0 ATG AGA 25.4 38.0 21.8 ATG TAA 23.9 22.5 31.9 30.1 31.3 36.1 25.7 GTG AGG 29.7 27.5 24.1 ATG TAA 25.4 23.8 ATG TAA 26.6 ATG TAA 24.9 ATG T– – 26.1 26.8 ATT TAA 29.0 24.6 ATG TAA 23.1 ATG T– – 27.5 23.4 29.2 23.1 GTG AGA 24.6 ATG TAA 29.0 34.3 42.2 ATG GTG 25.4 27.7
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
2
H. Wu et al.
shown in Table 1. All of the 13 protein-coding genes have three different start codons. However, the termination codons were of five different ends (Table 1). The Archangel mitogenome contains 22 tRNA genes (Table 1) which are interspersed along the genome and folded into the expected cloverleaf secondary structures with normal base pairing. The control region of the Archangel mitogenome was found to be 1663 bp, which is longer than those of other vertebrates. These features are applicable for the study of phylogenetic relationships in pigeons.
Declaration of interest
Downloaded by [NUS National University of Singapore] at 22:45 06 November 2015
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
Mitochondrial DNA, Early Online: 1–2
References Driscoll CA, Macdonald DW, O’Brien SJ. (2009). From wild animals to domestic pets, an evolutionary view of domestication. Proc Natl Acad Sci USA 106:9971–8. 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. Khan HA, Arif IA. (2013). COI barcodes and phylogeny of doves (Columbidae family). Mitochondrial DNA 24:1–2. Levi WM. (1965). Encyclopedia of pigeon breeds. Sumter, SC: Levi Publishing. Price TD. (2002). Domesticated birds as a model for the genetics of speciation by sexual selection. Genetica 116:311–27. Sossinka R. (1982). Domestication in birds. Volume 6. In: Farner DS, King AS, Parkes KC, editors. Avian Biology. London: Academic Press. p. 373–403.
ISSN: 1940-1736 (Print) 1940-1744 (Online) Journal homepage: http://www.tandfonline.com/loi/imdn20
The complete mitochondrial genome of Archangel pigeon Hua Wu, Bao-guang Liu, Gong-zheng Hu, Jian-hua Liu, Li Yuan & Yu-shan Pan To cite this article: Hua Wu, Bao-guang Liu, Gong-zheng Hu, Jian-hua Liu, Li Yuan & Yu-shan Pan (2014): The complete mitochondrial genome of Archangel pigeon, Mitochondrial DNA To link to this article: http://dx.doi.org/10.3109/19401736.2014.919479
Published online: 09 Jul 2014.
Submit your article to this journal
Article views: 33
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=imdn20 Download by: [NUS National University of Singapore]
Date: 06 November 2015, At: 22:45
http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2014 Informa UK Ltd. DOI: 10.3109/19401736.2014.919479
MITOGENOME ANNOUNCEMENT
The complete mitochondrial genome of Archangel pigeon Hua Wu1*, Bao-guang Liu1,2*, Gong-zheng Hu1, Jian-hua Liu1, Li Yuan1, and Yu-shan Pan1 College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, PR China and 2Department of Animal Husbandry and Veterinary, Tibetan Vocational and Technical College, Lhasa, Tibet, PR China
Downloaded by [NUS National University of Singapore] at 22:45 06 November 2015
1
Abstract
Keywords
The Archangel pigeon mitochondrial DNA has 17,235 bp and its structural organization is conserved compared to those of other birds. In this study, we report the basic characteristics of the Archangel mitochondrial genome, including structural organization and base composition of the rRNAs, tRNAs and protein-coding genes, as well as characteristics of tRNAs. These features are applicable for the study of phylogenetic relationships in pigeons.
Archangel pigeon, genome, mitochondrion
Pigeons were domesticated approximately 5000 years ago (Driscoll et al., 2009; Sossinka, 1982). They exhibited remarkable breed’s diversity, such as theatrical alterations in craniofacial formation, colors of plumage pigmentation, feather position and structure, vocalizations, flying capability, and several other characters (Levi, 1965; Price, 2002). The Archangel is a breed of fancy pigeon with remarkable metallic sheen of its feathers. The Archangel is a branch of descendants from the Rock Pigeon (Columba livia). Boasting the unusual appearance, it is always kept as an ornamental or fancy breed (Levi, 1965). Here, we reported Archangel pigeon mitochondrial genome for the first time. The complete mitochondrial DNA sequence of Archangel pigeon consisted of 17,235 bp and has been registered in GenBank with the accession number KJ722068. The structural organization of the complete mitogenome is shown in Table 1. It consisted two rRNAs, 22 tRNAs and 13 proteincoding genes with a control region and the overall characteristics including mitochondrial genome organization and gene arrangement pattern are identical to those of other birds (Kan et al., 2010; Khan & Arif, 2013). As expected, most coding genes as well as tRNAs and rRNAs are encoded on the H strand, although the ND6 gene and eight tRNA genes are encoded on the L strand. Of the 13 protein-coding genes of Archangel mtDNA. The genes in the Archangel mitogenome are in the same order as other vertebrates and no structural abnormalities were observed. The 12S and 16S ribosomal RNA genes contained 962 and 1507 bp, respectively. These genes are located between tRNAPhe and tRNALeu genes and are future separated by the gene tRNAVal. The start and stop codons of the 13 protein-coding genes in the Archangel mitogenome are
*These two authors contributed equally to this work. Correspondence: Hua Wu, College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou 450002, PR China. E-mail: [email protected]
History Received 19 April 2014 Accepted 26 April 2014 Published online 9 July 2014
Table 1. List of genes encoded by Archangel pigeon mitochondrial genome. Position Gene
From
To
Size (bp)
tRNAPhe 12S rRNA tRNAVal 16S rRNA 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
1 70 1043 1153 2701 2786 3769 3845 3915 3984 5024 5096 5167 5242 5308 5381 6923 6999 7070 7755 7827 7985 8668 9452 9521 9874 9944 10,234 11,612 11,683 11,746 11,818 13,644 14,787 14,862 14,980 15,502 15,573
69 1031 1114 2659 2774 3751 3839 3915 3983 5024 5094 5164 5239 5308 5379 6931 6996 7067 7753 7825 7994 8668 9451 9520 9872 9942 10,240 11,611 11,680 11,746 11,817 13,632 14,786 14,855 14,931 15,498 15,572 17,235
69 962 72 1507 74 966 71 71 69 1041 71 69 73 67 72 1551 74 69 684 71 168 684 784 69 351 69 297 1378 69 64 72 1815 1143 69 70 519 71 1663
Base composition (%) A
C
G
29.0 31.2 31.9 33.6 24.3 25.9 32.4 29.6 29.0 32.0 35.2 26.1 20.6 23.9 22.2 26.1 24.3 34.8 30.6 29.6 32.1 28.2 26.5 31.9 26.8 33.9 27.6 30.6 34.8 29.7 34.7 31.2 27.5 31.9 25.7 10.8 22.5 30.7
34.8 27.4 27.8 24.7 25.7 34.1 22.5 9.9 30.4 34.0 25.4 15.9 17.8 16.4 15.3 32.0 17.6 21.7 30.8 23.9 38.7 35.1 33.3 24.6 34.2 23.2 33.3 35.8 23.2 28.1 18.0 34.4 35.8 21.7 12.9 9.2 21.1 27.5
23.2 20.3 19.5 19.1 24.3 13.0 19.7 22.5 18.8 10.1 16.9 26.1 31.5 28.4 26.4 16.2 28.4 16.0 14.5 21.1 5.4 10.1 15.3 17.4 12.2 15.9 14.5 10.5 14.5 18.8 18.1 11.3 12.1 17.4 27.1 37.8 31.0 14.1
T
Start Stop codon codon Strand
13.0 21.1 20.8 22.6 25.7 27.0 ATG AGA 25.4 38.0 21.8 ATG TAA 23.9 22.5 31.9 30.1 31.3 36.1 25.7 GTG AGG 29.7 27.5 24.1 ATG TAA 25.4 23.8 ATG TAA 26.6 ATG TAA 24.9 ATG T– – 26.1 26.8 ATT TAA 29.0 24.6 ATG TAA 23.1 ATG T– – 27.5 23.4 29.2 23.1 GTG AGA 24.6 ATG TAA 29.0 34.3 42.2 ATG GTG 25.4 27.7
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
2
H. Wu et al.
shown in Table 1. All of the 13 protein-coding genes have three different start codons. However, the termination codons were of five different ends (Table 1). The Archangel mitogenome contains 22 tRNA genes (Table 1) which are interspersed along the genome and folded into the expected cloverleaf secondary structures with normal base pairing. The control region of the Archangel mitogenome was found to be 1663 bp, which is longer than those of other vertebrates. These features are applicable for the study of phylogenetic relationships in pigeons.
Declaration of interest
Downloaded by [NUS National University of Singapore] at 22:45 06 November 2015
The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
Mitochondrial DNA, Early Online: 1–2
References Driscoll CA, Macdonald DW, O’Brien SJ. (2009). From wild animals to domestic pets, an evolutionary view of domestication. Proc Natl Acad Sci USA 106:9971–8. 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. Khan HA, Arif IA. (2013). COI barcodes and phylogeny of doves (Columbidae family). Mitochondrial DNA 24:1–2. Levi WM. (1965). Encyclopedia of pigeon breeds. Sumter, SC: Levi Publishing. Price TD. (2002). Domesticated birds as a model for the genetics of speciation by sexual selection. Genetica 116:311–27. Sossinka R. (1982). Domestication in birds. Volume 6. In: Farner DS, King AS, Parkes KC, editors. Avian Biology. London: Academic Press. p. 373–403.
