Volume 38 Issue 4
Jul.  2017
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Xun-He Huang, Gui-Mei Li, Xing Chen, Ya-Jiang Wu, Wei-Na Li, Fu-Sheng Zhong, Wen-Zhi Wang, Zhao-Li Ding. Identification of a novel mtDNA lineage B3 in chicken (Gallus gallus domesticus). Zoological Research, 2017, 38(4): 208-210. doi: 10.24272/j.issn.2095-8137.2017.039
Citation: Xun-He Huang, Gui-Mei Li, Xing Chen, Ya-Jiang Wu, Wei-Na Li, Fu-Sheng Zhong, Wen-Zhi Wang, Zhao-Li Ding. Identification of a novel mtDNA lineage B3 in chicken (Gallus gallus domesticus). Zoological Research, 2017, 38(4): 208-210. doi: 10.24272/j.issn.2095-8137.2017.039

Identification of a novel mtDNA lineage B3 in chicken (Gallus gallus domesticus)

doi: 10.24272/j.issn.2095-8137.2017.039
Funds:  This work was supported by the Guangdong Natural Science Foundation (2014A030307018),Science and Technology Planning Project of Guangdong Province (2016A030303068),and Animal Branch of the Germplasm Bank of Wild Species (GBOWS)
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  • Corresponding author: Zhao-Li Ding, dingzl@mail.kiz.ac.cn
  • Received Date: 2017-03-09
  • Rev Recd Date: 2017-04-28
  • Publish Date: 2017-07-18
  • In this study, we sequenced the complete mitochondrial DNA genome (mitogenome) of the Zhengyang Yellow chicken (Gallus gallus domesticus) by next-generation sequencing technology. Samples were taken from Zhumadian city, Henan Province, China. The complete mitogenome was 16 785 bp in size, and had a nucleotide composition of 30.3% (A), 23.7% (T), 32.5% (C), and 13.5% (G), with a high AT content of 54.0%. The assembled mitogenome exhibited typical mitochondrial DNA (mtDNA) structure, including a non-coding control region, two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. Phylogenetic analysis indicated that this mitogenome defined a novel sub-haplogroup B3 within haplogroup B. These results should provide essential information for chicken domestication and insight into the evolution of genomes.
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  • [1] Chen X, Ni G, He K, Ding ZL, Li GM, Adeola AC, Murphy RW, Wang WZ, Zhang YP. 2016. An improved de novo pipeline for enrichment of high diversity mitochondrial genomes from Amphibia to high-throughput sequencing. bioRxiv, doi:  10.1101/080689.
    [2] China National Commission of Animal Genetic Resources. 2011. Animal Genetic Resources in China Poultry. Beijing: China Agriculture Press. (in Chinese)
    [3] Huang XH, Zhong FS, Li WN, Chen JB, Zhang AX, Yao QF. 2016.Complete mitochondrial genome of the Wuhua three-yellow chicken (Gallus gallus domesticus). Mitochondrial DNA Part A, 27(2): 1311-1312.
    [4] Liu LL, Xie HB, Yang YS, Yu QF, He JH. 2016. The complete mitochondrial genome of the Xuefeng black-boned chicken. Mitochondrial DNA Part A, 27(1): 30-31.
    [5] Liu YP, Wu GS, Yao YG, Miao YW, Luikart G, Baig M, Beja-Pereira A, Ding ZL, Palanichamy MG, Zhang YP. 2006. Multiple maternal origins of chickens: out of the Asian jungles. Molecular Phylogenetics and Evolution, 38(1): 12-19.
    [6] Miao YW, Peng MS, Wu GS, Ouyang YN, Yang ZY, Yu N, Liang JP, Pianchou G, Beja-Pereira A, Mitra B, Palanichamy MG, Baig M, Chaudhuri TK, Shen YY, Kong QP, Murphy RW, Yao YG, Zhang YP. 2013. Chicken domestication: an updated perspective based on mitochondrial genomes.Heredity, 110(3): 277-282.
    [7] Nishibori M, Shimogiri T, Hayashi T, Yasue H. 2005. Molecular evidence for hybridization of species in the genus Gallus except for Gallus varius. Animal Genetics, 36(5): 367-375.
    [8] Peng MS, Fan L, Shi NN, Ning T, Yao YG, Murphy RW, Wang WZ, Zhang YP. 2015. DomeTree: a canonical toolkit for mitochondrial DNA analyses in domesticated animals. Molecular Ecology Resources, 15(5): 1238-1242.
    [9] Shi NN, Fan L, Yao YG, Peng MS, Zhang YP. 2014. Mitochondrial genomes of domestic animals need scrutiny. Molecular Ecology, 23(22):5393-5397.
    [10] Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011.MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods.
    [11] Molecular Biology and Evolution, 28(10): 2731-2739.
    [12] Thorvaldsdóttir H, Robinson JT, Mesirov JP. 2013. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Briefings in Bioinformatics, 14(2): 178-192.
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Identification of a novel mtDNA lineage B3 in chicken (Gallus gallus domesticus)

doi: 10.24272/j.issn.2095-8137.2017.039
Funds:  This work was supported by the Guangdong Natural Science Foundation (2014A030307018),Science and Technology Planning Project of Guangdong Province (2016A030303068),and Animal Branch of the Germplasm Bank of Wild Species (GBOWS)
    Corresponding author: Zhao-Li Ding, dingzl@mail.kiz.ac.cn

Abstract: In this study, we sequenced the complete mitochondrial DNA genome (mitogenome) of the Zhengyang Yellow chicken (Gallus gallus domesticus) by next-generation sequencing technology. Samples were taken from Zhumadian city, Henan Province, China. The complete mitogenome was 16 785 bp in size, and had a nucleotide composition of 30.3% (A), 23.7% (T), 32.5% (C), and 13.5% (G), with a high AT content of 54.0%. The assembled mitogenome exhibited typical mitochondrial DNA (mtDNA) structure, including a non-coding control region, two rRNA genes, 13 protein-coding genes, and 22 tRNA genes. Phylogenetic analysis indicated that this mitogenome defined a novel sub-haplogroup B3 within haplogroup B. These results should provide essential information for chicken domestication and insight into the evolution of genomes.

Xun-He Huang, Gui-Mei Li, Xing Chen, Ya-Jiang Wu, Wei-Na Li, Fu-Sheng Zhong, Wen-Zhi Wang, Zhao-Li Ding. Identification of a novel mtDNA lineage B3 in chicken (Gallus gallus domesticus). Zoological Research, 2017, 38(4): 208-210. doi: 10.24272/j.issn.2095-8137.2017.039
Citation: Xun-He Huang, Gui-Mei Li, Xing Chen, Ya-Jiang Wu, Wei-Na Li, Fu-Sheng Zhong, Wen-Zhi Wang, Zhao-Li Ding. Identification of a novel mtDNA lineage B3 in chicken (Gallus gallus domesticus). Zoological Research, 2017, 38(4): 208-210. doi: 10.24272/j.issn.2095-8137.2017.039
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