Characterisation of the complete mitochondrial genome, genetic diversity and maternal origin of Huainan Partridge chicken

References

• Al-Jumaili, A. S., S. F. Boudali, A. Kebede, S. A. Al-Bayatti, A. A. Essa, A. Ahbara, R. S. Aljumaah, et al. 2020. “The Maternal Origin of Indigenous Domestic Chicken from the Middle East, the North and the Horn of Africa.” BMC Genetics 21 (1): 30. doi:10.1186/s12863-020-0830-0.
   PubMed Web of Science ®Google Scholar
• Allio, R., S. Donega, N. Galtier, and B. Nabholz. 2017. “Large Variation in the Ratio of Mitochondrial to Nuclear Mutation Rate across Animals: Implications for Genetic Diversity and the Use of Mitochondrial DNA as a Molecular Marker.” Molecular Biology and Evolution 34 (11): 2762–2772. doi:10.1093/molbev/msx197.
   PubMed Web of Science ®Google Scholar
• Anderson, S., A. T. Bankier, B. G. Barrell, M. H. De Bruijn, A. R. Coulson, J. Drouin, I. C. Eperon, et al. 1981. “Sequence and Organization of the Human Mitochondrial Genome.” Nature 290 (5806): 457–565. doi:10.1038/290457a0.
   PubMed Web of Science ®Google Scholar
• Avise, J. C. 2000. Phylogeography: The History and Formation of Species, 447. Cambridge: Harvard University Press.
   Google Scholar
• Bandelt, H. J., P. Forster, and A. Rohl. 1999. “Median-joining Networks for Inferring Intraspecific Phylogenies.” Molecular Biology and Evolution 16 (1): 37–48. doi:10.1093/oxfordjournals.molbev.a026036.
   PubMed Web of Science ®Google Scholar
• Bao, W. B., J. T. Shu, X. S. Wu, H. H. Musa, and G. H. Chen. 2009. “Genetic Diversity and Relationship between Genetic Distance and Geographical Distance in 14 Chinese Indigenous Chicken Breeds and Red Jungle Fowl.” Czech Journal of Animal Science 54 (2): 74–83. doi:10.17221/1666-CJAS.
   Web of Science ®Google Scholar
• Chan, P. P., and T. M. Lowe. 2019. “tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences.” Methods in Molecular Biology 1962: 1–14. doi:10.1007/978-1-4939-9173-0_1.
   PubMedGoogle Scholar
• Gao, Y. S., X. X. Jia, X. J. Tang, Y. F. Fan, J. X. Lu, S. H. Huang, and M. J. Tang. 2017. “The Genetic Diversity of Chicken Breeds from Jiangxi, Assessed with BCDO2 and the Complete Mitochondrial DNA D-loop Region.” PLoS One 12 (3): e0173192. doi:10.1371/journal.pone.0173192.
   PubMed Web of Science ®Google Scholar
• Guo, H. W., C. Li, X. N. Wang, Z. J. Li, G. R. Sun, G. X. Li, X. J. Liu, X. T. Kang, and R. L. Han. 2017. “Genetic Diversity of mtDNA D-loop Sequences in Four Native Chinese Chicken Breeds.” British Poultry Science 58 (5): 490–497. doi:10.1080/00071668.2017.1332403.
   PubMed Web of Science ®Google Scholar
• Gyllensten, U., D. Wharton, A. Josefsson, and A. C. Wilson. 1991. “Paternal Inheritance of Mitochondrial DNA in Mice.” Nature 352 (6332): 255–257. doi:10.1038/352255a0.
   PubMed Web of Science ®Google Scholar
• Halima, H., F. W. Neser, E. Van Marle-Koster, and A. De Kock. 2007. “Village-based Indigenous Chicken Production System in North-west Ethiopia.” Tropical Animal Health and Production 39 (3): 189–197. doi:10.1007/s11250-007-9004-6.
   PubMed Web of Science ®Google Scholar
• Herrera, M. B., S. Kraitsek, J. A. Alcalde, D. Quiroz, H. Revelo, L. A. Alvarez, M. F. Rosario, et al. 2020. “European and Asian Contribution to the Genetic Diversity of Mainland South American Chickens.” Royal Society Open Science 7 (2): 191558. doi:10.1098/rsos.191558.
   PubMed Web of Science ®Google Scholar
• Jia, X. X., J. X. Lu, X. J. Tang, Y. F. Fan, S. H. Huang, Q. L. Ge, and Y. S. Gao. 2018. “Genetic Diversity of Jiangsu Native Chicken Breeds Assessed with the Mitochondrial DNA D-loop Region.” British Poultry Science 59 (1): 34–39. doi:10.1080/00071668.2017.1395391.
   PubMed Web of Science ®Google Scholar
• Jiang, L., L. Peng, M. Tang, Z. You, M. Zhang, A. West, Q. Ruan, W. Chen, and J. Merila. 2019. “Complete Mitochondrial Genome Sequence of the Himalayan Griffon, Gyps Himalayensis (Accipitriformes: Accipitridae): Sequence, Structure, and Phylogenetic Analyses.” Ecology and Evolution 9 (15): 8813–8828. doi:10.1002/ece3.5433.
   PubMed Web of Science ®Google Scholar
• Kumar, S., G. Stecher, and K. Tamura. 2016. “Mega7: Molecular Evolutionary Genetics Analysis Version 7.0 For Bigger Datasets.” Molecular Biology and Evolution 33 (7): 1870–1874. doi:10.1093/molbev/msw054.
   PubMed Web of Science ®Google Scholar
• Labuschagne, C., A. Kotze, J. P. Grobler, and D. L. Dalton. 2014. “The Complete Sequence of the Mitochondrial Genome of the African Penguin (Spheniscus Demersus).” Gene 534 (1): 113–118. doi:10.1016/j.gene.2013.09.057.
   PubMed Web of Science ®Google Scholar
• Larkin, M. A., G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, et al. 2007. “Clustal W and Clustal X Version 2.0.” Bioinformatics 23 (21): 2947–2948. doi:10.1093/bioinformatics/btm404.
   PubMed Web of Science ®Google Scholar
• Lawal, R. A., R. M. Al-Atiyat, R. S. Aljumaah, P. Silva, J. M. Mwacharo, and O. Hanotte. 2018. “Whole-genome Resequencing of Red Junglefowl and Indigenous Village Chicken Reveal New Insights on the Genome Dynamics of the Species.” Frontiers in Genetics 9: 264. doi:10.3389/fgene.2018.00264.
   PubMed Web of Science ®Google Scholar
• Lawal, R. A., S. H. Martin, K. Vanmechelen, A. Vereijken, P. Silva, R. M. Al-Atiyat, R. S. Aljumaah, et al. 2020. “The Wild Species Genome Ancestry of Domestic Chickens.” BMC Biology 18 (1): 13. doi:10.1186/s12915-020-0738-1.
   PubMed Web of Science ®Google Scholar
• Li, Q., Q. Wang, X. Jin, Z. Chen, C. Xiong, P. Li, J. Zhao, and W. Huang. 2019. “The First Complete Mitochondrial Genome from the Family Hygrophoraceae (Hygrophorus Russula) by Next-generation Sequencing and Phylogenetic Implications.” International Journal of Biological Macromolecules 122: 1313–1320. doi:10.1016/j.ijbiomac.2018.09.091.
   PubMed Web of Science ®Google Scholar
• Liao, Y., G. Mo, J. Sun, F. Wei, and D. J. Liao. 2016. “Genetic Diversity of Guangxi Chicken Breeds Assessed with Microsatellites and the Mitochondrial DNA D-loop Region.” Molecular Biology Reports 43 (5): 415–425. doi:10.1007/s11033-016-3976-0.
   PubMed Web of Science ®Google Scholar
• Liu, Y. P., G. S. Wu, Y. G. Yao, Y. W. Miao, G. Luikart, M. Baig, A. Beja-Pereira, Z. L. Ding, M. G. Palanichamy, and Y. P. Zhang. 2006. “Multiple Maternal Origins of Chickens: Out of the Asian Jungles.” Molecular Phylogenetics and Evolution 38 (1): 12–19. doi:10.1016/j.ympev.2005.09.014.
   PubMed Web of Science ®Google Scholar
• Lohse, M., O. Drechsel, S. Kahlau, and R. Bock. 2013. “Organellargenomedraw—a Suite of Tools for Generating Physical Maps of Plastid and Mitochondrial Genomes and Visualizing Expression Data Sets.” Nucleic Acids Research 41 (W1): W575–W581. doi:10.1093/nar/gkt289.
   PubMed Web of Science ®Google Scholar
• Lorenzo, D. I., P., . S. Ceccobelli, F. Panella, G. Attard, and E. Lasagna. 2015. “The Role of Mitochondrial DNA to Determine the Origin of Domestic Chicken.” World’s Poultry Science Journal 71 (2): 311–318. doi:10.1017/S0043933915000318.
   Web of Science ®Google Scholar
• Miao, Y. W., M. S. Peng, G. S. Wu, Y. N. Ouyang, Z. Y. Yang, N. Yu, J. P. Liang, et al. 2013. “Chicken Domestication: An Updated Perspective Based on Mitochondrial Genomes.” Heredity 110 (3): 277–282. doi:10.1038/hdy.2012.83.
   PubMed Web of Science ®Google Scholar
• Mtileni, B. J., F. C. Muchadeyi, A. Maiwashe, E. Groeneveld, L. F. Groeneveld, K. Dzama, and S. Weigend. 2011. “Genetic Diversity and Conservation of South African Indigenous Chicken Populations.” Journal of Animal Breeding and Genetics 128 (3): 209–218. doi:10.1111/j.1439-0388.2010.00891.x.
   PubMed Web of Science ®Google Scholar
• Mukundan, L. P., S. Sukumaran, W. Sebastian, and A. Gopalakrishnan. 2020. “Characterization of the Whole Mitogenome of Largehead Hairtail Trichiurus Lepturus (Trichiuridae): Insights into Special Characteristics.” Biochemical Genetics 58 (3): 430–451. doi:10.1007/s10528-020-09956-z.
   PubMed Web of Science ®Google Scholar
• Ojala, D., J. Montoya, and G. Attardi. 1981. “tRNA Punctuation Model of Rna Processing in Human Mitochondria.” Nature 290 (5806): 470–474. doi:10.1038/290470a0.
   PubMed Web of Science ®Google Scholar
• Osman, S. A., T. Yonezawa, and M. Nishibori. 2016. “Origin and Genetic Diversity of Egyptian Native Chickens Based on Complete Sequence of Mitochondrial DNA D-loop Region.” Poultry Science 95 (6): 1248–1256. doi:10.3382/ps/pew029.
   PubMed Web of Science ®Google Scholar
• Perna, N. T., and T. D. Kocher. 1995. “Patterns of Nucleotide Composition at Fourfold Degenerate Sites of Animal Mitochondrial Genomes.” Journal of Molecular Evolution 41 (3): 353–358. doi:10.1007/BF01215182.
   PubMed Web of Science ®Google Scholar
• Rozas, J., A. Ferrer-Mata, J. C. Sanchez-DelBarrio, S. Guirao-Rico, P. Librado, S. E. Ramos-Onsins, and A. Sanchez-Gracia. 2017. “Dnasp 6: DNA Sequence Polymorphism Analysis of Large Data Sets.” Molecular Biology and Evolution 34 (12): 3299–3302. doi:10.1093/molbev/msx248.
   PubMed Web of Science ®Google Scholar
• Saitou, N., and M. Nei. 1987. “The Neighbor-joining Method: A New Method for Reconstructing Phylogenetic Trees.” Molecular Biology and Evolution 4: 406–525. doi:10.1093/oxfordjournals.molbev.a040454.
   PubMed Web of Science ®Google Scholar
• Suwannapoom, C., Y. J. Wu, X. Chen, A. C. Adeola, J. Chen, and W. Z. Wang. 2018. “Complete Mitochondrial Genome of the Thai Red Junglefowl (Gallus Gallus) and Phylogenetic Analysis.” Zoological Research 39 (2): 127–129. doi:10.24272/j..2095-8137.2017.028.
   PubMed Web of Science ®Google Scholar
• Wu, Z., and P. Kaiser. 2011. “Antigen Presenting Cells in a Non-mammalian Model System, the Chicken.” Immunobiology 216 (11): 1177–1183. doi:10.1016/j.imbio.2011.05.012.
   PubMed Web of Science ®Google Scholar
• Zhang, T., H. Liu, L. K. Yang, Y. J. Yin, H. Z. Lu, and L. Wang. 2018. “The Complete Mitochondrial Genome and Molecular Phylogeny of Lueyang Black-bone Chicken.” British Poultry Science 59 (6): 618–623. doi:10.1080/00071668.2018.1514581.
   PubMed Web of Science ®Google Scholar
• Zhong, Y., M. Zhou, B. Ouyang, C. Zeng, M. Zhang, and J. Yang. 2020. “Complete Mtdna Genome of Otus Sunia (Aves, Strigidae) and the Relaxation of Selective Constrains on Strigiformes mtDNA following Evolution.” Genomics 112 (5): 3815–3825. doi:10.1016/j.ygeno.2020.02.018.
   PubMed Web of Science ®Google Scholar