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Complete mitochondrial genome sequences of Korean native horse from Jeju Island: uncovering the spatio-temporal dynamics

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Abstract

The Korean native horse (Jeju horse) is one of the most important animals in Korean historical, cultural, and economical viewpoints. In the early 1980s, the Jeju horse was close to extinction. The aim of this study is to explore the phylogenomics of Korean native horse focusing on spatio-temporal dynamics. We determined complete mitochondrial genome sequences for the first Korean native (n = 6) and additional Mongolian (n = 2) horses. Those sequences were analyzed together with 143 published ones using Bayesian coalescent approach as well as three different phylogenetic analysis methods, Bayesian inference, maximum likelihood, and neighbor-joining methods. The phylogenomic trees revealed that the Korean native horses had multiple origins and clustered together with some horses from four European and one Middle Eastern breeds. Our phylogenomic analyses also supported that there was no apparent association between breed or geographic location and the evolution of global horses. Time of the most recent common ancestor of the Korean native horse was approximately 13,200–63,200 years, which was much younger than 0.696 My of modern horses. Additionally, our results showed that all global horse lineages including Korean native horse existed prior to their domestication events occurred in about 6000–10,000 years ago. This is the first study on phylogenomics of the Korean native horse focusing on spatio-temporal dynamics. Our findings increase our understanding of the domestication history of the Korean native horses, and could provide useful information for horse conservation projects as well as for horse genomics, emergence, and the geographical distribution.

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References

  1. Vilà C, Leonard JA, Götherström A, Marklund S, Sandberg K, Lidén K et al (2001) Widespread origins of domestic horse lineages. Science 291:474–477

    Article  PubMed  Google Scholar 

  2. Saccone C, Giorgi CD, Gissi C, Pesole G, Reyes A (1999) Evolutionary genomics in Metazoa: the mitochondrial DNA as a model system. Gene 238:195–209

    Article  CAS  PubMed  Google Scholar 

  3. Jansen T, Forster P, Levine MA, Oelke H, Hurles M, Renfrew C et al (2002) Mitochondrial DNA and the origins of the domestic horse. Proc Natl Acad Sci USA 99:10905–10910

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Cieslak M, Pruvost M, Benecke N, Hofreiter M, Morales A, Reissmann M et al (2010) Origin and history of mitochondrial DNA lineages in domestic horses. PLoS ONE 5:e15311

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Lippold S, Matzke NJ, Reissmann M, Hofreiter M (2011) Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication. BMC Evol Biol 11:328

  6. Achilli A, Olivieri A, Soares P, Lancioni H, Kashani BH, Perego UA et al (2012) Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. Proc Natl Acad Sci USA 109:2449–2454

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Der Sarkissian C, Ermini DL, Schubert M, Yang MA, Librado P, Fumagalli M et al (2015) Evolutionary genomics and conservation of the endangered Przewalski’s horse. Curr Biol 25:2577–2583

    Article  Google Scholar 

  8. Nam DY (1969) Horse production in Cheju during Lee dynasty. In: Studies on Korean History, Vol 4. Korea History Research Society, College of Letters Sciences, Seoul National University Press, Seoul, p 77–131

    Google Scholar 

  9. Shin T K, Lee CK, Kim SH, Yang KC, Ko CH, Lee BM et al. (1992) An anatomy study of animal bones excavated in the Kwakji archaeological site in Cheju Island. Go-Moon-Wha 40:31–42

    Google Scholar 

  10. Oh MY, Ko MH, Kim GO, Oh YS, Kim SJ, Hong SS (1994) Phylogenetic relationships of Cheju native horses by mitochondrial DNA sequences. Mol Cells 4:13–20

    CAS  Google Scholar 

  11. Kim K-I, Yang Y-H, Lee S-S, Park C, Ma R, Bouzat JL et al (1999) Phylogenetic relationships of Cheju horses to other horse breeds as determined by mtDNA D-loop sequence polymorphism. Anim Genet 30:102–108

    Article  CAS  PubMed  Google Scholar 

  12. Jung Y-H, Han S-H, Shin T, Oh M-Y (2002) Genetic characterization of horse bone excavated from the Kwakji archaeological site, Jeju, Korea. Mol Cells 14:224–230

    CAS  PubMed  Google Scholar 

  13. Yang YH, Kim KI, Cothran EG, Flannery AR (2002) Genetic diversity of Cheju horses (Equus caballus) determined by using mitochondrial DNA D-loop polymorphism. Biochem Genet 40:175–186

    Article  CAS  PubMed  Google Scholar 

  14. Xu S, Luosang J, Hua S, He J, Ciren A, Wang W et al (2007) High altitude adaptation and phylogenetic analysis of Tibetan horse based on the mitochondrial genome. J Genet Genomics 34:720–729

    Article  CAS  PubMed  Google Scholar 

  15. Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059–3066

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Hall TA (1999) BIOEDIT: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  17. Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818

    Article  CAS  PubMed  Google Scholar 

  18. Swofford DL (2003) PAUP: phylogenetic analysis using parsimony. Ver 4.0b10. Sinauer Associates, Sunderland

    Google Scholar 

  19. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574

    Article  CAS  PubMed  Google Scholar 

  20. Guindon S, Gascuel O (2003) A simple, fast and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52:696–704

    Article  PubMed  Google Scholar 

  21. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  22. Felsenstein J (1995) PHYLIP: phylogeny inference package. Ver 3.572c. University of Washington, Seattle

    Google Scholar 

  23. Kimura M (1980) A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  PubMed  Google Scholar 

  24. Strimmer K, von Haeseler A (1996) Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964–969

    Article  CAS  Google Scholar 

  25. Felsenstein J (1985) Confidence limits on the phylogenetics: an approach using the bootstrap. Evol Int J Org Evol 39:783–791

    Article  Google Scholar 

  26. Drummond AJ, Rambaut A (2007) BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214

    Article  PubMed  PubMed Central  Google Scholar 

  27. Forstén A (1992) Mitochondrial-DNA time-table and the evolution of Equus: comparison of molecular and paleontological evidence. Ann Zool Fenn 28:301–309

    Google Scholar 

  28. Drummond AJ, Ho SY, Phillips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. PLoS Bio 4:e88

    Article  Google Scholar 

  29. Suchard MA, Weiss RE, Sinsheimer JS (2001) Bayesian selection of continuous- time Markov chain evolutionary models. Mol Biol Evol 18:1001–1013

    Article  CAS  PubMed  Google Scholar 

  30. Rambaut A (2012) Available at http://evolve.zoo.ox.ac.uk/beast

  31. McGahern A, Bower M, Edwards C, Brophy PO, Sulimova G, Zakharov I et al (2006) Evidence for biogeographical patterning in mitochondrial DNA sequences in eastern horse populations. Anim Genet 37:494–497

    Article  CAS  PubMed  Google Scholar 

  32. Prystupa J, Hind P, Cothran E, Plante Y (2012) Maternal lineages in native Canadian equine populations and their relationship to the Nordic and Mountain and Moorland pony breeds. J Hered 103: 380–390

    Article  PubMed  Google Scholar 

  33. Winton CL, Hegarty MJ, McMahon R, Slavov GT, McEwan NR (2013) Genetic diversity and phylogenetic analysis of native mountain ponies of Britain and Ireland reveals a novel rare population. Ecol Evol 3:934–947

    Article  PubMed  PubMed Central  Google Scholar 

  34. Warmuth V, Campana M, Eriksson A, Bower M, Barker G, Manica A (2013) Ancient trade routes shaped the genetic structure of horses in eastern Eurasia. Mol Ecol 22:534–5351

    Article  Google Scholar 

  35. Rout PK, Joshi MB, Mandal A, Laloe D, Singh L, Thangaraj K (2008) Microsatellite-based phylogeny of Indian domestic goats. BMC Genet 9:11

    Article  PubMed  PubMed Central  Google Scholar 

  36. Olivieri A, Gandini F, Achilli A, Fichera A, Rizzi E, Bonfiglio S et al (2015) Mitogenomes from Egyptian cattle breeds: new clues on the origin of haplogroup Q and the early spread of Bos taurus from the near east. PLoS ONE 10:e0141170

    Article  PubMed  PubMed Central  Google Scholar 

  37. Achilli A, Bonfiglio S, Olivieri A, Malusà A, Pala M, Hooshiar Kashani B et al (2009) The multifaceted origin of taurine cattle reflected by the mitochondrial genome. PLoS ONE 4:e5753

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was carried out with the support of “Cooperative Research Program for Agriculture Science & Technology Development (Project No. PJ01040603)” Rural Development Administration, Republic of Korea.

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Authors and Affiliations

  1. Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-742, Republic of Korea

    Sook Hee Yoon, Jaemin Kim, Donghyun Shin & Heebal Kim

  2. C&K Genomics, Seoul National University Mt.4-2, Main Bldg. #514, SNU Research Park, NakSeoungDae, Gwanakgu, Seoul, 151-919, Republic of Korea

    Seoae Cho & Heebal Kim

  3. Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-742, Republic of Korea

    Woori Kwak

  4. The Animal Genomics and Breeding Center, Chonbuk National University, Jeonju, 561-756, Republic of Korea

    Hak-Kyo Lee

  5. Genomic Informatics Center, Hankyong National University, Anseong, 456-749, Republic of Korea

    Kyoung-Do Park

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  1. Sook Hee Yoon
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  2. Jaemin Kim
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  3. Donghyun Shin
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  7. Kyoung-Do Park
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  8. Heebal Kim
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Correspondence to Kyoung-Do Park or Heebal Kim.

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Yoon, S.H., Kim, J., Shin, D. et al. Complete mitochondrial genome sequences of Korean native horse from Jeju Island: uncovering the spatio-temporal dynamics. Mol Biol Rep 44, 233–242 (2017). https://doi.org/10.1007/s11033-017-4101-8

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  • DOI: https://doi.org/10.1007/s11033-017-4101-8

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