Mitogenome Characterization of Turkish Anatolian Donkey (Equus asinus) and Its Phylogenetic Relationships

Öz

The aim of this study was to characterize first mitogenome of Anatolian donkey in Turkey and to contribute to revealing its phylogenetics relationships. Whole mitogenome belonging to one sample of the Anatolian donkey was characterized with Long-Range PCR and Next-Generation Sequencing technique and phylogenetic analyses were performed using Bayesian, Maximum Likelihood and Neighbor-Joining methods. The complete mitogenome is a typical circular DNA molecule of 16.551 base pair in length that contained 13 protein coding genes (PCGs), 22 transfer RNA, two ribosomal RNA genes, and one non-coding control region (D-loop). The average nucleotide composition of the mitogenome is in the range of mammalian mitogenomes; 32.32% for adenine, 25.78% for thymine, 28.67% for cytosine and 13.23% for guanine; adenine + thymine content (58.10%) was higher than guanine + cytosine content (41.90%). A total of 14 transfer RNA, 12 protein coding and 2 ribosomal RNA genes were encoded on the heavy strand, and 8 transfer RNA and one protein coding (ND6) gene were encoded on the light strand. The gene structure, organization and compositions were similar to other equids. Phylogenetic analyses indicated that the Turkish Anatolian donkey was closer to the Chinese domestic donkey rather than to the European domestic donkeys, and it may have originated from the African wild donkeys (such as Somali wild donkey). This study provided reference mitogenomic data of Anatolian donkey for further molecular studies of the Turkish donkeys and other equids. 

Anahtar Kelimeler

• Equus asinus,Next-Generation Sequencing,mtDNA,phylogeny

Türkiye Anadolu Eşeği (Equus asinus)’nin Mitogenom Karakterizasyonu ve Filogenetik İlişkileri

Öz

Bu çalışmanın amacı, Türkiye Anadolu eşeği (Equus asinus)’nin ilk mitogenom karakterizasyonunu yapmak ve filogenetik ilişkilerinin ortaya çıkarılmasına katkı sağlamaktır. Anadolu eşeğine ait bir örneğin komple mitokondriyal genomu, Long-Range PCR ve Yeni Nesil Dizileme tekniği ile karakterize edilmiş ve Bayesian, Maksimum Likelihood ve Neighbor-Joining metotlarıyla filogenetik analizler yapılmıştır. Komple mitogenom, 13 protein kodlayan gen, 22 taşıyıcı RNA, 2 ribozomal RNA ve bir kodlama yapmayan kontrol bölgesi (D-loop) içeren, 16.551 baz çifti uzunluğunda tipik dairesel DNA moleküldür. Mitogenomun ortalama nükleotid kompozisyonu, memeli mitogenomları aralığında olup; adenin için % 32.32, timin için % 25.78, sitozin için % 28.67, guanin için % 13.23’tür; adenin+timin içeriği (% 58.10), guanin+sitozin içeriğinden (% 41.90) daha fazladır. Toplam 14 taşıyıcı RNA, 12 protein kodlayan ve 2 ribozomal RNA geni ağır zincir üzerinde kodlanmakta, 8 taşıyıcı RNA ve bir protein kodlayan gen (ND6) ise hafif zincir üzerinde kodlanmaktadır. Gen yapısı, organizasyonu ve kompozisyonu diğer atgillere benzerdir. Filogenetik analizler, Türkiye Anadolu eşeğinin, Çin evcil eşeklerine Avrupa evcil eşeklerinden daha yakın olduğunu ve Afrika yabani eşeklerinden (Somali yabani eşeği gibi) köken almış olabileceğini göstermiştir. Bu çalışma, Türkiye eşekleri ve diğer atgilleri içeren gelecekteki moleküler çalışmalar için Anadolu eşeğinin referans mitogenom verisini sunmuştur.

Anahtar Kelimeler

• Equus asinus,Yeni Nesil Dizileme,mtDNA,mtDNA,filogeni

Kaynakça

1. Achilli, A., Olivieri, A., Soares, P., Lancioni, H., Kashani, B.H., Perego, U.A., Felicetti, M., 2012. Mitochondrial genomes from modern horses reveal the major haplogroups that underwent domestication. Proceedings of the National Academy of Sciences, 109(7): 2449-2454.
2. Anonymous, 2014. Equus przewalskii Mitochondrial DNA, Complete Genome, Isolate: NOUMA1, GenBank: AP013094.1. (https://www.ncbi.nlm.nih. gov/nuccore/AP013094), (Erişim tarihi: 15.04.2019).
3. Anonymous, 2019. Domestic Animal Diversity Information System (DAD-IS). (http://www.fao. org/dad-is/en/), (Erişim tarihi: 05.05.2019).
4. Beja-Pereira, A., England, P.R., Ferrand, N., Jordan, S., Bakhiet, A.O., Abdalla, M.A., Mashkour, M., Jordana, J., Taberlet, P., Luikart, G., 2004. African origins of the domestic donkey. Science, 304(5678): 1781.
5. Benson, G., 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research, 27(2): 573-580.
6. Bernt, M., Donath, A., Jühling, F., Externbrink, F., Florentz, C., Fritzsch, G., Pütz, J., Middendorf, M., Stadler, P.F., 2013. MITOS: Improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution, 69(2): 313-319.
7. Bertolini, F., Scimone, C., Geraci, C., Schiavo, G., Utzeri, V.J., Chiofalo, V., Fontanesi, L., 2015. Next generation semiconductor based sequencing of the donkey (Equus asinus) genome provided comparative sequence data against the horse genome and a few millions of single nucleotide polymorphisms. PLoS one, 10(7): e0131925.
8. Boore, J.L., 1999. Animal mitochondrial genomes. Nucleic Acids Research, 27(8): 1767-1780.

9. Clutton-Brock, J., 1992., Horse Power: A History of the Horse and the Donkey in Human Societies. Harvard University Press, Cambridge, USA.
10. Cozzi, M.C., Valiati, P., Cherchi, R., Gorla, E., Prinsen, R.T.M.M., Longeri, M., Bagnato, A., Strillacci, M.G., 2018. Mitochondrial DNA genetic diversity in six Italian donkey breeds (Equus asinus). Mitochondrial DNA Part A, 29(3): 409-418.
11. Darriba, D., Taboada, G.L., Doallo, R., Posada, D., 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9(8): 772.
12. Der Sarkissian, C., Vilstrup, J. T., Schubert, M., Seguin-Orlando, A., Eme, D., Weinstock, J., Prieto, A., 2015. Mitochondrial genomes reveal the extinct Hippidion as an outgroup to all living equids. Biology letters, 11(3): 20141058.
13. Druzhkova, A.S., Makunin, A.I., Vorobieva, N.V., Vasiliev, S.K., Ovodov, N.D., Shunkov, M.V., Trifonov, V.A., Graphodatsky, A.S., 2017. Complete mitochondrial genome of an extinct Equus (Sussemionus) ovodovi specimen from Denisova cave (Altai, Russia). Mitochondrial DNA Part B, 2(1): 79-81.
14. Goto, H., Ryder, O.A., Fisher, A.R., Schultz, B., Kosakovsky Pond, S.L., Nekrutenko, A., Makova, K.D., 2011. A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses. Genome Biology and Evolution, 3: 1096-1106.
15. Guo, X., Bao, P., Pei, J., Ding, X., Liang, C., Yan, P., Lu, D., 2017. Complete mitochondrial genome of Qingyang donkey (Equus asinus). Conservation Genetics Resources, 9(2): 269-271.
16. Heintzman, P.D., Zazula, G.D., MacPhee, R.D., Scott, E., Cahill, J.A., McHorse, B.K., Kapp, J.D., Stiller, M., Wooller, M.J., Orlando, L., Southon, J., 2017. A new genus of horse from Pleistocene North America. Elife, 6: e29944.
17. Hou, H.Y., Chang, R.X., Cheng, Y.N., Jang-Liaw, N.H., 2018. Complete mitochondrial genome sequence for the somali wild ass Equus africanus somaliensis. Conservation Genetics Resources, 1-5.
18. Huggins, B., 2002. "Equus asinus" (On-line), animal diversity web. (https://animaldiversity.org/accounts/ Equus_asinus/), (Erişim tarihi: 10.05.2019). Jónsson, H., Schubert, M., Seguin-Orlando, A., Ginolhac, A., Petersen, L., Fumagalli, M., Lear, T., 2014. Speciation with gene flow in equids despite extensive chromosomal plasticity. Proceedings of the National Academy of Sciences, 111(52): 18655-18660.
19. 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 Research, 30(14): 3059-3066.
20. Krause, J., Unger, T., Noçon, A., Malaspinas, A.S., Kolokotronis, S.O., Stiller, M., Soibelzon, L., Spriggs, H., Dear, P.H., Briggs, A.W., Bray, S.C., O’Brien, S.J., Rabeder, G., Matheus, P., Cooper, A., Slatkin, M., Páábo, S., Hofreiter, M., 2008. Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary. BMC Evolutionary Biology, 8: 1-12.
21. Kul, B.C., Bilgen, N., Akyuz, B., Ertugrul, O., 2016. Molecular phylogeny of Anatolian and Cypriot donkey populations based on mitochondrial DNA and Y-chromosomal STRs. Ankara Üniversitesi Veteriner Fakültesi Dergisi, 63(2): 143-149.
22. Kumar, S., Stecher, G., Tamura, K., 2016. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7): 1870-1874.
23. Lippold, S., Matzke, N.J., Reissmann, M., Hofreiter, M., 2011. Whole mitochondrial genome sequencing of domestic horses reveals incorporation of extensive wild horse diversity during domestication. BMC Evolutionary Biology, 11: 1-10.
24. Luo, Y., Chen, Y., Liu, F., Jiang, C., Gao, Y., 2011. Mitochondrial genome sequence of the Tibetan wild ass (Equus kiang). Mitochondrial DNA, 22(1-2): 6-8.
25. Meimberg, H., Schachtler, C., Curto, M., Husemann, M., Habel, J.C., 2016. A new amplicon based approach of whole mitogenome sequencing for phylogenetic and phylogeographic analysis: An example of East African white-eyes (Aves, Zosteropidae). Molecular Phylogenetics and Evolution, 102: 74-85.
26. Ojala, D., Montoya, J., Attardi, G., 1981. tRNA punctuation model of RNA processing in human mitochondria. Nature, 290: 470-474.
27. Pengjia, B., Guo, X., Pei, J., Ding, X., Wu, X., Xiong, L., Liang, C., Chu, M., Yan, P., 2019. Characterization of the complete mitochondrial genome of the Liangzhou donkey (Equus asinus). Mitochondrial DNA Part B, 4(1): 1846-1847.
28. Rohland, N., Malaspinas, A.S., Pollack, J.L., Slatkin, M., Matheus, P., Hofreiter, M., 2007. Proboscidean mitogenomics: Chronology and mode of elephant evolution using mastodon as outgroup. PLoS Biology, 5(8): e207.
29. Ronquist, F., Teslenko, M., Mark, P.V.D., Ayres, D.L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M.A., Huelsenbeck, J.P., 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology, 61(3): 539-542.
30. Rosenbom, S., Costa, V., Al‐Araimi, N., Kefena, E., Abdel‐Moneim, A.S., Abdalla, M.A., Bakhiet, A., Beja‐Pereira, A., 2015. Genetic diversity of donkey populations from the putative centers of domestication. Animal Genetics, 46(1): 30-36.
31. Saccone, C., Pesole, G., Sbisa, E., 1991. The main regulatory region of mammalian mitochondrial DNA: structure-function model and evolutionary pattern. Journal of Molecular Evolution, 33(1): 83-91.
32. Schubert, M., Mashkour, M., Gaunitz, C., Fages, A., Seguin-Orlando, A., Sheikhi, S., Alfarhan, A.H., Alquraishi, S.A., Al-Rasheid, K.A.S., Chuang, R., Ermini, L., Gamba, C., Weinstock, J., Vedat, O., Orlando, L., 2017. Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages. Journal of Archaeological Science, 78: 147-157.
33. Steinberg, S., Cedergren, R., 1994. Structural compensation in a typical mitochondrial tRNAs. Nature Structural Biology, 1(8): 507-510.
34. Sun, Y., Jiang, Q., Yang, C., Wang, X., Tian, F., Wang, Y., Ma, Y., Ju, Z., Huang, J., Zhou, X., Zhong, J., Wang, C., 2016. Characterization of complete mitochondrial genome of Dezhou donkey (Equus asinus) and evolutionary analysis. Current Genetics, 62(2): 383-390.
35. Vilstrup, J.T., Seguin-Orlando, A., Stiller, M., Ginolhac, A., Raghavan, M., Nielsen, S.C., Weinstock, J., Froese, D., Vasiliev, S.K., Ovodov, N.D., Clary, J., Helgen, K.M., Fleischer, R.C., Cooper, A., Shapiro, B., Orlando, L., 2013. Mitochondrial phylogenomics of modern and ancient equids. PLoS One, 8(2): e55950.
36. Wada, K., Okumura, K., Nishibori, M., Kikkawa, Y., Yokohama, M., 2010. The complete mitochondrial genome of the domestic red deer (Cervus elaphus) of New Zealand and its phylogenic position within the family Cervidae. Animal Science Journal, 81(5): 551-557.
37. Wilson, D.E., Reeder, D.M., 2005. Mammal Species of the World: A Taxonomic and Geographic Reference (3. Edition). Johns Hopkins University Press, Baltimore.
38. Xu, X., Gullberg, A., Arnason, U., 1996. The complete mitochondrial DNA (mtDNA) of the donkey and mtDNA comparisons among four closely related mammalian species-pairs. Journal of Molecular Evolution, 43(5): 438-446.
39. Yalçın, E., 2016. Kırklareli ili eşek çiftliğindeki populasyonun çeşitli vücut ölçülerine göre morfometrik karakterizasyonu ve mtdna polimorfizmi yoluyla genetik çeşitliliğinin incelenmesi. Yüksek lisans tezi, Namık Kemal Üniversitesi Fen Bilimleri Enstitüsü, Tekirdağ.
40. Yang, X.S., Xue, D.Y., Han, H.X., 2013. The complete mitochondrial genome of Biston panterinaria (Lepidoptera, Geometridae), with phylogenetic utility of mitochondrial genome in the Lepidoptera. Gene, 515(2): 349-358.
41. Yılmaz, O., Ertuğrul, M., 2011. Eşeğin (Equus asinus) evcilleştirilmesi. Iğdır Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 1(3): 111-115.
42. Yılmaz, O., Ertuğrul, M., 2014. Türkiye’de yetiştirilen kimi tek tırnaklılara ait bazı morfolojik özellikler. Çanakkale Onsekizmart Üniversitesi Ziraat Fakültesi Dergisi, 2(2): 9-16.
43. Yilmaz, O., Wilson, R.T., 2013. The domestic livestock resources of Turkey: Notes on donkeys. Journal of Animal and Plant Sciences, 23(2): 651-656.
44. Zhang, J., Chiodini, R., Badr, A., Zhang, G., 2011. The impact of next-generation sequencing on genomics. Journal of Genetics and Genomics, 38(3): 95-109.