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

Year 2019, , 257 - 267, 31.10.2019

Osman İbiş

https://doi.org/10.19159/tutad.569435

Cited By: 2

Abstract

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. 

Keywords

Equus asinus, Next-Generation Sequencing, mtDNA, phylogeny

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

Abstract

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.

Keywords

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

References

• 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.
• 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).
• Anonymous, 2019. Domestic Animal Diversity Information System (DAD-IS). (http://www.fao. org/dad-is/en/), (Erişim tarihi: 05.05.2019).
• 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.
• Benson, G., 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research, 27(2): 573-580.
• 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.
• 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.
• Boore, J.L., 1999. Animal mitochondrial genomes. Nucleic Acids Research, 27(8): 1767-1780.
• Clutton-Brock, J., 1992., Horse Power: A History of the Horse and the Donkey in Human Societies. Harvard University Press, Cambridge, USA.
• 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.
• Darriba, D., Taboada, G.L., Doallo, R., Posada, D., 2012. jModelTest 2: more models, new heuristics and parallel computing. Nature Methods, 9(8): 772.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• Ojala, D., Montoya, J., Attardi, G., 1981. tRNA punctuation model of RNA processing in human mitochondria. Nature, 290: 470-474.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• Steinberg, S., Cedergren, R., 1994. Structural compensation in a typical mitochondrial tRNAs. Nature Structural Biology, 1(8): 507-510.
• 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.
• 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.
• 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.
• Wilson, D.E., Reeder, D.M., 2005. Mammal Species of the World: A Taxonomic and Geographic Reference (3. Edition). Johns Hopkins University Press, Baltimore.
• 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.
• 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.
• 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.
• Yılmaz, O., Ertuğrul, M., 2011. Eşeğin (Equus asinus) evcilleştirilmesi. Iğdır Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 1(3): 111-115.
• 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.
• 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.
• 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.