Abstract
Recently, there has been considerable interest in genetic differentiation in the Cervidae family. A common tool used to determine genetic variation in different species, breeds and populations is mitochondrial DNA analysis, which can be used to estimate phylogenetic relationships among animal taxa and for molecular phylogenetic evolution analysis. With the development of sequencing technology, more and more mitochondrial sequences have been made available in public databases, including whole mitochondrial DNA sequences. These data have been used for phylogenetic analysis of animal species, and for studies of evolutionary processes.
We determined the complete mitochondrial genome of a Central European red deer, Cervus elaphus hippelaphus, from Hungary by a next generation sequencing technology. The mitochondrial genome is 16 354 bp in length and contains 13 protein-coding genes, two rRNA genes, 22 tRNA genes and a control region, all of which are arranged similar as in other vertebrates. We made phylogenetic analyses with the new sequence and 76 available mitochondrial sequences of Cervidae, using Bos taurus mitochondrial sequence as outgroup. We used ‘neighbor joining’ and ‘maximum likelihood’ methods on whole mitochondrial genome sequences; the consensus phylogenetic trees supported monophyly of the family Cervidae; it was divided into two subfamilies, Cervinae and Capreolinae, and five tribes, Cervini, Muntiacini, Alceini, Odocoileini, and Capreolini. The evolutionary structure of the family Cervidae can be reconstructed by phylogenetic analysis based on whole mitochondrial genomes; which method could be used broadly in phylogenetic evolutionary analysis of animal taxa.
Article PDF
Similar content being viewed by others
Explore related subjects
Discover the latest articles, news and stories from top researchers in related subjects.Avoid common mistakes on your manuscript.
References
Bán, I. (1998) The Hungarian Wonder Deer. EP Systema, Debrecen.
Douzery, E., Randi, E. (1997) The mitochondrial control region of Cervidae: Evolutionary patterns and phylogenetic content. Mol. Biol. Evol. 14, 1154–1166.
Feulner, P. G. D., Bielfeldt, W., Zachos, F. E., Bradvarovic, J., Eckert, I., Hartl, G. B. (2004) Mitochondrial DNA and microsatellite analyses of the genetic status of the presumed subspecies Cervus elaphus montanus (Carpathian red deer). Heredity 93, 299–306.
Flegontov, P., Gray, M. W., Burger, G., Lukes, J. (2011) Gene fragmentation: a key to mitochondrial genome evolution in Euglenozoa? Curr. Genet. 57, 225–232.
Gilbert, C., Ropiquet, A., Hassanin, A. (2006) Mitochondrial and nuclear phylogenies of Cervidae (Mammalia, Ruminantia). Systematics, morphology, and biogeography. Mol. Phylogenet. Evol. 40, 101–117.
Hahn, C., Bachmann, L., Chevreux, B. (2013) Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads–a baiting and iterative mapping approach. Nucl. Acids Res. 41, e129.
Hassanin, A., Delsuc, F., Ropiquet, A., Hammer, C., Jansen van Vuuren, B., Matthee, C., Ruiz-Garcia, M., Catzeflis, F., Areskoug, V., Nguyen, T. T., Couloux, A. (2012) Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes. C. R. Biol. 335, 32–50.
Ju, Y., Liu, H., Rong, M., Yang, Y., Wei, H., Shao, Y., Chen, X., Xing, X. (2016) Complete mitochondrial genome sequence of Aoluguya reindeer (Rangifer tarandus). Mitochondrial DNA 27, 2261–2262.
Kuwayama, R., Ozawa, T. (2000) Phylogenetic relationships among European red deer, wapiti, and sika deer inferred from mitochondrial DNA sequences. Mol. Phylogenet. Evol. 15, 115–123.
Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., Higgins, D. G. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948.
Lartillot, N., Lepage, T., Blanquart, S. (2009) PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating. Bioinformatics 25, 2286–2288.
Li, Y., Ba, H., Yang, F. (2016) Complete mitochondrial genome of Cervus elaphus songaricus (Cetartiodactyla: Cervinae) and a phylogenetic analysis with related species. Mitochondrial DNA 620–621.
Liu, Z., Wang, J., Sun, Y., Hou, Z., Teng, L. (2015) Complete mitochondrial genome of a wild Alashan Red Deer (Cervus elaphus alxaicus). Mitochondrial DNA Early Online.
Lowe, T. M., Eddy, S. R. (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucl. Acids Res. 25, 955–964.
Mahmut, H., Masuda, R., Onuma, M., Takahashi, M., Nagata, J., Suzuki, M., Ohtaishi, N. (2002) Molecular phylogeography of the red deer (Cervus elaphus) populations in Xinjiang of China: Comparison with other Asian, European, and North American populations. Zool. Sci. 19, 485–495.
Marincs, F., Molnár, J., Tóth, G., Stéger, V., Barta, E. (2013) Introgression and isolation contributed to the development of Hungarian Mangalica pigs from a particular European ancient bloodline. Genet. Sel. Evol. 45, 22.
Matosiuk, M., Sheremetyeva, I. N., Sheremetyev, I. S., Saveljev, A. P., Borkowska, A. (2014) Evolutionary neutrality of mtDNA introgression: evidence from complete mitogenome analysis in roe deer. J. Evol. Biol. 27, 2483–2494.
Milner, J. M., Bonenfant, C., Mysterud, A., Gaillard, J. M., Csányi, S., Stenseth, N. C. (2006) Temporal and spatial development of red deer harvesting in Europe: biological and cultural factors. J. Appl. Ecol. 43, 721–734.
Molnár, J., Tóth, G., Stéger, V., Zsolnai, A., Jánosi, A., Mohr, A., Szántó-Egész, R., Tóth, P., Micsinai, A., Rátky, J., Marincs, F. (2013) Mitochondrial D-loop analysis reveals low diversity in Mangalica pigs and their relationship to historical specimens. J. Anim. Breed. Genet. 130, 312–320.
Olivieri, C., Marota, I., Rizzi, E., Ermini, L., Fusco, L., Pietrelli, A., De Bellis, G., Rollo, F., Luciani, S. (2014) Positioning the red deer (Cervus elaphus) hunted by the Tyrolean Iceman into a mitochondrial DNA phylogeny. PLoS ONE 9, e100136.
Pang, H., Liu, W., Chen, Y., Fang, L., Zhang, X., Cao, X. (2008) Identification of complete mitochondrial genome of the tufted deer. Mitochondrial DNA 19, 411–417.
Pitra, C., Fickel, J., Meijaard, E., Groves, P. C. (2004) Evolution and phylogeny of old world deer. Mol. Phylogenet. Evol. 33, 880–895.
Radko, A., Zalewski, D., Rubiś, D., Szumec, A. (2014) Genetic differentiation among 6 populations of red deer (Cervus elaphus L.) in Poland based on microsatellite DNA polymorphism. Acta Biol. Hung. 65, 414–427.
Sbisà, E., Tanzariello, F., Reyes, A., Pesole, G., Saccone, C. (1997) Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. Gene 205, 125–140.
Shao, Y., Su, W., Liu, H., Zha, D., Zhang, R., Xing, X. (2016) Complete mitochondrial genome sequence of northeastern red deer (Cervus elaphus xanthopygus). Mitochondrial DNA Early Online.
Shao, Y., Xing, X., Zha, D., Yang, F. (2016) Complete mitochondrial genome sequence of tarim red deer (Cervus elaphus yarkandensis). Mitochondrial DNA 547–548.
Shao, Y., Zha, D., Xing, X., Su, W., Liu, H., Zhang, R. (2016) Complete mitochondrial genome sequence of northeastern sika deer (Cervus nippon hortulorum). Mitochondrial DNA 469–470.
Skog, A., Zachos, F. E., Rueness, E. K., Feulner, P. G. D., Mysterud, A., Langvatn, R., Lorenzini, R., Hmwe, S. S., Lehoczky, I., Hartl, G. B., Stenseth, N. C., Jakobsen, K. S. (2009) Phylogeography of red deer (Cervus elaphus) in Europe. J. Biogeogr. 36, 66–77.
Szabolcsi, Z., Egyed, B., Zenke, P., Pádár, Zs., Borsy, A., Stéger, V., Pásztor, E., Csányi, S., Buzás, Zs., Orosz, L. (2014) Constructing STR multiplexes for individual identification of Hungarian red deer. J. Forensic Sci. 59, 1090–1099.
Tamura, K., Dudley, J., Nei, M., Kumar, S. (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24, 1596–1599.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., Kumar, S. (2013) MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol. Biol. Evol. 30, 2725–2729.
Wada, K., Nishibori, M., Yokohama, M. (2007) The complete nucleotide sequence of mitochondrial genome in Japanese Sika deer (Cervus nippon), and a phylogenetic analysis between Cervidae and Bovidae. Small Rum. Res. 69, 46–54.
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. Anim. Sci. J. 81, 551–557.
Wang, Q., Yang, C. (2013) The phylogeny of the Cetartiodactyla based on complete mitochondrial genomes. Internat. J. Biol. 5, 30–36.
Yang, C., Li, P., Zhang, X., Guo, Y., Gao, Y., Xiong, Y., Wang, L., Qi, W., Yue, B. (2012) The complete mitochondrial genome of the Chinese Sika deer (Cervus nippon Temminck, 1838), and phylogenetic analysis among Cervidae, Moschidae and Bovidae. J. Nat. Hist. 46, 1747–1759.
Zachos, F. E., Hartl, G. B. (2011) Phylogeography, population genetics and conservation of the European red deer Cervus elaphus. Mammal Rev. 41, 138–150.
Zhang, W-Q., Zhang, M-H. (2012) Phylogeny and evolution of Cervidae based on complete mitochondrial genomes. Genet. Mol. Res. 11, 628–635.
Zsolnai, A., Lehoczky, I., Gyurmán, A., Nagy, J., Sugár, L., Anton, I., Horn, P., Magyary, I. (2009) Development of eight-plex microsatellite PCR for parentage control in deer. Archiv Tierzucht 52, 143–149.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
About this article
Cite this article
Frank, K., Barta, E., Bana, N.Á. et al. Complete Mitochondrial Genome Sequence of a Hungarian Red Deer (Cervus Elaphus Hippelaphus) from High-Throughput Sequencing Data and Its Phylogenetic Position within the Family Cervidae. BIOLOGIA FUTURA 67, 133–147 (2016). https://doi.org/10.1556/018.67.2016.2.2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1556/018.67.2016.2.2