Proceedings of the National Institute of Ecology of the Republic of Korea

National Institute of Ecology (국립생태원)
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Complete Mitochondrial Genome and Phylogenetic Analysis for the Korean Field Mouse Apodemus peninsulae Found on Baengnyeong Island in South Korea

  • Jung A Kim (Division of Animal Resources, National Institute of Biological Resources) ;
  • Hye Sook Jeon (Division of Animal Resources, National Institute of Biological Resources) ;
  • Seung Min Lee (Division of Animal Resources, National Institute of Biological Resources) ;
  • Hong Seomun (Division of Animal Resources, National Institute of Biological Resources) ;
  • Junghwa An (Division of Animal Resources, National Institute of Biological Resources)
  • Received : 2022.12.06
  • Accepted : 2023.01.16
  • Published : 2023.05.01
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Abstract

The Korean field mouse, Apodemus peninsulae mitochondrial genome has previously been reported for mice obtained from mainland Korea and China. In this investigation the complete mitochondrial genome sequence for a mouse obtained from Baengnyeong Island (BI) in South Korea was determined using high-throughput whole-genome sequencing for the first time. The circular genome was determined to be 16,268 bp in length. It was found to be composed of a typical complement gene that encodes 13 protein subunits of enzymes involved in oxidative phosphorylation, two ribosomal RNAs, 22 transfer RNAs, and one control region. Phylogenetic analysis involved 13 amino acid sequences and demonstrated that the A. peninsulae genome from BI was more closely grouped with two Korean samples (HQ660074 and JN546584) than the Chinese (KP671850) sample. This study verified the evolutionary status of A. peninsulae inhabiting the BI at the molecular level, and could be a significant supplement to the genetic background.

Keywords

Acknowledgement

This work was supported by a grant (NIBR202104102) from the National Institute of Biological Resources (NIBR) funded by the Ministry of Environment (MOE), Republic of Korea. Genetic samples were collected with legal permits (2021-6ho, Ongjin-gun) from the MOE, Republic of Korea.

References

  1. Batsaikhan, A., Tinnin, D., Lhagvasuren, B., and Sukhchuluun, G. (2016). Apodemus peninsulae. The IUCN Red List of Threatened Species 2016: e.T1899A115058828. International Union for Conservation of Nature and Natural Resources.
  2. Cho, M., Lee, E., You, H., Kang, N.G., and Yoo, D.G. (2013). Late quaternary sedimentation in the Yellow sea off Baegryeong Island, Korea. Geophysics and Geophysical Exploration, 16, 145-153. https://doi.org/10.7582/GGE.2013.16.3.145
  3. Hahn, C., Bachmann, L., and Chevreux, B. (2013). Reconstructing mitochondrial genomes directly from genomic nextgeneration sequencing reads--a baiting and iterative mapping approach. Nucleic Acids Research, 41, e129. https://doi.org/10.1093/nar/gkt371
  4. Jeon, M.G., Kim, J.Y., and Park, Y.C. (2016). Phylogenetic analysis of the complete mitochondrial genome of the Korean field mouse Apodemus peninsulae (Rodentia, Murinae) from China. Mitochondrial DNA. Part A, DNA Mapping, Sequencing, and Analysis, 27, 2408-2409. https://doi.org/10.3109/19 401736.2015.1030618
  5. Jo, Y.S., Baccus, J.T., Koprowski, J.L. (2018). Mammals of Korea. National Institute of Biological Resources.
  6. Kang, J.H., Kim, D.W., Suh, J.H., and Park, J.Y. (2012). Breeding and wintering of the light-vented Bulbul (Pycnonotus sinensis) in Baengnyeong Island, Incheon, South Korea. The Korean Journal of Ornithology, 19, 237-241.
  7. Kim, H.R., and Park, Y.C. (2011). The complete mitochondrial genome of the Korean field mouse Apodemus peninsulae (Rodentia, Murinae) from Korea. Mitochondrial DNA, 22, 97-98. https://doi.org/10.3109/19401736.2011.624610
  8. Laslett, D., and Canback, B. (2008). ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences. Bioinformatics, 24, 172-175. https://doi.org/10.1093/bioinformatics/btm573
  9. Lee, E.J., Lee, W.S., and Rhim, S.J. (2008). Characteristics of small rodent populations in post-fire silvicultural management stands within pine forest. Forest Ecology and Management, 255, 1418-1422. https://doi.org/10.1016/j.foreco.2007.10.055
  10. Lee, E.J., Rhim, S.J., and Lee, W.S. (2012). Seasonal movements and home range sizes of Korean field mouse Apodemus peninsulae in unburned and post-fire pine planted stands within a pine forest. Journal of Animal and Veterinary Advances, 11, 3834-3839. https://dx.doi.org/10.3923/javaa.2012.3834.3839
  11. Lu, J., and Zhang, Z. (2005). Food hoarding behaviour of large field mouse Apodemus peninsulae. Acta Theriologica, 50, 51-58. https://doi.org/10.1007/BF03192618
  12. Meng, G., Li, Y., Yang, C., and Liu, S. (2019). MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic Acids Research, 47, e63. https://doi.org/10.1093/nar/gkz173
  13. Musser, G.G., and Carleton, M.D. (2005). Family Muridae. In D.E. Wilson, and D.M., Reeder (Eds.), Mammal Species of the World: A Taxonomic and Geographic Reference, 3rd ed. (pp. 1189-1531). Johns Hopkins University Press.
  14. Oh, D.J., Kim, T.W., Chang, M.H., Han, S.H., Oh, H.S., and Kim, S.J. (2011). The mitochondrial genome of Apodemus peninsulae (Rodentia, Muridae). Mitochondrial DNA, 22, 99-101. https://doi.org/10.3109/19401736.2011.624612
  15. Park, C.D., Do, M.S., Lee, J.H., and Suh, J.H. (2019). Herpetofauna in Socheong, Daecheong and Baengnyeong islands, Korea. Korean Journal of Herpetology, 10, 1-7.
  16. Park, G., and Lee, H.M. (2007). The Landforms of Baengnyeongdo Island. 3rd National Natural Environment Survey. Ministry of Environment.
  17. Won, C., and Smith, K.G. (1999). History and current status of mammals of the Korean Peninsula. Mammal Review, 29, 3-36. https://doi.org/10.1046/j.1365-2907.1999.00034.x
  18. Wyman, S.K., Jansen, R.K., and Boore, J.L. (2004). Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 20, 3252-3255. https://doi.org/10.1093/bioinformatics/bth352
  19. Yoon, M.H., Phillips, C.J., Kim, I., and Oh, H.S. (2004). Biogeography, genetic structure, and speciation in the striped field mouse, Apodemus agarius, in Southern Korea. Korean Journal Genetics, 26, 15-28.