식물분류학회지 (Korean Journal of Plant Taxonomy)

  • 제51권1호
  • /
  • Pages.109-114
  • /
  • 2021
  • /
  • 1225-8318(pISSN)
  • /
  • 2466-1546(eISSN)
한국식물분류학회 (The Korean Society of Plant Taxonomists)
권호 표지
DOI QR코드

DOI QR Code

A report of the second chloroplast genome sequence in Veronica nakaiana (Plantaginaceae), an endemic species in Korea

  • 투고 : 2021.03.03
  • 심사 : 2021.03.26
  • 발행 : 2021.03.31
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

Veronica nakaiana Ohwi (Plantaginaceae) is an endemic taxon on Ulleungdo Island, Korea. We report the second complete chloroplast genome sequence of V. nakaiana. Its genome size is 152,319 bp in length, comprising a large single-copy of 83,195 bp, a small single-copy of 17,702 bp, and a pair of inverted repeat regions of 25,711 bp. The complete genome contains 115 genes, including 51 protein-coding genes, four rRNA genes, and 31 tRNA genes. When comparing the two chloroplast genomes of V. nakaiana, 11 variable sites are recognized: seven SNPs and four indels. Two substitutions in the coding regions are recognized: rpoC2 (synonymous substitution) and rpl22 (nonsynonymous substitution). In nine noncoding regions, one is in the tRNA gene (trnK-UUU), one is in the intron of atpF, and seven are in the intergenic spacers (trnH-GUG~psbA, trnK-UUU, rps16~trnQ-UUG, trnC-GCA~petN, psbZ~trnG-GCC, ycf3~trnS-GGA, ycf4~cemA, and psbB~psbT). The data provide the level of genetic variation in V. nakaiana. This result will be a useful resource to formulate conservation strategies for V. nakaiana, which is a rare endemic species in Korea.

키워드

참고문헌

  1. Albach, D. C. 2008. Further arguments for the rejection of paraphyletic taxa: Veronica subgen. Pseudolysimachium (Plantaginaceae). Taxon 57: 1-6.
  2. Albach, D. C. and H. M. Meudt. 2010. Phylogeny of Veronica in the Southern and Northern Hemispheres based on plastid, nuclear ribosomal and nuclear low-copy DNA. Molecular Phylogenetics and Evolution 54: 457-471. https://doi.org/10.1016/j.ympev.2009.09.030
  3. Albach, D. C., M. M. Martinez-Ortega, M. A. Fischer and M. W. Chase. 2004a. A new classification of the tribe Veroniceae: problems and a possible solution. Taxon 53: 429-452. https://doi.org/10.2307/4135620
  4. Albach, D. C., M. M. Martinez-Ortega, M. A. Fischer and M. W. Chase. 2004b. Evolution of Veroniceae: a phylogenetic perspective. Annals of the Missouri Botanical Garden 91: 275-302.
  5. Cheong, W. Y., S.-H. Kim, J. Yang, W. Lee, J.-H. Pak and S.-C. Kim. 2020. Insights from chloroplast DNA into the progenitor-derivative relationship between Campanula punctata and C. takesimana (Campanulaceae) in Korea. Journal of Plant Biology 63: 433-444.
  6. Choi, K. S., M. G. Chung and S. Park. 2016. The complete chloroplast genome sequences of three Veroniceae species (Plantaginaceae): comparative analysis and highly divergent regions. Frontiers in Plant Science 7: 355. https://doi.org/10.3359/fpls.2016.00355
  7. Greiner, S., P. Lehwark and R. Bock. 2019. Organellar Genome-DRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research 47: W59-W64.
  8. Jeong, K. S., M. S. Kim, W. Lee and J.-H. Pak. 2014. Infraspecific variation and geographic study of Lonicera insularis (Caprifoliaceae) based on chloroplast DNA sequences. Korean Journal of Plant Taxonomy 44: 202-207. https://doi.org/10.11110/kjpt.2014.44.3.202
  9. Katoh, K. and D. M. Standley. 2013. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Phylogenetics and Evolution 30: 772-780.
  10. Kearse, M., R. Moir, A. Wilson, S. Stones-Havas, M. Cheung, S. Sturrock, S. Buxton, A. Cooper, S. Markowitz, C. Duran, T. Thierer, B. Ashton, P. Meintjes and A. Drummond. 2012. Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28: 1647-1649. https://doi.org/10.1093/bioinformatics/bts199
  11. Kim, K.-J. and H.-G. Choi. 2007. Scrophylariaceae Juss. In The Genera of Vascular Plants of Korea. Park, C.-W. (ed.), Academy Publishing Co., Seoul. Pp. 861-891.
  12. Kim, S. 2018. Psudolysimachion (W. D. J. Koch) Opiz. In Flora of Korea. Vol. 6b. Asteridae: Scurophulariaceae to Dipsacaceae. Park, C.-W. (ed.), Doohyun Publishing Co., Seoul. Pp. 23-28.
  13. Kumar, S., G. Stecher and K. Tamura. 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution. 33: 1870-1874. https://doi.org/10.1093/molbev/msw054
  14. Lee, T. B. and T. Yamazaki. 1983. A revision of the Scrophulariaceae in Korea. Bulletin of the Kwanak Arboretum 4: 34-70.
  15. Lee, W., J. Yang, K.-S. Jung, J.-H. Pak, M. Maki and S.-C. Kim. 2017. Chloroplast DNA assessment of anagenetic speciation in Rubus takesimensis (Rosaceae) on Ulleung Island, Korea. Journal of Plant Biology 60: 163-174. https://doi.org/10.1007/s12374-016-0421-9
  16. Oh, S.-H. 2015. Sea, wind, or bird: origin of Fagus multinervis (Fagaceae) inferred from chloroplast DNA sequences. Korean Journal of Plant Taxonomy 45: 213-220. https://doi.org/10.11110/kjpt.2015.45.3.213
  17. Opiz, F.M. 1852. Seznam Rostlin Kveteny Ceske. Fr. Rivnace, Prague, 220 pp.
  18. Park, J., H. Xi and S.-H. Oh. 2020. Comparative chloroplast genomics and phylogenetic analysis of the Viburnum dilatatum complex (Adoxaceae) in Korea. Korean Journal of Plant Taxonomy 50: 8-16. https://doi.org/10.11110/kjpt.2020.50.1.8
  19. Posada D. and K. A. Crandall. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14: 817-818. https://doi.org/10.1093/bioinformatics/14.9.817
  20. Refulio-Rodriguez, N. F. and R. G. Olmstead. 2014. Phylogeny of Lamiidae. American Journal Botany 101: 287-299. https://doi.org/10.3732/ajb.1300394
  21. Salehi, B., M. S. Shetty, N. V. A. Kumar, J. Zivkovic, D. Calina, A. O. Docea, S. Emamzadeh-Yazdi, C. S. Kilic, T. Goloshvili, S. Nicola, G. Pignata, F. Sharopov, M. M. Contreras, W. C. Cho, N. Martins and J. Sharifi-Rad. 2019. Veronica plants: drifting from farm to traditional healing, food application, and phytopharmacology. Molecules 24: 2454. https://doi.org/10.3390/molecules24132454
  22. Silvestro, D. and I. Michalak. 2012. RaxmlGUI: a graphical frontend for RAxML. Organisms Diversity and Evolution 12: 335-337. https://doi.org/10.1007/s13127-011-0056-0
  23. Yamazaki, T. 1968. On the genus Pseudolysimachion. Journal of Japanease Botany 43: 405-412.