DOI QR코드

DOI QR Code

The complete chloroplast genome of Aruncus aethusifolius (Rosaceae), a species endemic to Korea

  • 투고 : 2022.02.25
  • 심사 : 2022.03.14
  • 발행 : 2022.06.30

초록

Aruncus aethusifolius (H. Lév.) Nakai is an endemic species in Korea and is economically important as an ornamental herb. The complete chloroplast genome of A. aethusifolius is 157,217 bp long with four subregions consisting of 85,207 bp of large singlecopy and 19,222 bp of small single-copy regions separated by 26,394 bp of inverted repeat regions. The genome includes 131 genes (86 protein-coding genes, eight rRNAs, and 37 tRNAs). Phylogenetic analyses demonstrates that the chloroplast genome of A. aethusifolius was sister to A. dioicus var. kamtschaticus, forming the strongly supported clade of Aruncus. This is the first report of the chloroplast genome of A. aethusifolius.

키워드

과제정보

This work was supported, in part, by research grants from the National Institute of Biological Resources of Korea (NIBR-202104201).

참고문헌

  1. Baek, J., S. Park, J. Lee, J. Min, J. Park and G. W. Lee. 2021. The complete chloroplast genome of Chrysanthemum zawadskii Herbich (Asteraceae) isolated in Korea. Mitochondrial DNA Part B Resources 6: 1956-1958. https://doi.org/10.1080/23802359.2021.1934148
  2. Bolger, A. M., M. Lohse and B. Usadel. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120. https://doi.org/10.1093/bioinformatics/btu170
  3. Darriba, D., G. L. Taboada, R. Doallo and D. Posada. 2012. jModelTest 2: More models, new heuristics and parallel computing. Nature Methods 9: 772.
  4. Greiner, S., P. Lehwark and R. Bock. 2019. OrganellarGenome-DRAW (OGDRAW) version 1.3.1: Expanded toolkit for thegraphical visualization of organellar genomes. Nucleic Acids Research 47: W59-W64. https://doi.org/10.1093/nar/gkz238
  5. Kim, M.-H., S. Park, J. Lee, J, Baek, J. Park and G. W. Lee. 2021. The complete chloroplast genome of Glycyrrhiza uralensis Fisch. isolated in Korea (Fabaceae). Korean Journal of Plant Taxonomy 51: 353-362. https://doi.org/10.11110/kjpt.2021.51.4.353
  6. Kumar, S., G. Stecher, M. Li, C. Knyaz and K. Tamura. 2018. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution 35: 1547-1549. https://doi.org/10.1093/molbev/msy096
  7. Hara, H. 1955. Critical notes on some type specimens of East-Asiatic plants in foreign herbaria (2). Journal of Japanese Botany 30: 65-72.
  8. Lee, B and J. Park. 2021. The complete chloroplast genome of Zoysia japonica Steud. isolated in Korea (Poaceae): Investigation of potential molecular markers on Z. japonica chloroplast genomes. Plant Biotechnology Reports 15: 707-715. https://doi.org/10.1007/s11816-021-00708-y
  9. Lee, T. B. 1980. Illustrated Flora of Korea. Hyang-mun Pub. Co., Seoul, 990 pp.
  10. Lee, Y. N. 2006. New Flora of Korea. Kyo-Hak Publishing Co., Seoul, Vol. 1, 975 pp, Vol. 2, 885 pp. (in Korean)
  11. Li, H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint at: https://arxiv.org/abs/1303.3997.
  12. Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis and R. Durbin. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079. https://doi.org/10.1093/bioinformatics/btp352
  13. Nakai, T. 1912. Notulae ad plantas Japoniae et Coreae VIII. Botanical Magazine (Tokyo) 26: 321-328. https://doi.org/10.15281/jplantres1887.26.303_57
  14. Park, J., Y. Kim and M. Kwon. 2019a. The complete mitochondrial genome of tulip tree, Liriodendron tulipifera L. (Magnoliaceae): Intra-species variations on mitochondrial genome. Mitochondrial DNA Part B Resources 4: 1308-1309. https://doi.org/10.1080/23802359.2019.1591242
  15. Park, J., Y. Kim, W. Kwon, H. Xi and C.-H. Park. 2021. The complete chloroplast genome sequence of new species candidate of Plantago depressa Willd. in Korea (Plantaginaceae). Mitochondrial DNA Part B Resources 6: 1961-1963. https://doi.org/10.1080/23802359.2021.1935356
  16. Park, J., Y. Kim, H. Xi and K.-I. Heo. 2019b. The complete chloroplast genome of ornamental coffee tree, Coffea arabica L. (Rubiaceae). Mitochondrial DNA Part B Resources 4: 1059-1060. https://doi.org/10.1080/23802359.2019.1584060
  17. Park, J., H. Xi and Y. Kim. 2020a. The complete chloroplast genome of Arabidopsis thaliana isolated in Korea (Brassicaceae): An investigation of intraspecific variations of the chloroplast genome of Korean A. thaliana. International Journal of Genomics 3236461.
  18. Park, J., H. Xi, Y. Kim, S. Nam, K.-I. Heo. 2020b. The complete mitochondrial genome of new species candidate of Rosa rugosa (Rosaceae). Mitochondrial DNA Part B Resources 5: 3435-3437. https://doi.org/10.1080/23802359.2020.1821820
  19. Park, J., H. Xi and S.-H. Oh. 2020c. 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
  20. Park, J., N. Yun and S.-H. Oh. 2019c. The complete chloroplast genome of an endangered species in Korea, Halenia corniculata (L.) Cornaz (Gentianaceae). Mitochondrial DNA Part B Resources 4: 1539-1540. https://doi.org/10.1080/23802359.2019.1601532
  21. Potter, D., T. Eriksson, R. C. Evans, S. Oh, J. E. F. Smedmark, D. R. Morgan, M. Kerr, K. M. Robertson, M. Arsenault, T. A. Dickinson and C. Campbell. 2007. Phylogeny and classification of Rosaceae. Plant Systematics and Evolution 266: 5-43. https://doi.org/10.1007/s00606-007-0539-9
  22. Ronquist, F., M. Teslenko, P. Van Der Mark, D. L. Ayres, A. Darling, S. Hohna, B. Larget, L. Liu, M. A. Suchard and J. P. Huelsenbeck. 2012. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539-542. https://doi.org/10.1093/sysbio/sys029
  23. Suh, H.-J., J. Min, J. Park and S.-H. Oh. 2021. The complete chloroplast genome of Aruncus dioicus var. kamtschaticus (Rosaceae). Mitochondrial DNA Part B Resources 6: 1256-1258. https://doi.org/10.1080/23802359.2021.1906173
  24. Tatusova, T. A. and T. L. Madden. 1999. BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiology Letters 174: 247-250. https://doi.org/10.1016/S0378-1097(99)00149-4
  25. Yoo, S.-C., S.-H. Oh and J. Park. 2021. Phylogenetic position of Daphne genkwa (Thymelaeaceae) inferred from complete chloroplast data. Korean Journal of Plant Taxonomy 51: 171-175. https://doi.org/10.11110/kjpt.2021.51.2.171
  26. Yun, N., H.-J. Suh and S.-H. Oh. 2017. Sexuality of Aruncus aethusifolius (Rosaceae). Korean Journal of Plant Taxonomy 47: 189-195. https://doi.org/10.11110/kjpt.2017.47.3.189
  27. Zerbino, D. R. and E. Birney. 2008. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18: 821-829. https://doi.org/10.1101/gr.074492.107
  28. Zhang, S.-D., J.-J. Jin, S.-Y. Chen, M. W. Chase, D. E. Soltis, H.-T. Li, J.-B. Yang, D.-Z. Li and T.-S. Yi. 2017. Diversification of Rosaceae since the Late Cretaceous based on plastid phylogenomics. New Phytologist 214: 1355-1367. https://doi.org/10.1111/nph.14461
  29. Zhao, Q.-Y., Y. Wang, Y.-M. Kong, D. Luo, X. Li and P. Hao. 2011. Optimizing de novo transcriptome assembly from shortread RNA-Seq data: A comparative study. BMC Bioinformatics 12(Suppl 14): S2.