Browse > Article
http://dx.doi.org/10.11110/kjpt.2022.52.4.262

Complete chloroplast genome sequence of Clematis calcicola (Ranunculaceae), a species endemic to Korea  

Beom Kyun PARK (Division of Forest Biodiversity, Korea National Arboretum)
Young-Jong JANG (Division of Forest Biodiversity, Korea National Arboretum)
Dong Chan SON (Division of Forest Biodiversity, Korea National Arboretum)
Hee-Young GIL (Division of Forest Biodiversity, Korea National Arboretum)
Sang-Chul KIM (Division of Forest Biodiversity, Korea National Arboretum)
Publication Information
Korean Journal of Plant Taxonomy / v.52, no.4, 2022 , pp. 262-268 More about this Journal
Abstract
The complete chloroplast genome (cp genome) sequence of Clematis calcicola J. S. Kim (Ranunculaceae) is 159,655 bp in length. It consists of large (79,451 bp) and small (18,126 bp) single-copy regions and a pair of identical inverted repeats (31,039 bp). The genome contains 92 protein-coding genes, 36 transfer RNA genes, eight ribosomal RNA genes, and two pseudogenes. A phylogenetic analysis based on the cp genome of 19 taxa showed high similarity between our cp genome and data published for C. calcicola, which is recognized as a species endemic to the Korean Peninsula. The complete cp genome sequence of C. calcicola reported here provides important information for future phylogenetic and evolutionary studies of Ranunculaceae.
Keywords
Clematis; C. calcicola; Korean endemic species; phylogenetic relationships; plastome; simple sequence repeats;
Citations & Related Records
Times Cited By KSCI : 2  (Citation Analysis)
연도 인용수 순위
1 Chang, C. S. 2007. Clematis L. In The Genera of Vascular Plants of Korea. Flora of Korea Editorial Committee (ed.), Academy Publishing Co., Seoul. Pp. 191-195.
2 Chang, C. S. and H. Kim. 2018. Clematis L. In The Genera of Vascular Plants of Korea. Flora of Korea Editorial Committee (ed.), Hongneung Science Publishing Co., Seoul. Pp. 253-259.
3 Choi, K. S., Y. -H. Ha, H.-Y. Gil, K. Choi, D.-K. Kim and S.-H. Oh. 2021. Two Korean endemic Clematis chloroplast genomes: inversion, reposition, expansion of the inverted repeat region, phylogenetic analysis, and nucleotide substitution rates. Plants 10: 397.   DOI
4 Chung, G. Y., K. S. Chang, J.-M. Chung, H. J. Choi, W.-K. Paik and J.-O. Hyun. 2017. A checklist of endemic plants on the Korean Peninsula. Korean Journal of Plant Taxonomy 47: 264-288.   DOI
5 Fu, P.-C., Y.-Z. Zhang, H.-M. Geng and S.-L. Chen. 2016. The complete chloroplast genome sequence of Gentiana lawrencei var. farreri (Gentianaceae) and comparative analysis with its congeneric species. PeerJ 4: e2540.   DOI
6 Golenberg, E. M., M. T. Clegg, M. L. Durbin, J. Doebley and D. P. Ma. 1993. Evolution of a noncoding region of the chloroplast genome. Molecular Phylogenetics and Evolution 2: 52-64.   DOI
7 Gray, M. W. 1989. The evolutionary origins of organelles. Trends in Genetics 5: 294-299.   DOI
8 Howe, C. J., A. C. Barbrook, V. L. Koumandou, R. E. R. Nisbet, H. A. Symington and T. F. Wightman. 2003. Evolution of the chloroplast genome. Philosophical Transactions of the Royal Society of London Series B Biology Sciences 358: 99-107.   DOI
9 Kadota, Y. 2006. Clematis L. In Flora of Japan. Vol. IIa. Angiospermae, Dicotyledoneae, Archichlamydeae. Iwatsuki, K., D. E. Boufford and H. Ohba (eds.), Kodansha, Tokyo. Pp. 298-308.
10 Kalyaanamoorthy, S., B. Q. Minh, T. K. F. Wong, A. von Haeseler and L. S. Jermiin. 2017. ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature Methods 14: 587-589.   DOI
11 Katoh, K., K. Misawa, K.-I. Kuma and T. Miyata. 2002. MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Research 30: 3059-3066.   DOI
12 Katoh, K and D. M. Standley. 2013. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution 30: 772-780.   DOI
13 Kim, J.-S., J.-M. Chung, S.-Y. Kim and J.-H. Park. 2009. Clematis calcicola J. S. Kim: A new species of Clematis sect. Atragene (Ranunculaceae) from Korea. Korean Journal of Plant Taxonomy 39: 1-3.   DOI
14 Kim, J. S. 2017a. Clematis L. In Flora of Korea Vol. 2a. National Institute of Biological Resources (ed.), Incheon. Pp. 69-76.
15 Kim, M. 2017b. Korean Endemic Plants. Haejin Media Co. Ltd., Seoul. P. 76.
16 Lee, J. K. and H. S. Kim. 2018. Clematis calcicola J. S. Kim. In Silvics of Korea. Vol. 2. Oh, B. U. and S. H. Oh (eds.), Korea National Arboretum of the Korea Forest Service, Pocheon. Pp. 63-71.
17 Park, B. K., B. Ghimire, Y.-H. Ha, D. C. Son and D.-K. Kim. 2021. Complete chloroplast genome of Clematis taeguensis (Ranunculaceae), an endemic species from South Korea. Mitochondrial DNA Part B Resources 6: 1496-1497.   DOI
18 Maier, R. M., K. Neckermann, G. L. Igloi and H. Kossel. 1995. Complete sequence of the maize chloroplast genome: Gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. Journal of Molecular Biology 251: 614-628.   DOI
19 National Institute of Biological Resources. 2011. Endemic Species of Korea. Geobook, Incheon. P. 331.
20 Palmer, J. D. 1985. Comparative organization of chloroplast genomes. Annual Review of Genetics 19: 325-354.   DOI
21 Park, B. K., J.-S. Kim, G. Y. Chung, J.-H. Kim, D. C. Son and C.- G. Jang. 2022. Clematis pseudotubulosa (Ranunculaceae), a new species from Korea. Korean Journal of Plant Taxonomy 52: 35-44.   DOI
22 Reith, M. and J. Munholland. 1995. Complete nucleotide sequence of the Porphyra purpurea chloroplast genome. Plant Molecular Biology Reporter 13: 333-335.   DOI
23 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.   DOI
24 Tamura, M. 1955. Systema clematidis Asiae Orientalis. Science Reports, Vol. 4. College of General Education, Osaka University, Osaka. Pp. 43-55.
25 Tamura, M. 1967. Morphology, Ecology and Phylogeny of the Ranunculaceae VII. Science Reports, Vol. 16. College of General Education, Osaka University, Osaka. Pp. 21-43.
26 Tamura, M. 1987. A classification of genus Clematis. Acta Phytotaxonomica et Geobotanica 38: 33-44.
27 Wang, R.-J., C.-L. Cheng, C.-C. Chang, C.-L. Wu, T.-M. Su and S.-M. Chaw. 2008. Dynamics and evolution of the inverted repeat-large single copy junctions in the chloroplast genomes of monocots. BMC Evolutionary Biology 8: 36.   DOI
28 Tamura, M. 1995. Clematis. In Die Naturlichen Pflanzenfamilien. Zweite Aufl, Vol. 17a. IV. Hiepko, P. (ed.), Dunker & Humbolt, Berlin. Pp. 368-387.
29 Tillich, M., P. Lehwark, T. Pellizzer, E. S. Ulbricht-Jones, A. Fischer, R. Bock and S. Greiner. 2017. GeSeq: Versatile and accurate annotation of organelle genomes. Nucleic Acids Research 45: W6-W11.   DOI
30 Trifinopoulos, J., L.-T. Nguyen, A. von Haeseler and B. Q. Minh. 2016. W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research 44: W232-W235.   DOI
31 Wang, W. T. and B. Bartholomew. 2001. Clematis L. In Flora of China. Vol. 6. Caryophyllaceae through Lardizabalaceae. Wu, Z. Y., P. H. Raven and D. Y. Hong (eds.), Science Press, Beijing and Missouri Botanical Garden Press, St. Louis, MO. Pp. 333-386.
32 Wang, W.-T. and L.-Q. Li. 2005. A new system of classification of the genus Clematis (Ranunculaceae). Acta Phytotaxonomica Sinica 43: 431-488.
33 Yang, W.-J., L.-Q. Li and L. Xie. 2009. A revision of Clematis sect. Atragene (Ranunculaceae). Journal of Systematics and Evolution 47: 552-580.   DOI
34 Zhang, D., F. Gao, I. Jakovlic, H. Zou, J. Zhang, W. X. Li and G. T. Wang. 2020. PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Molecular Ecology Resources 20: 348-355.   DOI