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http://dx.doi.org/10.11110/kjpt.2021.51.4.345

The complete chloroplast genome of Diarthron linifolium (Thymelaeaceae), a species found on a limestone outcrop in eastern Asia  

KIM, Sang-Tae (Department of Medical & Biological Sciences, The Catholic University of Korea)
OH, Sang-Hun (Department of Biology, Daejeon University)
PARK, Jongsun (InfoBoss Research Center)
Publication Information
Korean Journal of Plant Taxonomy / v.51, no.4, 2021 , pp. 345-352 More about this Journal
Abstract
Diarthron linifolium Turcz. is an annual herb usually found in sandy soil or limestone areas. Plants in the genus Diarthron are known to have toxic chemicals that may, however, be potentially useful as an anticancer treatment. Diarthron linifolium is a unique species among the species of the genus distributed in Korea. Here, we determine the genetic variation of D. linifolium collected in Korea with a full chloroplast genome and investigate its evolutionary status by means of a phylogenetic analysis. The chloroplast genome of Korean D. linifolium has a total length of 172,644 bp with four subregions; 86,158 bp of large single copy and 2,858 bp of small single copy (SSC) regions are separated by 41,814 bp of inverted repeat (IR) regions. We found that the SSC region of D. linifolium is considerably short but that IRs are relatively long in comparison with other chloroplast genomes. Various simple sequence repeats were identified, and our nucleotide diversity analysis suggested potential marker regions near ndhF. The phylogenetic analysis indicated that D. linifolium from Korea is a sister to the group of Daphne species.
Keywords
chloroplast genomes; Diarthron linifolium; phylogenetic analysis; simple sequence repeats; Thymelaeaceae;
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1 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
2 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.   DOI
3 Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin and 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics 25: 2078-2079.   DOI
4 Loeuille, B., V. Thode, C. Siniscalchi, S. Andrade, M. Rossi and J. R. Pirani. 2021. Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences from Aldama (Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera. PeerJ 9: e10886.   DOI
5 Jeon, J.-H. and S.-C. Kim. 2019. Comparative analysis of the complete chloroplast genome sequences of three closely related East-Asian wild roses (Rosa sect. Synstylae; Rosaceae). Genes 10: 23.   DOI
6 Jiang, D., Z. Zhao, T. Zhang, W. Zhong, C. Liu, Q. Yuan and L. Huang. 2017. The chloroplast genome sequence of Scutellaria baicalensis provides insight into intraspecific and interspecific chloroplast genome diversity in Scutellaria. Genes 8: 227.   DOI
7 Kim, M., H. Xi and J. Park. 2021a. Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors. PLoS ONE 16: e0252181.   DOI
8 Kim, M., H. Xi, S. Park, Y. Yun and J. Park. 2021b. Genome-wide comparative analyses of GATA transcription factors among seven Populus genomes. Scientific Reports 11: 16578.   DOI
9 Kim, Y., J. Park and Y. Chung. 2019. Comparative analysis of chloroplast genome of Dysphania ambrosioides (L.) Mosyakin & Clemants understanding phylogenetic relationship in genus Dysphania R. Br. Korean Journal of Plant Resources 32: 644-668.   DOI
10 Kwon, W., Y. Kim, C.-H. Park and J. Park. 2019. The complete chloroplast genome sequence of traditional medical herb, Plantago depressa Willd. (Plantaginaceae). Mitochondrial DNA Part B Resources 4: 437-438.   DOI
11 Huelsenbeck, J. P. and F. Ronquist. 2001. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.   DOI
12 Shukla, N., H. Kuntal, A. Shanker and S. N. Sharma. 2018. Mining and analysis of simple sequence repeats in the chloroplast genomes of genus Vigna. Biotechnology Research and Innovation 2: 9-18.   DOI
13 Qian, S., Y. Zhang and S. Y. Lee. 2021. Comparative analysis of complete chloroplast genome sequences in Edgeworthia (Thymelaeaceae) and new insights into phylogenetic relationships. Frontiers in Genetics 12: 643552.   DOI
14 Roberts, R. J., M. O. Carneiro and M. C. Schatz. 2013. The advantages of SMRT sequencing. Genome Biology 14: 405.   DOI
15 Schattner, P., A. N. Brooks and T. M. Lowe. 2005. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Research 33(Suppl): W686-W689.   DOI
16 Tan, K. 1982. Studies in the Thymelaeaceae. III. The status of Diarthon, Dendrostellera, Stelleropsis and Stellera. Notes from the Royal Botanic Garden Edinburgh 40: 213-221.
17 Liu, W., H. Kong, J. Zhou, P. W. Fritsch, G. Hao and W. Gong. 2018. Complete chloroplast genome of Cercis chuniana (Fabaceae) with structural and genetic comparison to six species in Caesalpinioideae. International Journal of Molecular Sciences 19: 1286.   DOI
18 Li, B., F. Lin, P. Huang, W. Guo and Y. Zheng. 2020a. Development of nuclear SSR and chloroplast genome markers in diverse Liriodendron chinense germplasm based on low-coverage whole genome sequencing. Biological Research 53: 21.   DOI
19 Li, H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint at https://arxiv.org/abs/1303.3997.
20 Li, W., C. Zhang, X. Guo, Q. Liu and K. Wang. 2019. Complete chloroplast genome of Camellia japonica genome structures, comparative and phylogenetic analysis. PLoS ONE 14: e0216645.   DOI
21 Min, J., W. Kwon, H. Xi and J. Park. 2019. The complete chloroplast genome of Leucobryum juniperoideum (brid.) C. Mull. (Leucobryaceae, Bryophyta). Mitochondrial DNA Part B Resources 4: 2962-2963.   DOI
22 Cho, W.-B., E.-K. Han, G. Choi and J.-H. Lee. 2018. The complete chloroplast genome of Daphne kiusiana, an evergreen broad-leaved shrub on Jeju Island. Conservation Genetics Resources 10: 103-106.   DOI
23 Nei, M. and W. H. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proceedings of the National Academy of Sciences of the United States of America 76: 5269-5273.   DOI
24 Li, C., Y. Zheng and P. Huang. 2020b. Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling. Scientific Reports 10: 12188.   DOI
25 Beaumont, A. J., T. J. Edwards, J. Manning, O. Maurin, M. Rautenbach, M. C. Motsi, M. F. Fay, M. W. Chase and M. Van der Bank. 2009. Gnidia (Thymelaeaceae) is not monophyletic: Taxonomic implications for Thymelaeoideae and a partial new generic taxonomy for Gnidia. Botanical Journal of the Linnean Society 160: 402-417.   DOI
26 Bolger, A. M., M. Lohse and B. Usadel. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120.   DOI
27 Chen, J., Z. Hao, H. Xu, L. Yang, G. Liu, Y. Sheng, C. Zheng, W. Cheng, T. Cheng and J. Shi. 2015. The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng. Frontiers in Plant Science 6: 447.   DOI
28 Choi, N. J., H. Xi and J. Park. 2021. A comparative analyses of the complete mitochondrial genomes of fungal endosymbionts in Sogatella furcifera, white-backed planthoppers. International Journal of Genomics 2021: 6652508.
29 de Souza, U. J. B., R. Nunes, C. P. Targueta, J. A. F. Diniz-Filho and M. P. de Campos Telles. 2019. The complete chloroplast genome of Stryphnodendron adstringens (Leguminosae-Caesalpinioideae): Comparative analysis with related Mimosoid species. Scientific Reports 9: 14206.   DOI
30 Deamer, D., M. Akeson and D. Branton. 2016. Three decades of nanopore sequencing. Nature Biotechnology 34: 518-524.   DOI
31 Dong, W., C. Xu, C. Li, J. Sun, Y. Zuo, S. Shi, T. Cheng, J. Guo and S. Zhou. 2015. ycf1, the most promising plastid DNA barcode of land plants. Scientific Reports 5: 8348.   DOI
32 Wang, Q., L.-H. Mao, B. Ding, M.-T. Li, Z.-X. Fu and H.-P. Deng. 2020. The complete chloroplast genome of Plantago fengdouensis (Plantaginaceae): An endemic and endangered species from China. Mitochondrial DNA Part B Resources 5: 51-52.   DOI
33 Gandhi, S. G., P. Awasthi and Y. S. Bedi. 2010. Analysis of SSR dynamics in chloroplast genomes of Brassicaceae family. Bioinformation 5: 16-20.   DOI
34 Cheng, J., Z. Zhao, B. Li, C. Qin, Z. Wu, D. L. Trejo-Saavedra, X. Luo, J. Cui, R. F. Rivera-Bustamante, S. Li and K. Hu. 2016. A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum. Scientific Reports 6: 18919.   DOI
35 Galicia-Herbada, D. 2006. Origin and diversification of Thymelaea (Thymelaeaceae): Inferences from a phylogenetic study based on ITS (rDNA) sequences. Plant Systematics and Evolution 257: 159-187.   DOI
36 Yan, F., X. Tao, Q.-L. Wang, Z. Y. Juan, C.-M. Zhang and H. L. Yu. 2019a. The complete chloroplast genome sequence of the medicinal shrub Daphne giraldii Nitsche. (Thymelaeaceae). Mitochondrial DNA Part B Resources 4: 2685-2686.   DOI
37 Yan, F., Q.-L. Wang, Y.-J. Zhang, C.-M. Zhang and Y. Chen. 2019b. The complete chloroplast genome sequence of medicinal plant, Daphne tangutica Maxim. (Thymelaeaceae). Mitochondrial DNA Part B Resources 4: 1776-1777.   DOI
38 Lee, J., J. Park, H. Xi and J. Park. 2020. Comprehensive analyses of the complete mitochondrial genome of Figulus binodulus (Coleoptera: Lucanidae). Journal of Insect Science 20: 10.
39 Van der Bank, M., M. F. Fay and M. W. Chase. 2002. Molecular phylogenetics of Thymelaeaceae with particular reference to African and Australian genera. Taxon 51: 329-339.   DOI
40 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.   DOI
41 Hishamuddin, M. S., S. Y. Lee, W. L. Ng, S. I. Ramlee, D. U. Lamasudin and R. Mohamed. 2020. Comparison of eight complete chloroplast genomes of the endangered Aquilaria tree species (Thymelaeaceae) and their phylogenetic relationships. Scientific Reports 10: 13034.   DOI
42 Neubig, K. M., W. M. Whitten, B. S. Carlsward, M. A. Blanco, L. Endara, N. H. Williams and M. Moore. 2009. Phylogenetic utility of ycf 1 in orchids: A plastid gene more variable than matK. Plant Systematics and Evolution 277: 75-84.   DOI
43 Park, J., J. Min, Y. Kim and Y. Chung. 2021a. The comparative analyses of six complete chloroplast genomes of morphologically diverse Chenopodium album L. (Amaranthaceae) collected in Korea. International Journal of Genomics 2021: 6643444.
44 Park, J., and H. Xi. 2021. Investigation of nucleotide diversity based on 17 sea cucumber mitochondrial genomes and assessment of sea cucumber mitochondrial gene markers. Advances in Oceanography and Marine Biology 2: 2021.
45 Goodwin, S., J. D. McPherson and W. R. McCombie. 2016. Coming of age: Ten years of next-generation sequencing technologies. Nature Reviews Genetics 17: 333-351.   DOI
46 He, L., Y. Zhang and S. Y. Lee. 2021. Complete plastomes of six species of Wikstroemia (Thymelaeaceae) reveal paraphyly with the monotypic genus Stellera. Scientific Reports 11: 13608.   DOI
47 Hong, S.-Y., K.-S. Cheon, K.-O. Yoo, H.-O. Lee, K.-S. Cho, J.-T. Suh, S.-J. Kim, J.-H. Nam, H.-B. Sohn and Y.-H. Kim. 2017. Complete chloroplast genome sequences and comparative analysis of Chenopodium quinoa and C. album. Frontiers in Plant Science 8: 1696.   DOI
48 Huang, J., X. Yang, C. Zhang, X. Yin, S. Liu and X. Li. 2015. Development of chloroplast microsatellite markers and analysis of chloroplast diversity in Chinese jujube (Ziziphus jujuba Mill.) and wild jujube (Ziziphus acidojujuba Mill.). PLoS ONE 10: e0134519.   DOI
49 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.   DOI
50 Yan, F., C.-Y. Zhang, Q.-L. Wang, J.-D. Wang, H.-P. Wang, T. Xu, E.-J. Wang and L.-Y. Hou. 2021. Characterization of the complete chloroplast genome sequence of Daphne retusa Hemsl. (Thymelaeaceae), a rare alpine plant species in northwestern China. Mitochondrial DNA Part B Resources 6: 2139-2141.   DOI
51 Zerbino, D. R. and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18: 821-829.   DOI
52 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.
53 Yun, N., J. Park and S.-H. Oh. 2019. The complete chloroplast genome of the traditional medicinal plant Stellera chamaejasme L. (Thymelaeaceae). Mitochondrial DNA Part B Resources 4: 1796-1797.   DOI
54 Park, J., H. Xi, Y. Kim, S. Nam and K.-I. Heo. 2020b. The complete mitochondrial genome of new species candidate of Rosa rugosa (Rosaceae). Mitochondrial DNA Part B Resources 5: 3435-3437.   DOI
55 Sun, D.-X., D. Zhao, H.-Y. Wei, X.-L. Ma, L.-L. Shi and J. Zhang. 2018. Four new sesquiterpenoids from the roots of Diarthron tianschanica with their antineoplastic activity. Molecules 23: 1383.   DOI
56 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 2020: 3236461.
57 Park, J., H. Xi and Y. Kim. 2021b. The complete mitochondrial genome of Arabidopsis thaliana (Brassicaceae) isolated in Korea. Korean Journal of Plant Taxonomy 51: 176-180.   DOI
58 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.   DOI