Biologia Plantarum 63: 565-574, 2019 | DOI: 10.32615/bp.2019.101

Comparative analysis of complete chloroplast genomes sequencesof Arctium lappa and A. tomentosum

Y.-P. XING1, L. XU1,*, S.-Y. CHEN1, Y.-M. LIANG1, J.-H. WANG1, C.-S. LIU2, T. LIU3, T.-G. KANG1,*
College of Traditional Chinese Medicine, Liaoning University of Traditional Chinese Medicine,
1 Dalian 116600, P.R. China
2 College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100102, P.R. China
3 School of Pharmacy, China Medical University, Shenyang 110122, P.R. China

Arctium lappa and A. tomentosum are known medicinal plants in China. The complete chloroplast genomes from A. lappa and A. tomentosum were sequenced using Illumina sequencing technology. The total genome sizes of the complete chloroplast genomes of A. lappa and A. tomentosum were 152 767 bp and 152 688 bp, respectively, and contained a pair of inverted repeats of the same length (15,181 bp). The small single-copies were 18 584 bp and 18 582 bp, and the large single-copies were 83 821 bp and 83 744 bp, respectively. We identified and annotated 134 and 126 genes from A. lappa and A. tomentosum including, respectively, 90 and 89 protein-coding genes, 36 and 29 tRNAs, and eight rRNAs. A. lappa was found to have 10 tRNAs different from those in A. tomentosum, and A. tomentosum had three tRNAs different from those in A. lappa. There were only two types of simple sequence repeats of two species, mononucleotide and dinucleotide, and the sequences were A and T rich. In addition, the two ways of phylogenetic analysis show that the position of A. lappa and A. tomentosum is consistent within Asteraceae.

Keywords: medicinal plants, phylogenetic analysis, simple sequence repeats.

Received: March 1, 2018; Revised: October 7, 2018; Accepted: December 11, 2018; Published online: August 2, 2019Show citation

ACS AIP APA ASA Harvard Chicago IEEE ISO690 MLA NLM Turabian Vancouver
XING, Y.-P., XU, L., CHEN, S.-Y., LIANG, Y.-M., WANG, J.-H., LIU, C.-S., LIU, T., & KANG, T.-G. (2019). Comparative analysis of complete chloroplast genomes sequencesof Arctium lappa and A. tomentosum. Biologia plantarum, 63, 565-574. doi: 10.32615/bp.2019.101.
Download citation
  • BibTeX (.bib)
  • Bookends (.ris)
  • EasyBib (.ris)
  • EndNote (.enw)
  • EndNote 8 (.xml)
  • ISI WoS (.isi)
  • Medlars (.medlars)
  • Mendeley (.ris)
  • MODS (.xml)
  • Papers (.ris)
  • RefWorks (.txt)
  • RefManager (.ris)
  • RIS (.ris)
  • MS Word (.xml)
  • Zotero (.ris)

    • Open full article

    Supplementary files

    Download fileXING5684 Suppl.pdf

    File size: 2.06 MB

    References

    1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W., Lipman, D.J.: Basic local alignment search tool. - J. mol. Biol. 215: 403-410, 1990. Go to original source...
    2. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S., Eppig, J., Harris, M., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G.: Gene ontology: tool for the unification of biology. - Nat. Genet. 25: 25-29, 2000. Go to original source...
    3. Borgstrom, E., Lundin, S., Lundeberg, J.: Large scale library generation for high throughput sequencing. - PLoS ONE 6: e19119, 2011. Go to original source...
    4. Chan, Y.S., Cheng, L.N., Wu, J.H., Chan, E., Kwan, Y.W., Lee, S.M., Leung, G.P., Yu, P.H., Chan, S.W.: A review of the pharmacological effects of A. lappa (burdock). - Inflammopharmacology 19: 245-254, 2011. Go to original source...
    5. Choi, K.S., Park, S.: The complete chloroplast genome sequence of Aster spathulifolius (Asteraceae); genomic features and relationship with Asteraceae. - Gene 572: 214-221, 2015. Go to original source...
    6. Chumley, T.W., Palmer, J.D., Mower, J.P., Fourcade, H.M., Calie, P.J., Boore, J.L., Jansen, R.K.: The complete chloroplast genome sequence of Pelargonium × hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. - Mol. Biol. Evol. 23: 2175-2190, 2006. Go to original source...
    7. Chung, S.M., Deena S.D.W., Jack, E.S.: Genetic relationships within the Cucurbitaceae as assessed by consensus chloroplast simple sequence repeats (ccSSR) marker and sequence analyses. - Can. J. Bot. 81: 814-832, 2003. Go to original source...
    8. Conea, S., Mogoan, C., Vostinaru, O., Toma, C.C., Hepcal, I.C., Cazacu, I., Pop, C., Vlase., L.: Polyphenolic profile, anti-inflammatory and antinociceptive activity of an extract from A. lappa L. roots. - Not. Bot. Hort. Agrobot. 45: 59-64, 2017. Go to original source...
    9. Cronn, R., Liston, A., Parks, M., Gernandt, D.S., Shen, R.K.: Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by- synthesis technology. - Nucl. Acids Res. 36: e122, 2008. Go to original source...
    10. Curci, P.L., De, P.D., Danzi, D., Vendramin, G.G., Sonnante, G.: Complete chloroplast genome of the multifunctional crop globe artichoke and comparison with other Asteraceae. - PLoS ONE 10: e0120589, 2015. Go to original source...
    11. Frazer, K.A., Pachter, L., Poliakov, A., Rubin, E.M., Dubchak, A.I.: VISTA: computational tools for comparative genomics. - Nucl. Acids Res. 32: W273-W279, 2004. Go to original source...
    12. He, L., Qian, J., Li, X.W., Sun, Z.Y., Xu, X.L., Chen, S.L.: Complete chloroplast genome of medicinal plant Lonicera japonica: genome rearrangement, intron gain and loss, and implications for phylogenetic studies. - Molecules 22: 249, 2017. Go to original source...
    13. Jansen, R.K., Raubeson, L.A., Boore, J.L., De Pamphilis, C.W., Chumley, T.W., Haberle, R.C., Wyman, S.K., Alverson, A.J., Peery, R., Herman, S.J., Fourcade, H.M., Kuehl, J.V., McNeal, J.R., Leebens M.J., Cui, L.: Methods for obtaining and analyzing whole chloroplast genome sequences. - Methods Enzymol. 395: 348-384, 2005. Go to original source...
    14. Jiao, Y., Jia, H.M., Li, X.W., Chai, M.L., Jia, H.J., Chen, Z., Wang, G.Y., Chai, C.Y., Van de Weg, E., Gao, Z.S.: Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry (Myrica rubra). - BMC Genomics 13: 201, 2012. Go to original source...
    15. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., Hattori, M.: The KEGG resource for deciphering the genome. - Nucl. Acids Res. 32: D277-D280, 2004. Go to original source...
    16. Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K.F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., Hirakawa, M.: From genomics to chemical genomics: new developments in KEGG. - Nucl. Acids Res. 34: D354-D357, 2006. Go to original source...
    17. Kanehisa, M.: A database for post-genome analysis. - Trends Genet. 13: 375, 1997. Go to original source...
    18. Kang, J.S., Lee, B.Y., Kik, M.: The complete chloroplast genome sequences of Lychnwas wilfordii and Silene capitata and comparative analyses with other Caryophyllaceae genomes. - PLoS ONE 12: e0172924, 2017. Go to original source...
    19. Khakhlova, O., Bock, R.: Elimination of deleterious mutations in plastid genomes by gene conversion. - Plant J. 46: 85-94, 2006. Go to original source...
    20. Kim, K.J., Lee, H.L.: Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. - DNA Res. 11: 247-261, 2004. Go to original source...
    21. Kim, K.J., Choi, K.S., Jansen, R.K.: Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae). - Mol. Biol. Evol. 22: 1783-1792, 2005. Go to original source...
    22. Kim, W.J., Moon, B.C., Yang, S., Han, K.S., Choi, G., Lee, A.Y.: Rapid authentication of the herbal medicine plant species Aralia continentalis Kitag., and Angelica bwaserrata C.Q. Yuan and R.H. Shan using ITS2 sequences and multiple x-SCAR markers. - Molecules 21: 270, 2016. Go to original source...
    23. Koren, S., Schatz, M.C., Walenz, B.P., Martin, J., Howard, J., Ganapathy, G., Wang, Z., Rasko, D.A., McCombie, W. R., Jarvis, E.D., Phillippy, A.M.: Hybrid error correction and de novo assembly of single-molecule sequencing reads. - Nat. Biotechnol. 30: 693-700, 2012. Go to original source...
    24. Li, X.W., Gao, H.H., Wang, Y.T., Song, J.Y., Robert, H., Wu, H.Z., Hu, Z.G., Yao, H., Luo, H.M., Luo, K., Pan, H.L., Chen, S.L.: Complete chloroplast genome sequence of Magnolia grandiflora and comparative analysis with related species. - Sci. China Life Sci. 56: 189-198, 2013. Go to original source...
    25. Liu, L.P., Wan, Q., Guo, Y.P., Yang, J., Rao, G.Y.: Phylogeny of the genus Chrysanthemum L.: evidence from single-copy nuclear gene and chloroplast DNA sequences. - PLoS ONE 7: e48970, 2012. Go to original source...
    26. Lohse, M., Drechsel O., Kahlau, S., Bock, R.: Organellar Genome DRAW - a suite of tools for generating physical maps of plastid and mitochondrial genomes visualizing expression data sets. - Nucl. Acids Res. 41: W575-W581, 2013. Go to original source...
    27. Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., Tang, J., Wu, G., Zhang, H., Shi, Y., Liu, Y., Yu, C., Wang, B., Lu, Y., Han, C., Cheung D.W., Yiu, S., Peng, S., Zhu, X., Liu, G., Liao, X., Li, Y., Yang, H., Wang, J., Lam T.W., Wang, J.: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. - Gigascience 1: 18, 2012. Go to original source...
    28. Masalih, R.H., Majesky, L., Schwarzacher, T., Gornall, R., Heslop-Harrison, P.: Complete chloroplast genomes from apomictic Taraxacum (Asteraceae): Identity and variation between three microspecies. - PLoS ONE 12: e0168008, 2017. Go to original source...
    29. Magrane, M., Consortium, U.: UniProt knowledge base: a hub of integrated protein data database. - Databases (Oxford) 2011: bar009, 2011.
    30. McPherson, H., Van der Merwe, M., Delaney, S.K., Edwards, M.A., Henry, H.R., McIntosh, E., Robert, J.H., McIntosh, E., Rymer, P.D., Milner, M.L., Siow, J., Rossetto, M.: Capturing chloroplast variation for molecular ecology studies: a simple next generation sequencing approach applied to a rainforest tree. - BMC Ecol. 13: 8, 2013. Go to original source...
    31. Ohyama, K., Fukuzai, H., Kohchi, T., Shirai, H., Sano, T., Sano, S., Umesono, K., Shiki,Y., Takeuchi, M., Chang, Z., Aota, S.I., Inokuchi, H., Ozeki, H.: Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. - Nature 322: 572-574, 1986. Go to original source...
    32. Palmer, J.D., Thompson, W.F.: Chloroplast DNA rearrangements are more frequent when a large inverted repeat sequence was lost. - Cell 29: 537-550, 1982. Go to original source...
    33. Raubeson, L.A., Jansen, R.K.: Chloroplast genomes of plants, plant diversity and evolution: genotypic and phenotypic variation in higher plants. - Mol. Phylogenet. Evol. 3: 45-68, 2005.
    34. Raubeson, L.A., Peery, R., Chumley, T.W., Dziubek, C., Fourcade, H.M., Boore, J.L., Jansen, R.K.: Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. - BMC Genomics 8: 174, 2007. Go to original source...
    35. Ravi, V., Khurana, J.P., Tyagi, A.K., Khurana, P.: An update on chloroplast genomes. - Plant Syst. Evol. 271: 101-122, 2008. Go to original source...
    36. Tatusov, R.L., Koonin, E.V., Lipman, D. J.: A genomic perspective on protein families. - Science 278: 631-637, 1997. Go to original source...
    37. Tatusov, R.L., Fedorova, N.D., Jackson, J.D., Jacobs, A.R., Kiryutin, B., Koonin, E.V., Krylov, D.M., Mazumder, R., Mekhedov, S.L., Nikolskaya, A.N., Bachoti,S., Smirnov,S., Sverdlov, A.V., Vasudevan, S., Wolf, Y.I.,Yin, J.J., Natale, D.A., Yin, J.J., Natale, D.A.: The COG database: an updated version includes eukaryotes. - BMC Bioinformatics 4: 41, 2003. Go to original source...
    38. Tseng, M.C., Wong, S.L., Hsiung, D.S., Hwang, J.H., Lee, S.C., Chen, F.H.: Genetic diversity of the chloroplast trnL-trnF intergenic spacer and nuclear internal transcribed spacer of great burdock (Arctium Lappa L.) in Taiwan. - J. med. Plants Res. 6: 5086-5093, 2012.
    39. Wang, M., Cui, L., Feng, K., Deng, P., Du, X., Wan, F., Song, W., Nie, X.: Comparative analysis of Asteraceae chloroplast genomes: structural organization, RNA editing and evolution. - Plant mol. Biol. Rep. 33: 1526-1538, 2015. Go to original source...
    40. Wicke, S., Schneeweiss, G.M., De Pamphilis, C.W., Muller, K.F., Quandt, D.: The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. - Plant mol. Biol. 76: 273-297, 2017.
    41. Wills, D.M., Hester, M.L., Liu, A., Burke, J. M.: Chloroplast SSR polymorphisms in the Compositae and the mode of organellar inheritance in Helianthus annuus. - Theor. appl. Genet. 110: 941-947, 2005. Go to original source...
    42. Wu, M.L., Li, Q., Xu, J., Li, X.W.: Complete chloroplast genome of the medicinal plant Amomum compactum: gene organization, comparative analysis, and phylogenetic relationships within Zingiberales. - Chin. Med. 13: 10, 2018. Go to original source...
    43. Wu, Z.Q., Ge, S.: The phylogeny of the BEP clade in grasses revisited: evidence from the whole genome sequences of chloroplasts. - Mol. Phylogenet. Evol. 62: 573-578, 2012. Go to original source...
    44. Wyman, S.K., Jansen, R.K., Boore, J.L.: Automatic annotation of organellar genomes with DOGMA. - Bioinformatics 20: 3252-3255, 2004. Go to original source...
    45. Xu, L., Dou, D.Q., Wan, B., Yang, Y.Y., Kang, T.G., Liu, Y.: [Identification of traditional Medicine Fructus Arctii by nuclear ribosomal DNA ITS sequences.] - China J. Chin. Mater. Med. 36: 45, 2011. [In Chin.]
    46. Yang, J.B., Tang, M., Li, H.T., Zhang, Z.R., Li, D.Z.: Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses. - BMC Evol. Biol. 13: 84, 2013. Go to original source...
    47. Yang, J.B., Yang, S.X., Li, H.T., Yang, J., Li, D.Z.: Comparative chloroplast genomes of Camellia species. - PLoS ONE 8: e73053, 2013. Go to original source...
    48. Yao, X., Tang, P., Li, Z., Li, D., Liu, Y., Huang, H.: The first complete chloroplast genome sequences in Actinidiaceae: genome structure and comparative analysis. - PLoS ONE 10: e0129347, 2015. Go to original source...

    Return to the content