Abstract
Three species of Gentiana (Gentiana manshurica kitag., Gentiana scabra bunge., and Gentiana triflora pall.) were the main source for an important traditional Chinese medicine, "Longdan", which was first mentioned in " Shennong materia medica Sutra " 2000 years ago. Until recently, there were very few reports on taxonomic classification of these three traditional medicinal Gentiana species. In the current study, chloroplast genomes of the three Gentiana species were sequenced and the phylogenetic analyses were performed in combination with 31 NCBI downloaded Gentiana species sequences and two species of Swertia as outgroup. Based on the phylogenetic results, a new taxonomic classification for Gentiana was proposed, including 4 independent clades with 6 subdivisions (Group 1–Group 6). All the general features, SSR characteristics and gene composition of Gentiana chloroplast genomes strongly supported such a new classification system for Gentiana, which could lay a theoretical foundation for Gentiana in the molecular evolutionary research. Finally, phylogenetic analyisis also demonstrated that the three examined species from Gentiana could cluster together into one group (Group 6), which was far away from the evolutionary position of the medicinal species, Gentiana rigescens Franch, which was consistent with the traditional classification in traditional medicinal uses and taxonomy.
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Abbreviations
- LSC:
-
Large single copy region
- SSC:
-
Small single copy region
- IRA:
-
Inverted repeat region A
- IRB:
-
Inverted repeat region B
- tRNA:
-
Transfer RNA
- rRNA:
-
Ribosomal RNA
References
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Brown J, Pirrung M, McCue LA (2017) FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. Bioinformatics 33(19):3137–3139. https://doi.org/10.1093/bioinformatics/btx373
Beier S, Thiel T, Münch T, Scholz U, Mascher M (2017) MISA-web: a web server for microsatellite prediction. Bioinformatics 33(16):2583–2585. https://doi.org/10.1093/bioinformatics/btx198
Darling AC, Mau B, Blattner FR, Perna NT (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14(7):1394–1403. https://doi.org/10.1101/gr.2289704
Daniell H, Lin CS, Yu M, Chang WJ (2016) Chloroplast genomes: diversity, evolution, and applications in genetic engineering. Genome Biol 17(1):134. https://doi.org/10.1186/s13059-016-1004-2
Dong LP, Ni LH, Zhao ZL, Wu JR (2017) Research progress on iridoids in Gentiana L. Chin Tradit Herbal Drugs 48(10):2116–2128. https://doi.org/10.7501/j.issn.0253-2670.2017.10.030
Dong BR, Zhao ZL, Ni LH, Wu JR, Dan ZG (2020) Comparative analysis of complete chloroplast genome sequences within Gentianaceae and significance of identifying species. Chin Tradit Herbal Drugs 51(06):1641–1649
Editorial Committee of flora of China (2013) Chinese Academy of Sciences Flora of China. Science Press, Beijing. http://frps.iplant.cn/
Enescu RE, Vechiu E, Cântar I (2018) Herbarium survey of genus Gentiana L. Res J Agric Sci 50(2):51–59
Favre A, Michalak I, Chen CH, Wang JC, Pringle JS, Matuszak S, Sun H, Yuan YM, Struwe LN, Muellner-Riehl A (2016) Out-of-Tibet: the spatio-temporal evolution of Gentiana (Gentianaceae). J Biogeogr 43:1967–1978. https://doi.org/10.1111/jbi.12840
Favre A, Pringle JS, Heckenhauer J, Kozuharova E, Gao QB, Lemmon EM, Lemmon AR, Sun H, Tkach N, Gebauer S, Sun SS, Fu PC (2020) Phylogenetic relationships and sectional delineation within Gentiana (Gentianaceae). Syst Phylogeny 69(6):1221–1238. https://doi.org/10.1002/tax.12405
Favre A, Paule J, Ebersbach J (2022) Incongruences between nuclear and plastid phylogenies challenge the identifcation of correlates of diversifcation in Gentiana in the European Alpine System. Alp Bot 132:29–50. https://doi.org/10.1007/s00035-021-00267-6
Fu PC, Twyford AD, Sun SS, Wang HY, Xia MZ, Tan CX, Zhou XJ, Chen SL (2020) Recurrent hybridization underlies the evolution of novelty in Gentiana (Gentianaceae) in the Qinghai-Tibetan Plateau. AoB Plants 13(1):plaa068. https://doi.org/10.1093/aobpla/plaa068
Greiner S, Lehwark P, Bock R (2019) OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Res 47(W1):W59–W64. https://doi.org/10.1093/nar/gkz238
Jiao Y, Jia HM, Li XW, Chai ML, Jia HJ, Chen Z et al (2012) Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry (Myrica rubra). BMC Genomic 13:201. https://doi.org/10.1186/1471-2164-13-201
Jin JJ, Yu WB, Yang JB, Song Y, dePamphilis CW, Yi TS, Li DZ (2020) GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biol 21(1):241. https://doi.org/10.1186/s13059-020-02154-5
Kurtz S, Choudhuri JV, Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R (2001) REPuter: the manifold applications of repeat analysis on a genomic scale. Nucl Acids Res 29(22):4633–4642. https://doi.org/10.1093/nar/29.22.4633
Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucl Acids Res 32(1):11–16. https://doi.org/10.1093/nar/gkh152
Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11):1451–1452. https://doi.org/10.1093/bioinformatics/btp187
Liu J, Yan HF, Ge XJ (2016) The use of DNA barcoding on recently diverged species in the genus Gentiana (Gentianaceae) in China. PLoS ONE 11(4):e0153008. https://doi.org/10.1371/journal.pone.0153008
Mirzaee F, Hosseini A, Jouybari HB, Davoodi A, Azadbakht M (2017) Medicinal biological and phytochemical properties of Gentiana species. J Tradit Complement Med 7(4):400–408. https://doi.org/10.1016/j.jtcme.2016.12.013
Muellner-Riehl AN (2019) Mountains as evolutionary arenas: patterns, emerging approaches, paradigm shifts, and their implications for plant phylogeographic research in the tibeto-himalayan region. Front Plant Sci 10:195. https://doi.org/10.3389/fpls.2019.00195
National Pharmacopoeia Commission (2020) Chinese pharmacopoeia. China Medical Science and Technology Press, Beijing
Pan Y, Zhao YL, Zhang J, Li WY, Wang YZ (2016) Phytochemistry and Pharmacological Activities of the Genus Gentiana (Gentianaceae). Chem Biodivers 13(2):107–150. https://doi.org/10.1002/cbdv.201500333
Pan X, Zhu HY, Zhang CH, Feng B (2020) Advances in studies on chemical constituents and pharmacological actions of Gentiana scabra. J Jilin Med Univ 41(02):150–151
Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Höhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP (2012) MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 61(3):539–542. https://doi.org/10.1093/sysbio/sys029
Stamatakis A (2014) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30(9):1312–1313. https://doi.org/10.1093/bioinformatics/btu033
Sun SS, Fu PC, Zhou XJ, Cheng YW, Zhang FQ, Chen SL, Gao QB (2018) The complete plastome sequences of seven species in Gentiana Sect. Kudoa (Gentianaceae): insights into plastid gene loss and molecular evolution. Front Plant Sci 9:493. https://doi.org/10.3389/fpls.2018.00493
Tillich M, Lehwark P, Pellizzer T, Ulbricht-Jones ES, Fischer A, Bock R, Greiner S (2017) GeSeq - versatile and accurate annotation of organelle genomes. Nucl Acids Res 45(W1):W6–W11. https://doi.org/10.1093/nar/gkx391
Tao Z, Wang J, Jia Y, Li W, Xu F, Wang X (2018) Comparative Chloroplast Genome Analyses of Species in Gentiana section Cruciata (Gentianaceae) and the Development of Authentication Markers. Int J Mol Sci 19(7):1962. https://doi.org/10.3390/ijms19071962
Yuan YM, Kupfer P, Doyle JJ (1996) Infrageneric phylogeny of the genus Gentiana (Gentianaceae) inferred from nucleotide sequences of the internal transcribed spacers (ITS) of nucle-ar ribosomal DNA. Am J Bot 83(5):641–652. https://doi.org/10.2307/2445924
Yang JB, Yang SX, Li HT, Yang J, Li DZ (2013) Comparative Chloroplast Genomes of Camellia Species. PLoS ONE 8:e73053. https://doi.org/10.1371/journal.pone.0073053
Zhu A, Guo W, Gupta S, Fan W, Mower JP (2016) Evolutionary dynamics of the plastid inverted repeat: the effects of expansion, contraction, and loss on substitution rates. New Phytol 209(4):1747–1756. https://doi.org/10.1111/nph.13743
Zhao ZP, Yan Y, Zheng MM, Liu XL (2019) Genetic evaluation of Gentiana rigescens based on the chloroplast psbA-trnH, trnL-trnF sequence polymorphism. Lishizhen Med Mater Med Res 30(05):1203–1206
Zhang JH, Yin HB, Zhang JK, Wang N, Ren X (2019) Herbal Textual Analysis of Gentianae Radix et Rhizoma. Chin J Exp Tradit Med Formulae 25(13):163–169. https://doi.org/10.13422/j.cnki.syfjx.20191213
Zhang Q, Zhang WW, Ding Y et al (2020) DNA barcode identification of Changbai Mountain Gentiana. Modern Chin Med 17:1817–1821
Acknowledgements
The authors thank professor Zhang Hui from Institute of Botany, Chinese Academy of Sciences for the suggestions on the revision of the draft.
Funding
This research was funded by "General Survey of Traditional Chinese Medicine Resources in Ganjingzi District of Dalian and Xinfu District of Fushun" by the Health Commission of Liaoning Province (2019001), Liaoning Provincial Department of Science and Technology Project "Technical Dispatch of Chinese Medicinal Materials in Kazuo County, Liaoning Province" (2020JH5/10400122), “Major increase and decrease of expenditure at the central level” (2060302).
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HY: Conceptualization and proofreading. RZ & SY: Formal analysis, Writing – review and editing. CL and JC: Methodology. YX: Software. XR and DJ: Writing – original draft. JX: later revision of the manuscript.
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Zhao, R., Yin, S., Xue, J. et al. Sequencing and comparative analysis of chloroplast genomes of three medicinal plants: Gentiana manshurica, G. scabra and G. triflora. Physiol Mol Biol Plants 28, 1421–1435 (2022). https://doi.org/10.1007/s12298-022-01217-0
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DOI: https://doi.org/10.1007/s12298-022-01217-0