Skip to main content
SpringerLink
Log in

Characterization of the Complete Chloroplast Genome and Evolutionary Position of Clematis tomentella

  • Published:
Cytology and Genetics Aims and scope Submit manuscript

Abstract

Clematis tomentella 2001 (Ranunculaceae) is a typical drought-tolerant sand-fixing plant in desert ecosystem in northwest China. To elucidate the phylogenetic status of C. tomentella and its related species, we determined the complete chloroplast (cp) genome and analyzed their interspecific relationships. The result showed that the cp genome of C. tomentella was 159 816 bp in length, including two inverted repeats of 31 045 bp, a large single copy region of 79 535 bp, and a small single copy region of 18 191 bp. 136 genes were annotated across the whole cp genome, including 92 protein-coding genes, 8 rRNA genes, and 36 tRNA genes, as well as the GC content accounted for 38%. Crucially, we found that the regions of psbE-petL, trnG_UCC-atpA, ndhF-rpl32, and rps8-infA were highly divergent, which could be marked as DNA barcodes for the identification of C. tomentella in Ranunculaceae. A maximum likelihood phylogenetic tree revealed that C. tomentella was closely related to C. fruticosa. Our results provide the references and implications for the phylogenetic study of Clematis in Ranunculaceae in the future.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.
Fig. 5.
Fig. 6.
Fig. 7.

Similar content being viewed by others

DATA AVAILABILITY

The data is openly available in the NCBI database at https://www.ncbi.nlm.nih.gov/, accession number ON854662. The associated SRA, BioSample, and BioProject numbers are SRR20647951, SAMN29333046, and PRJNA852531, respectively.

REFERENCES

  1. Altschul, S., Madden, T., Schäffer, A., Zhang, J., Zhang, Z., and Miller, W., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 1997, vol. 25, pp. 3389–3402. https://doi.org/10.1093/nar/25.17.3389

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Alzahrani, D., Albokhari, E., Abba, A., and Yaradua, S., The first complete chloroplast genome sequences in Resedaceae: Genome structure and comparative analysis, Sci. Prog., 2021, vol. 104, no. 4, p. 368504211059973. https://doi.org/10.1177/00368504211059973

    Article  CAS  PubMed  Google Scholar 

  3. Amiryousefi, A., Hyvonen, J., and Poczai, P., IRscope: an online program to visualize the junction sites of chloroplast genomes, Bioinformatics, 2018, vol. 34, no. 17, pp. 3030–3031. https://doi.org/10.1093/bioinformatics/bty220

    Article  CAS  PubMed  Google Scholar 

  4. Beier, S., Thiel, T., Münch, T., Scholz, U., and Mascher, M., MISA-web: a web server for microsatellite prediction, Bioinformatics, 2017, vol. 33, pp. 2583–2585. https://doi.org/10.1093/bioinformatics/btx198

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Chase, M.W., Christenhusz, M.J.M., Fay, M.F., Byng, J.W., Judd, W.S., Soltis, D.E., Mabberley, D.J., Sennikov, A.N., Soltis, P.S., and Stevens, P.F., An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV, Bot. J. Linn. Soc., 2016, vol. 181, no. 1, pp. 1–20. https://doi.org/10.1111/boj.12385

    Article  Google Scholar 

  6. Chen, X., Chang, Q., Xia, P., Liang, Z., and Yan, K., The complete chloroplast genome of Clematis henryi var. ternate (Ranunculaceae), Mitochondrial DNA, Part B: Resources, 2021, vol. 6, no. 4, pp. 1319–1320. https://doi.org/10.1080/23802359.2021.1907807

    Article  PubMed  PubMed Central  Google Scholar 

  7. Choi, K.S., Ha, Y.H., Gil, H.Y., Choi, K., Kim, D.K., and Oh, S.H., Two Korean endemic Clematis chloroplast genomes: Inversion, reposition, expansion of the inverted repeat region, phylogenetic analysis, and nucleotide substitution rates, Plants (Basel), 2021, vol. 10, no. 2, p. 397. https://doi.org/10.3390/plants10020397

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Cui, N., Liao, B., Liang, C., Li, S., Zhang, H., Xu, J., Li, X., and Chen, S., Complete chloroplast genome of Salvia plebeia: organization, specific barcode and phylogenetic analysis, Chin. J. Nat. Med., 2020, vol. 18, no. 8, pp. 563–572. https://doi.org/10.1016/S1875-5364(20)30068-6

    Article  PubMed  Google Scholar 

  9. Dong, W., Liu, J., Yu, J., Wang, L., and Zhou, S., Highly variable chloroplast markers for evaluating plant phylogeny at low taxonomic levels and for DNA barcoding, PLoS One, 2012, vol. 7, no. 4, p. e35071. https://doi.org/10.1371/journal.pone.0035071

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Frazer, K., Pachter, L., Poliakov, A., Rubin, E.M., and Dubchak, I., VISTA: computational tools for comparative genomics, Nucleic Acids Res., 2004, vol. 32, pp. W273–W279. https://doi.org/10.1093/nar/gkh458

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Greiner, S., Lehwark, P., and Bock, R., OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes, Nucleic Acids Res., 2019, vol. 47, pp. W59–W64. https://doi.org/10.1101/545509

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Guan, K.J., Xiao, P.G., and Pan, K.Y., Flora of China: Ranunculaceae, Beijing: Sci. Press (China), 1979.

    Google Scholar 

  13. Guo, Y.Q., Shi, J.N., Liu, B., Na W.H., Guo, J., and Shao, F., Studies on seeding and cutting propagating of Clematis canescens, an endangered wild plant (in Chinese), For. Res., 2006, vol. 19, no. 5, pp. 672–674. https://doi.org/10.3321/j.issn:1001-1498.2006.05.026

    Article  Google Scholar 

  14. Guo, Y.Q., Ding, X.L., Liu, B., Shao, F., and Na, W.H., Clematis canescens, an endangered wild ornamental plant in Ningxia, China (in Chinese), China Seed Ind., 2007, vol. 3, p. 55. https://doi.org/10.19462/j.cnki.1671-895x.2007.03.033

    Article  Google Scholar 

  15. Huang, D. and Cronk, Q.C.B., Plann: A command-line application for annotating plastome sequences, Appl. Plant Sci., 2015, vol. 3, p. 1500026. https://doi.org/10.3732/apps.1500026

    Article  Google Scholar 

  16. Jiang, M., Wang, J., and Zhang, H., The complete plastome sequence of Clematis guniuensis (Ranunculaceae), a new plant species endemic to China, Mitochondrial DNA, Part B: Resources, 2020, vol. 5, no. 1, pp. 408–409. https://doi.org/10.1080/23802359.2019.1704662

    Article  PubMed  PubMed Central  Google Scholar 

  17. Katoh, K. and Standley, D., MAFFT multiple sequence alignment software version 7: improvements in performance and usability, Mol. Biol. Evol., 2013, vol. 30, pp. 772–780. https://doi.org/10.1093/molbev/mst010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Konhar, R., Debnath, M., Vishwakarma, S., Bhattacharjee, A., Sundar, D., Tandon, P., Dash, D., and Biswal, D.K., The complete chloroplast genome of Dendrobium nobile, an endangered medicinal orchid from north-east India and its comparison with related Dendrobiumspecies, PeerJ, 2019, vol. 7, p. e7756. https://doi.org/10.7717/peerj.7756

    Article  PubMed  PubMed Central  Google Scholar 

  19. Kühn, I. and Klotz, S., Urbanization and homogenization-comparing the floras of urban and rural areas in Germany, Biol. Conserv., 2005, vol. 127, no. 3, pp. 292–300. https://doi.org/10.1016/j.biocon.2005.06.033

    Article  Google Scholar 

  20. Kumar, S., Stecher, G., Li, M., Knyaz, C., and Tamura, K., MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms, Mol. Biol. Evol., 2018, vol. 35, no. 6, pp. 1547–1549. https://doi.org/10.1093/molbev/msy096

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Li, M., Yang, B., Chen, Q., Zhu, W., Ma, J., and Tian, J., The complete chloroplast genome sequence of Clematis terniflora DC. (Ranunculaceae), Mitochondrial DNA, Part A, 2016, vol. 27, no. 4, pp. 2470–2472. https://doi.org/10.3109/19401736.2015.1033702

    Article  CAS  Google Scholar 

  22. Li, J., Li, H., Zhi, J., Shen, C., Yang, X., and Xu, J., Codon usage of expans in genes in Populus trichocarpa, Curr. Bioinf., 2017, vol. 12, no. 5, pp. 452–461. https://doi.org/10.2174/1574893611666161008195145

    Article  CAS  Google Scholar 

  23. Liu, B., Guo, J., Guo, Y.Q., Shao, F., and Na, W.H., Effects of different substrates and different chemicals on rooting of Clematis canescenscuttings (in Chinese), Ningxia Agric. For. Sci. Technol., 2007, vol. 4, pp. 11–13.

    Google Scholar 

  24. Mishra, P., Kumar, A., Nagireddy, A., Daya, N., and Ashutosh, M., DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market, Plant Biotechnol. J., 2015, vol. 14, pp. 8–21. https://doi.org/10.1111/pbi.12419

    Article  CAS  PubMed  Google Scholar 

  25. Nurk, S., Bankevich, A., Antipov, D., Gurevich, A., Korobeynikov, A., Lapidus, A., Prjibelski, A., Pyshkin, A., Sirotkin, A., and Sirotkin, Y., Assembling single-cell genomes and mini-metagenomes from chimeric MDA products, J. Comput. Biol., 2013, vol. 20, no. 10, pp. 714–737. https://doi.org/10.1089/cmb.2013.0084

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Park, B.K., Ghimire, B., Ha, Y.H., Son, D.C., and Kim, D.K., Complete chloroplast genome of Clematis taeguensis (Ranunculaceae), an endemic species from South Korea, Mitochondrial DNA, Part B: Resources, 2021, vol. 6, no. 4, pp. 1496–1497. https://doi.org/10.1080/23802359.2021.1910080

    Article  PubMed  PubMed Central  Google Scholar 

  27. Powell, W., Morgante, M., Mcdevitt, R., Vendra-min, G.G., and Rafalski, J.A., Polymorphic simple sequence repeat regions in chloroplast genomes: Applications to the population genetics of pines, Proc. Natl. Acad. Sci. U. S. A., 1995, vol. 92, pp. 7759–7763. https://doi.org/10.1073/pnas.92.17.7759

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Rozas, J., Ferrermata, A., Sánchezdelbarrio, J., Guiraorico, S., Librado, P., Ramosonsins, S., and Sánchezgracia, A., DnaSP 6: DNA sequence polymorphism analysis of large datasets, Mol. Biol. Evol., 2017, vol. 34, pp. 3299–3302. https://doi.org/10.1093/molbev/msx248

    Article  CAS  PubMed  Google Scholar 

  29. Stefanova, P., Taseva, M., Georgieva, T., Gotcheva, V., and Angelov, A., A modified CTAB method for DNA extraction from soybean and meat products, Biotechnol. Biotechnol. Equip., 2013, vol. 27, no. 3, pp. 3803–3810. https://doi.org/10.5504/BBEQ.2013.0026

    Article  CAS  Google Scholar 

  30. VanDo, T., Xu, B., and Gao, X., Molecular phylogeny and character evolution of Flemingia (Leguminosae, Papilionoideae, Phaseoleae, Cajaninae) inferred from three cpDNA and nrITS sequence data, Plant Syst. Evol., 2021, vol. 307, p. 30. https://doi.org/10.1007/S00606-021-01749-0

    Article  CAS  Google Scholar 

  31. Wang, Z. and Ren, H., The role of native plants in vegetation restoration (in Chinese), Hubei Agric. Sci., 2018, vol. 57, no. 10, pp. 83–87. https://doi.org/10.14088/j.cnki.issn0439-8114.2018.10.020

    Article  Google Scholar 

  32. Wei, F., Tang, D., Wei, K., Qin, F., Li, L., Lin, Y., Zhu, Y., Aziz, K., Haneef, K., and Miao, J., The complete chloroplast genome sequence of the medicinal plant Sophora tonkinensis, Sci. Rep., 2020, vol. 10, p. 12473. https://doi.org/10.1038/s41598-020-69549-z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Wei, H., Pan, L., Tian, S., Tang, Z., He, H., Zhang, H., and Jiang, M., Chloroplast genome sequence characterization and phylogenetic analysis of Clematis henryi, Chin. Tradit. Herbal Drugs, 2022, vol. 53, no. 12, pp. 3766–3773. https://doi.org/10.7501/j.issn.0253-2670.2022.12.023

    Article  Google Scholar 

  34. Xiang, Q.-H., He, J., Liu, H.-J., Lyu, R.-D., Yao, M., Guan, W.-B., and Xie, L., The complete chloroplast genome sequences of three Clematis species (Ranunculaceae), Mitochondrial DNA, Part B: Resources, 2019, vol. 4, no. 1, pp. 834-835. https://doi.org/10.1080/23802359.2019.1567290

    Article  Google Scholar 

  35. Yang, Z., Huang, Y., An, W., Zheng, X., Huang, S., and Liang, L., Sequencing and structural analysis of the complete chloroplast genome of the medicinal plant Lycium chinense Mill, Plants (Basel), 2019, vol. 8, no. 4, p. 87. https://doi.org/10.3390/plants8040087

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Yang, Y.-C., Wang, N., Zhang, W., and Zhou, T., The complete chloroplast genome of Clematis fruticosa Turcz. (Ranunculaceae), Mitochondrial DNA, Part B: Resources, 2020, vol. 5, no. 2, pp. 1908–1909. https://doi.org/10.1080/23802359.2020.1754951

    Article  Google Scholar 

Download references

Funding

This study was financially supported by the China Forage and Grass Research System (CARS-34), the Innovative Demonstration Projects for High-quality Agricultural Development and Ecological Protection (NGSB-2021-14-6), the Special Project for Youth Top-notch Talents of Ningxia Hui Autonomous Region ([2017] 186), and Natural Science Foundation of Ningxia Province [2020AAC03273, 2022AAC03641].

Author information

Authors and Affiliations

  1. Ningxia Technical College of Wine and Desertification Prevention, Yinchuan, 750199, Ningxia, China

    Wangsuo Liu

  2. Institute of Forestry and Grassland Ecology, Ningxia Academy of Agriculture and Forestry Science, Yinchuan, 750011, Ningxia, China

    Wangsuo Liu, Zhanjun Wang, Ying Tian & Bo Ji

  3. Ningxia Key Laboratory of Desertification Control and Soil and Water Conservation, Ningxia Academy of Agriculture and Forestry Science, Yinchuan, 750011, Ningxia, China

    Zhanjun Wang, Ying Tian & Bo Ji

Authors
  1. Wangsuo Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhanjun Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ying Tian
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Bo Ji
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Zhanjun Wang.

Ethics declarations

ETHICS APPROVAL AND CONSENT TO PARTICIPATE

This article does not contain any studies involving animals or human participants performed by any of the authors.

CONFLICT OF INTEREST

The authors of this work declare that they have no conflicts of interest.

Additional information

Publisher’s Note.

Allerton Press remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Liu, W., Wang, Z., Tian, Y. et al. Characterization of the Complete Chloroplast Genome and Evolutionary Position of Clematis tomentella. Cytol. Genet. 58, 126–135 (2024). https://doi.org/10.3103/S0095452724020075

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.3103/S0095452724020075

Keywords:

Search

Navigation