Skip to main content
SpringerLink
Log in

The Complete Chloroplast Genome Sequence of Staphylea holocarpa (Staphyleaceae)

  • Original Article
  • Published:
Molecular Biotechnology Aims and scope Submit manuscript

Abstract

Staphylea holocarpa (Hemsley 1895) is an ornamental deciduous shrub or tree in the family Staphyleaceae. As the shortage of the wild resources, S. holocarpa is also a rare plant. The revelation of the species origin and evolution progress and the relation. Therefore, the S. holocarpa complete chloroplast genome sequence was completed and characterized by de novo assembly. The cp genome length of S. holocarpa was 160,461 bp and it has a typical quadripartite structure, consisted of an 89,760 bp large single-copy region and a 18,639 bp small single-copy region, which were divided by two inverted repeat regions of 26,031 bp. After genome annotation, it comes to 130 genes that were predicted, which includes 85, 8, and 37 encoded proteins, rRNA, and tRNA, respectively. A phylogenetic analysis has shown that the S. holocarpa cp genome is related to the Staphylea trifolia. This work will be useful for further population genomic and phylogenetic studies of S. holocarpa.

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

Similar content being viewed by others

Data Availability

Staphylea holocarpa cp genome sequence and structure information data that are associated with the findings and results has been now available at NCBI website publicly. The corresponding accession number was MZ493339. And the relevant numbers of BioProject, SRA, and Bio-Sample are PRJNA753259, SRR15404045, and SAMN20692242, respectively.

References

  1. Lubica, L., Jan, M., Irena, M., & Daniel, G. (2007). Antioxidant activity and total phenols in different extracts of four Staphylea L. species. Molecules, 12, 28–35.

    Google Scholar 

  2. Lacikova, L., Pferschy-Wenzig, E.-M., Masterova, I., Grancai, D., & Bauer, R. (2009). Antiinflammatory potential and fatty acid content of lipophilic leaf extracts of four Staphylea L. species. Natural Product Communications, 4, 543–546.

    Article  CAS  PubMed  Google Scholar 

  3. Vothknecht, U. C., & Westhoff, P. (2001). Biogenesis and origin of thylakoid membranes. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 1541, 91–101.

    Article  CAS  PubMed  Google Scholar 

  4. Uthaipaisanwong, P., Chanprasert, J., Shearman, J. R., Sangsrakru, D., Yoocha, T., Jomchai, N., Jantasuriyarat, C., Tragoonrung, S., & Tangphatsornruang, S. (2012). Characterization of the chloroplast genome sequence of oil palm (Elaeis guineensis Jacq.). Gene, 500, 172–180.

    Article  CAS  PubMed  Google Scholar 

  5. Sandoval-Vargas, J. M., Jiménez-Clemente, L. A., Macedo-Osorio, K. S., Oliver-Salvador, M. C., Fernández-Linares, L. C., Durán-Figueroa, N. V., & Badillo-Corona, J. A. (2019). Use of the ptxD gene as a portable selectable marker for chloroplast transformation in Chlamydomonas reinhardtii. Molecular Biotechnology, 61, 461–468.

    Article  CAS  PubMed  Google Scholar 

  6. Shinozaki, K., Ohme, M., Tanaka, M., Wakasugi, T., & Sugiura, M. (1986). The complete nucleotide sequence of the tobacco chloroplast genome: Its gene organization and expression. Plant Molecular Biology Reporter, 5, 2043–2049.

    CAS  Google Scholar 

  7. Castro, I., Pinto-Carnide, O., & Ortiz, J. M. (2013). Chloroplast genome diversity in Portuguese grapevine (Vitis vinifera L.) cultivars. Molecular Biotechnology, 54, 528–540.

    Article  CAS  PubMed  Google Scholar 

  8. Wang, X., Wang, D., Gao, N., Han, Y., Wang, X., Shen, X., & You, C. (2022). Identification of the complete chloroplast genome of Malus zhaojiaoensis Jiang and its comparison and evolutionary analysis with other Malus species. Genes, 13, 560–566.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Xu, B., Shi, X. H., Sun, Y., & Li, N. (2002). Study on Dormancy and Germination of Staphylea holocarpa Hemsl. Seed, 3, 174–180.

    Google Scholar 

  10. Bankevich, A. (2006). A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Journal of Computational Biology, 1, 2320–2325.

    Google Scholar 

  11. Duan, H., Zhang, Q., Tian, F., Hu, Y., Wang, C., Lu, Y., Yuan, H., Yang, H., & Cui, G. (2022). Complete chloroplast genome of Calligonum mongolicum Turcz. and comparative analysis with other Calligonum species. Journal of Applied Research on Medicinal and Aromatic, 27, 100370.

    CAS  Google Scholar 

  12. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., & Prjibelski, A. D. (2012). SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19, 455–477.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Wang, J., Tian, T., Han, X., Ye, B., & Zhou, H. (2021). The complete chloroplast genome and phylogenetic analysis of Syringa reticulata subsp. amurensis (Rupr.) P.S. Green & M.C. Chang from Qinghai Province, China. Mitochondrial DNA Part B: Resources, 6, 1844–1846.

    Article  PubMed  PubMed Central  Google Scholar 

  14. Huang, D. I., & Cronk, Q. (2015). Plann: A command-line application for annotating plastome sequences. Applications in Plant Sciences, 3, 1500026.

    Article  Google Scholar 

  15. Liu, S., Feng, S., Huang, Y., An, W., Yang, Z., Xie, C., & Zheng, X. (2021). Characterization of the complete chloroplast genome of Buddleja lindleyana. Journal of AOAC International, 105, 202–210.

    Article  Google Scholar 

  16. Mower, J. P. (2009). The PREP suite: Predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments. Nucleic Acids Research, 37, 253–259.

    Article  Google Scholar 

  17. Michael, T., Pascal, L., Tommaso, P., Ulbricht-Jones, E. S., Axel, F., Ralph, B., & Stephan, G. (2017). GeSeq—Versatile and accurate annotation of organelle genomes. Nucleic Acids Research, 45, 6–11.

    Article  Google Scholar 

  18. Standley, D. M. (2013). MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Molecular Biology and Evolution, 30, 772–776.

    Article  PubMed  PubMed Central  Google Scholar 

  19. Lam-Tung, N., Schmidt, H. A., Arndt, V. H., & Quang, M. B. (2015). IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution, 1, 268–274.

    Google Scholar 

  20. Thi, H. D., Olga, C., Arndt, V. H., Quang, M. B., & Sy, V. L. (2017). UFBoot2: Improving the ultrafast bootstrap approximation. Molecular Biology and Evolution, 2, 2–7.

    Google Scholar 

  21. Peng, Y. L., Chen, Z. D., Gong, X., Zhong, Y., & Shi, S. H. (2003). Phylogenetic position of Dipentodon sinicus: Evidence from DNA sequences of chloroplast rbcL, nuclear ribosomal 18S, and mitochondria matR genes. Botanical Bulletin of Academia Sinica, 44, 217–222.

    CAS  Google Scholar 

  22. Pan, D. K., Huang, B. H., Wang, Q., Dai, S. Q., & Fan, X. B. (2020). A comparison of classifications between Flora Reipublicae Popularis Sinicae and flora of China. Chinese Wild Plant Resources, 39, 66–72.

    Google Scholar 

  23. Manchester, S. R. (1988). Fruits and seeds of Tapiscia (Staphyleaceae) from the Middle Eocene of Oregon, USA. Tertiary Research, 9, 59–66.

    Google Scholar 

Download references

Funding

The manuscript has been supported and funded by the Research on the synchronicity of dichogamy in Scirpus planiculmis [NSFC31800348], Major Basic Research Project of the Natural Science Foundation of the Jiangsu Higher Education Institutions [Number: 2018JQ3052] and Comprehensive evaluation of soil quality of Taxus forest in Shaanxi Province [BG2022002].

Author information

Authors and Affiliations

  1. Department of Ecological Environmental Engineering, Yangling Vocational and Technical College, Yangling, 712100, Shaanxi, People’s Republic of China

    Sihui Chen

  2. College of Chemistry and Pharmacy, Northwest A&F University, Yangling, 712100, Shaanxi, People’s Republic of China

    Ruiting Xu

  3. College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, People’s Republic of China

    Yulin Liu

  4. Infrastructure Construction Office, Taibai Mountain National Nature Reserve Administration, Yangling, 712100, Shanxi, People’s Republic of China

    Wentao Tong

  5. Ordos Forestry and Grassland Development Center, Ordos, 017000, Inner Mongolia, People’s Republic of China

    Jing Wang

  6. International Office, Yangling Vocational and Technical College, Yangling, 712100, Shaanxi, People’s Republic of China

    Kun Qian

  7. Civil Engineering Department, Yangling Vocational and Technical College, Yangling, 712100, Shaanxi, People’s Republic of China

    Wei Bo

Authors
  1. Sihui Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ruiting Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wentao Tong
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jing Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Kun Qian
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Wei Bo
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yulin Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

SC, RX, WT, JW, KQ and WB performed the experiments. SC and YL were responsible for the data analysis, the drafts writing and revision progress. In this study, all authors have taken part in and approved the final manuscript.

Corresponding author

Correspondence to Yulin Liu.

Ethics declarations

Ethical Approval

This study was approved by the Museum Garden, Northwest A&F University, Yangling, Shaanxi, PR China. Field studies comply with local legislation, and authors have obtained necessary permits for access to the land. In addition, the trees of Staphylea holocarpa are planted here for ornamental and scientific research for several years.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chen, S., Xu, R., Tong, W. et al. The Complete Chloroplast Genome Sequence of Staphylea holocarpa (Staphyleaceae). Mol Biotechnol 66, 1458–1463 (2024). https://doi.org/10.1007/s12033-023-00780-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12033-023-00780-5

Keywords

Search

Navigation