A DNA barcode reference library of native seed plants in the Guangdong-Hong Kong-Macao Greater Bay Area


  • Ren, H., Lu, H., Wang, J., Liu, N. & Guo, Q. Forest restoration in China: advances, obstacles, and perspectives. Tree For. Sci. Biotech. 6, 7–16 (2012).


    Google Scholar
     

  • Yang, C. et al. Rapid urbanization induced extensive forest loss to urban land in the Guangdong-Hong Kong-Macao Greater Bay Area, China. Chin. Geogr. Sci. 31, 93–108 (2021).


    Google Scholar
     

  • Mishra, P. et al. DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market. Plant Biotech. J. 14, 8–21 (2016).

    CAS 

    Google Scholar
     

  • Dasmahapatra, K. K. & Mallet, J. Taxonomy: DNA barcodes: recent successes and future prospects. Heredity 97, 254–255 (2006).

    CAS 
    PubMed 

    Google Scholar
     

  • Hubert, N. & Hanner, R. DNA Barcoding, species delineation and taxonomy: a historical perspective. DNA Barcodes 3, 44–58 (2015).


    Google Scholar
     

  • Zhu, S., Liu, Q., Qiu, S., Dai, J. & Gao, X. DNA barcoding: an efficient technology to authenticate plant species of traditional Chinese medicine and recent advances. Chin. Med. 17, 112 (2022).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hebert, P. D. N., Cywinska, A., Ball, S. L. & deWaard, J. R. Biological identifications through DNA barcodes. Proc. Biol. Sci. 270, 313–321 (2003).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kress, W. J., Wurdack, K. J., Zimmer, E. A., Weigt, L. A. & Janzen, D. H. Use of DNA barcodes to identify flowering plants. Proc. Natl. Acad. Sci. USA. 102, 8369–8374 (2005).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kress, W. J. & Erickson, D. L. A two-locus global DNA barcode for land plants: The coding rbcL gene complements the noncoding trnH–psbA spacer region. PLoS One 2, e508 (2007).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Burgess, K. et al. Discriminating plant species in a local temperate flora using the rbcL plus matK DNA barcode. Methods Ecol. Evol. 2, 333–340 (2011).


    Google Scholar
     

  • de Boer, H. J., Ouarghidi, A., Martin, G., Abbad, A. & Kool, A. DNA barcoding reveals limited accuracy of identifications based on folk taxonomy. PLoS One 9, e84291 (2014).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • CBOL Plant Working Group. et al. A DNA barcode for land plants. Proc. Natl. Acad. Sci. USA. 106, 12794–12797 (2009).

    ADS 
    PubMed Central 

    Google Scholar
     

  • China Plant BOL Group. et al. Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants. Proc. Natl. Acad. Sci. USA. 108, 19641–19646 (2011).

    ADS 
    PubMed Central 

    Google Scholar
     

  • Yao, H. et al. Use of ITS2 region as the universal DNA barcode for plants and animals. PLoS One 5, e13102 (2010).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen, S. et al. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One 5, e8613 (2010).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schoch, C. L. et al. From the cover: nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi. Proc Natl Acad Sci USA. 109, 6241–6246 (2012).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Jones, L. et al. Barcode UK: A complete DNA barcoding resource for the flowering plants and conifers of the United Kingdom. Mol. Ecol. Resour. 21, 2050–2062 (2021).

    CAS 
    PubMed 

    Google Scholar
     

  • deWaard, J. R., Hebert, P. D. & Humble, L. M. A comprehensive DNA barcode library for the looper moths (Lepidoptera: Geometridae) of British Columbia, Canada. PLoS One 6, e18290 (2011).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Costion, C. et al. Building a plant DNA barcode reference library for a diverse tropical flora: an example from Queensland, Australia. Diversity 8, 5 (2016).


    Google Scholar
     

  • Jin, L. et al. A DNA barcode library for woody plants in tropical and subtropical China. Sci Data 10, 819 (2023).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Song, F. et al. Plant DNA barcode library for native flowering plants in the arid region of northwestern China. Mol. Ecol. Resour. 23, 1389–1402 (2023).

    CAS 
    PubMed 

    Google Scholar
     

  • Zhang, J. Plantlist: Looking Up the Status of Plant Scientific Names based on The Plant List Database. R package version (0.8.0), https://github.com/helixcn/plantlist (2022).

  • Zuntini, A. R. et al. Phylogenomics and the rise of the angiosperms. Nature 629, 843–850 (2024).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Yang, Y. et al. Recent advances on phylogenomics of gymnosperms and a new classification. Plant Divers. 44, 340–350 (2022).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Le, T. M. T. et al. A DNA barcode reference of seed plants in the Guangdong-Hong Kong-Macao Greater Bay Area. Figshare https://doi.org/10.6084/m9.figshare.27909693 (2024).

  • Liu, J. et al. The use of DNA barcoding as a tool for the conservation biogeography of subtropical forests in China. Divers. Distrib. 21, 188–199 (2015).


    Google Scholar
     

  • Doyle, J. J. & Doyle, J. L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull. 19, 11–15 (1987).


    Google Scholar
     

  • Kress, W. J. et al. Plant DNA barcodes and a community phylogeny of a tropical forest dynamics plot in Panama. Proc Natl Acad Sci USA. 106, 18621–18626 (2009).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Filichkin, S. A. & Gelvin, S. B. Effect of dimethyl sulfoxide concentration on specificity of primer matching in PCR. Biotechniques 12, 828–830 (1992).

    CAS 
    PubMed 

    Google Scholar
     

  • Kearse, M. et al. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28, 1647–1649 (2012).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ripma, L. A., Simpson, M. G. & Kristen, H. L. Geneious! Simplified genome skimming methods for phylogenetic systematic studies: A case study in Oreocarya (Boraginaceae). Appl. Plant Sci. 2, 1400062 (2014).


    Google Scholar
     

  • Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gill, B. A. et al. Plant DNA-barcode library and community phylogeny for a semi-arid East African savanna. Mol. Ecol. Resour. 19, 838–846 (2019).

    PubMed 

    Google Scholar
     

  • Wright, E. S. Using Decipher v2.0 to analyze big biological sequence data in R. R J 8, 352–359 (2016).


    Google Scholar
     

  • Meier, R., Shiyang, K., Vaidya, G. & Ng, P. K. DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Syst. Biol. 55, 715–728 (2006).

    PubMed 

    Google Scholar
     

  • Stamatakis, A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30, 1312–1313 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Le, T. M. T. et al. Dataset: DS-GHMGBA. https://doi.org/10.5883/DS-GHMGBA (2024).

  • Feliner, G. N. & Rosselló, J. A. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol. Phyl. Evol. 44, 911–919 (2007).


    Google Scholar
     

  • Lahaye, R. et al. DNA barcoding the floras of biodiversity hotspots. Proc Natl Acad Sci USA. 105, 2923–2928 (2008).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gong, L. et al. Constructing a DNA barcode reference library for southern herbs in China: A resource for authentication of southern Chinese medicine. PLoS One 13, e0201240 (2018).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hu, J. L. et al. Assessing candidate DNA barcodes for Chinese and internationally traded timber species. Mol. Ecol. Resour. 22, 1478–1492 (2022).

    CAS 
    PubMed 

    Google Scholar
     

  • Wirta, H. et al. Establishing a community-wide DNA barcode library as a new tool for arctic research. Mol. Ecol. Resour. 16, 809–822 (2016).

    CAS 
    PubMed 

    Google Scholar
     

  • Mao, X. et al. Establishing community-wide DNA barcode references for conserving mangrove forests in China. BMC Plant Biol. 21, 571 (2021).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Harris, A. J. et al. A molecular phylogeny of Staphyleaceae: Implications for generic delimitation and classical biogeographic disjunctions in the family. J. Syst. Evol. 55(2), 124–141 (2017).


    Google Scholar
     

  • Zhou, B. F. et al. Phylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere. Nat. Commun. 13, 1320 (2022).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, Z. F. et al. DNA barcoding evaluation and implications for phylogenetic relationships in Lauraceae from China. PLoS One 12, e0175788 (2017).

    PubMed 
    PubMed Central 

    Google Scholar
     



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