Skip to main content
SpringerLink
Log in

Assessment of candidate plant DNA barcodes using the Rutaceae family

  • Research Papers
  • Published:
Science China Life Sciences Aims and scope Submit manuscript

Abstract

DNA barcoding is a rapidly developing frontier technology that is gaining worldwide attention. Here, seven regions (psbA-trnH, matK, ycf5, rpoC1, rbcL, ITS2, and ITS) with potential for use as DNA barcodes were tested for their ability to identify 300 samples of 192 species from 72 genera of the family Rutaceae. To evaluate each barcode’s utility for species authentication, PCR amplification efficiency, genetic divergence, and barcoding gaps were assessed. We found that the ITS2 region exhibited the highest inter-specific divergence, and that this was significantly higher than the intra-specific variation in the “DNA barcoding gap” assessment and Wilcoxon two-sample tests. The ITS2 locus had the highest identification efficiency among all tested regions. In a previous study, we found that ITS2 was able to discriminate a wide range of plant taxa, and here we confirmed that ITS2 was also able to discriminate a number of closely related species. Therefore, we propose that ITS2 is a promising candidate barcode for plant species identification.

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

Similar content being viewed by others

References

  1. Hebert P D, Cywinska A, Ball S L, et al. Biological identifications through DNA barcodes. Proc R Soc Biol Sci SerB, 2003, 270: 313–321 10.1098/rspb.2002.2218, 1:CAS:528:DC%2BD3sXktVWiu7g%3D

    Article  CAS  Google Scholar 

  2. Gregory T R. DNA barcoding does not compete with taxonomy. Nature, 2005, 434: 1067 10.1038/4341067b, 15858548, 1:CAS:528:DC%2BD2MXjsF2ltrk%3D

    Article  PubMed  CAS  Google Scholar 

  3. Miller S E. DNA barcoding and the renaissance of taxonomy. Proc Natl Acad Sci USA, 2007, 104: 4775–4776 10.1073/pnas.0700466104, 17363473, 1:CAS:528:DC%2BD2sXjvFCjsLo%3D

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  4. Hebert P D, Ratnasingham S, deWaard J R. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Biol Sci SerB, 2003, 270: S96–S99 10.1098/rsbl.2003.0025, 1:CAS:528:DC%2BD3sXns1Smsbo%3D

    Article  CAS  Google Scholar 

  5. Vences M, Thomas M, Bonett R M, et al. Deciphering amphibian diversity through DNA barcoding: chances and challenges. Philos Trans R Soc Lond B Biol Sci, 2005, 360: 1859–1868 10.1098/rstb.2005.1717, 16221604, 1:CAS:528:DC%2BD2MXhtlSjsrjE

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  6. Janzen D H, Hajibabaei M, Burns J M, et al. Wedding biodiversity inventory of a large and complex Lepidoptera fauna with DNA barcoding. Philos Trans R Soc Lond B Biol Sci, 2005, 360: 1835–1845 10.1098/rstb.2005.1715, 16214742, 1:CAS:528:DC%2BD2MXhtlSjsrjI

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  7. Ward R D, Zemlak T S, Innes B H, et al. DNA barcoding Australia’s fish species. Philos Trans R Soc Lond B Biol Sci, 2005}, 360}: 1847–1 10.1098/rstb.2005.1716, 16214743, 1:CAS:528:DC%2BD2MXhtlSjsrjK

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  8. Kress W J, Wurdack K J, Zimmer E A, et al. Use of DNA barcodes to identify flowering plants. Proc Natl Acad Sci USA, 2005, 102: 8369–8374 10.1073/pnas.0503123102, 15928076, 1:CAS:528:DC%2BD2MXlsV2mtbY%3D

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  9. Newmaster S G, Fazekas A J, Ragupathy S. DNA barcoding in land plants: evaluation of rbcL in a multigene tiered approach. Can J Bot, 2006, 84: 335–341 10.1139/B06-047, 1:CAS:528:DC%2BD28XotFeis7c%3D

    Article  CAS  Google Scholar 

  10. Chase M W, Cowan R S, Hollingsworth P M, et al. A proposal for a standardised protocol to barcode all land plants. Taxon, 2007, 56: 295–299

    Google Scholar 

  11. Kress W J, Erickson D L. A two-locus global DNA barcode for land plants: The coding rbcL gene complements the non-coding trnH-psbA spacer region. PLoS ONE, 2007, 2: e508 10.1371/journal.pone.0000508, 17551588, 1:CAS:528:DC%2BD2sXmvFyrs7Y%3D

    Article  PubMed  PubMed Central  Google Scholar 

  12. Pennisi E. Wanted: a barcode for plants. Science, 2007, 318: 190–191 10.1126/science.318.5848.190, 17932267, 1:CAS:528:DC%2BD2sXhtFyrs7rE

    Article  PubMed  CAS  Google Scholar 

  13. CBOL Plant Working Group. A DNA barcode for land plants. Proc Natl Acad Sci USA, 2009, 106: 12794–12797 10.1073/pnas.0905845106

    Article  PubMed Central  Google Scholar 

  14. Chen S L, Yao H, Han J P, et al. Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species. PLoS ONE, 2010, 5: e8613 10.1371/journal.pone.0008613, 20062805, 1:CAS:528:DC%2BC3cXmtlertQ%3D%3D

    Article  PubMed  PubMed Central  Google Scholar 

  15. Song J Y, Yao H, Li Y, et al. Authentication of the family Polygonaceae in Chinese pharmacopoeia by DNA barcoding technique. J Ethnopharmacol, 2009, 124: 434–439 10.1016/j.jep.2009.05.042, 19505556, 1:CAS:528:DC%2BD1MXptVSisbg%3D

    Article  PubMed  CAS  Google Scholar 

  16. Lahaye R, van der Bank M, Bogarin D, et al. DNA barcoding the floras of biodiversity hotspots. Proc Natl Acad Sci USA, 2008, 105: 2923–2928 10.1073/pnas.0709936105, 18258745

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  17. Sass C, Little D P, Stevenson D W, et al. DNA Barcoding in the Cycadales: Testing the potential of proposed barcoding markers for species identification of Cycads. PLoS ONE, 2007, 2: e1154 10.1371/journal.pone.0001154, 17987130, 1:CAS:528:DC%2BD1cXjslShsg%3D%3D

    Article  PubMed  PubMed Central  Google Scholar 

  18. Zhu Y J, Chen S L, Yao H, et al. DNA barcoding for the identification plants of the genus Paris. Acta Pharmaceutica Sinica, 2010, 45: 376–382.

    PubMed  CAS  Google Scholar 

  19. Keller A, Schleicher T, Schultz J, et al. 5.8S–28S rRNA interaction and HMM-based ITS2 annotation. Gene, 2009, 430: 50–57 10.1016/j.gene.2008.10.012, 19026726, 1:CAS:528:DC%2BD1MXovV2l

    Article  PubMed  CAS  Google Scholar 

  20. Meyer C P, Paulay G. DNA barcoding: error rates based on comprehensive sampling. PLoS Biol, 2005, 3: e422 10.1371/journal.pbio.0030422, 16336051, 1:CAS:528:DC%2BD2MXhtlWls7nL

    Article  PubMed  PubMed Central  Google Scholar 

  21. Slabbinck B, Dawyndt P, Martens M, et al. TaxonGap: a visualization tool for intra- and inter-species variation among individual biomarkers. Bioinformatics, 2008, 24: 866–867 10.1093/bioinformatics/btn031, 18227116, 1:CAS:528:DC%2BD1cXjsVaktLw%3D

    Article  PubMed  CAS  Google Scholar 

  22. Ross H A, Murugan S, Li W L. Testing the reliability of genetic methods of species identification via simulation. Syst Biol, 2008, 57: 216–230 10.1080/10635150802032990, 18398767

    Article  PubMed  Google Scholar 

  23. Chase M W, Salamin N, Wilkinson M, et al. Land plants and DNA barcodes: short-term and long-term goals. Philos Trans R Soc Lond B Biol Sci, 2005, 360: 1889–1895 10.1098/rstb.2005.1720, 16214746, 1:CAS:528:DC%2BD2MXhtlSjsrnP

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  24. Gonzalez M A, Baraloto C, Engel J, et al. Identification of Amazonian trees with DNA barcodes. PLoS One, 2009, 4: e7483 10.1371/journal.pone.0007483, 19834612, 1:CAS:528:DC%2BD1MXhtlWqtbnI

    Article  PubMed  PubMed Central  Google Scholar 

  25. Müller T, Philippi N, Dandekar T, et al. Distinguishing species. RNA, 2007, 13: 1469–1472 10.1261/rna.617107, 17652131, 1:CAS:528:DC%2BD2sXhtVSqt7jO

    Article  PubMed  PubMed Central  Google Scholar 

  26. Miao M, Warren A, Song W, et al. Analysis of the internal transcribed spacer 2 (ITS2) region of scuticociliates and related taxa (Ciliophora, Oligohymenophorea) to infer their evolution and phylogeny. Protist, 2008, 159: 519–533 10.1016/j.protis.2008.05.002, 18675585, 1:CAS:528:DC%2BD1MXjs1Khsg%3D%3D

    Article  PubMed  CAS  Google Scholar 

  27. Shaw J, Lickey E B, Beck J T, et al. The tortoise and the hare. II. Relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. Am J Bot, 2005, 92: 142–166 10.3732/ajb.92.1.142, 1:CAS:528:DC%2BD2MXht1Klsbc%3D

    Article  PubMed  CAS  Google Scholar 

  28. Yao H, Song J Y, Ma X Y, et al. Identification of Dendrobium species by a candidate DNA barcode sequence: The chloroplast psbA-trnH intergenic region. Planta Med, 2009, 75: 667–669 10.1055/s-0029-1185385, 19235685, 1:CAS:528:DC%2BD1MXmsFWhu7g%3D

    Article  PubMed  CAS  Google Scholar 

  29. Walter R, Herbert J W, Leon D B. The Citrus industry (Vol I). California: University of California Press, 1967. 190–430

  30. Tanaka T. Taxonomic problem of Citrus fruits in the Orient. Bull Univ Osaka Pref Ser B, 1969, 21: 133–138

    Google Scholar 

  31. Zeng M. The knowledge comprehension and arrangement of Citrus. China Fruit, 1960, (2): 31–37

    Google Scholar 

  32. Francois L, Frederic L, Joseph M B, et al. DNA amplified fingerprinting, a useful tool for determination of genetic origin and diversity analysis in Citrus. Hort Sci, 1995, 30: 1063–1067

    Google Scholar 

  33. Chen S L, Song J Y, Yao H, et al. Strategy and key technique of identification of Chinese herbal medicine using DNA barcoding, Chin J Nat Med, 2009, 7: 322–327 10.3724/SP.J.1009.2009.00322, 1:CAS:528:DC%2BC3cXhtFKktbc%3D

    Article  CAS  Google Scholar 

  34. Ning S P, Yan H Y, Hao G, et al. Current advances of DNA barcoding study in plants. Biodiversity Science, 2008, 16: 417–425 1:CAS:528:DC%2BD1MXotVWktLg%3D

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Medicinal Plant Development, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100193, China

    Kun Luo, ShiLin Chen, JingYuan Song, Hui Yao, Xinye Ma, XiaoHui Pang, Hua Yu & XiWen Li

  2. College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430061, China

    Kun Luo, KeLi Chen & Zhen Liu

  3. School of Bioscience and Engineering, Southwest Jiaotong University, Chengdu, 610031, China

    YingJie Zhu

  4. Department of Chemistry, Tsinghua University, Beijing, 100084, China

    XiWen Li

Authors
  1. Kun Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. ShiLin Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. KeLi Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. JingYuan Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hui Yao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Xinye Ma
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. YingJie Zhu
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. XiaoHui Pang
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Hua Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. XiWen Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Zhen Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to ShiLin Chen.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Luo, K., Chen, S., Chen, K. et al. Assessment of candidate plant DNA barcodes using the Rutaceae family. Sci. China Life Sci. 53, 701–708 (2010). https://doi.org/10.1007/s11427-010-4009-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11427-010-4009-1

Keywords

Search

Navigation