DNA barcoding of plants: Selection of core markers for taxonomic groups
DOI:
https://doi.org/10.14719/pst.2018.5.1.356Keywords:
DNA barcoding, rbcL, matK, ITS2Abstract
Plant identification is a crucial and routine taxonomic procedure in order to understand and conserve the biodiversity. Anthropogenic activity, pollution, deforestation, and exploitation of natural resources have been threatening to the plant biodiversity. Unfortunately, the major concern of traditional identification of plants is the gradual declined number of taxonomic expertise and lack of tools which accurately discriminate plant seeds, plant parts and seedling, and herbal adulterant. Presently, it is of utmost importance that plant biodiversity to be preserved. To overcome this issues the advent of molecular marker based technique which utilized short fragment of DNA and correctly assign plant taxa to their taxonomic group, called as DNA barcoding. First time, single marker based taxon identification successfully implemented to an animal taxa using mitochondrial cytochrome I (COI) gene fragment. However, Plant DNA barcoding is more complex and it often requires more than one set of DNA markers. In the present review, we have compiled the recent progress of plant DNA barcoding in various taxonomic groups and utility of plastids and nuclear DNA based markers for plant identification.
Downloads
Download data is not yet available.
References
1. Hebert PDN, Ratnasingham S, deWaard JR. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Biol Sci SerB. 2003; 270: S96-S99. https://doi.org/10.1098/rsbl.2003.0025
2. Hebert PDN, Cywinska A, Ball SL, deWaard JR. Biological identifications through DNA barcodes. Proc R Soc Biol Sci SerB. 2003; 270: 313-321. https://doi.org/10.1098/rspb.2002.2218
3. CBOL Plant Working Group. A DNA barcode for land plants. Proc Natl Acad Sci USA. 2009; 106: 12794-12797. https://doi.org/10.1073/pnas.0905845106
4. China Plant BOL Group, Li DZ, Gao LM, Li HT, Wang H, Ge XJ, 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. 2011; 108: 19641-19646. https://doi.org/10.1073/pnas.1104551108
5. Chen S, Yao H, Han J, Liu C, Song J, et al. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. Plos One. 2010; 5: e8613. https://doi.org/10.1371/journal.pone.0008613
6. Mohammed Abubakar B, MohdSalleh F, Shamsir Omar MS, Wagiran A. DNA Barcoding and Chromatography Fingerprints for the Authentication of Botanicals in Herbal Medicinal Products. Evid Based Complement Alternat Med. 2017.1352948.
7. Li HQ, Chen JY, Wang S, Xiong SZ. Evaluation of six candidate DNA barcoding loci in Ficus (Moraceae) of China. Mol Ecol Resour. 2012; 12: 783-790. https://doi.org/10.1111/j.1755-0998.2012.03147.x
8. Chen J, Zhao J, Erickson DL, Xia N, Kress WJ. Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China. Mol Ecol Resour. 2015; 15: 337-348. https://doi.org/10.1111/1755-0998.12319
9. Xiang XG, Hu H, Wang W, Jin XH. DNA barcoding of the recently evolved genus Holcoglossum (Orchidaceae: Aeridinae): a test of DNA barcode candidates. Mol Ecol Resour. 2011; 11: 1012-1021. https://doi.org/10.1111/j.1755-0998.2011.03044.x
10. Zhang CY, Wang FY, Yan HF, Hao G, Hu CM, et al. Testing DNA barcoding in closely related groups of Lysimachia L. (Myrsinaceae). Mol Ecol Resour. 2012; 12: 98-108. https://doi.org/10.1111/j.1755-0998.2011.03076.x
11. Mishra P, Kumar A, Nagireddy A, Mani DN, Shukla AK, Tiwari R, Sundaresan V. DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market. Plant biotechnol J. 2016; 14: 8-21. https://doi.org/10.1111/pbi.12419
12. Janjua S, Fakhar-I-Abbas, William K, Malik IU, Mehr J. DNA Mini-barcoding for wildlife trade control: a case study on identification of highly processed animal materials. Mitochondrial DNA. 2017; 28: 544-6. https://doi.org/10.3109/24701394.2016.1155051
13. Manoylov KM. Taxonomic identification of algae (morphological and molecular): species concepts, methodologies, and their implications for ecological bioassessment. J phycol. 2014; 50: 409-24. https://doi.org/10.1111/jpy.12183
14. Subhadra B. Algal biorefinery?based industry: an approach to address fuel and food insecurity for a carbon?smart world. J Sci Food Agric. 201; 91: 2-13. https://doi.org/10.1002/jsfa.4207
15. Hadi SIIA, Santana H, Brunale PPM, Gomes TG, Oliveira MD, Matthiensen A, et al. (2016) DNA barcoding green microalgae isolated from neotropical inland waters. Plos One 11(2): e0149284. https://doi.org/10.1371/journal.pone.0149284
16. Hall JD, Fucikova K, Lo C, Lewis LA, Karol KG. An assessment of proposed DNA barcodes in freshwater green algae. Cryptogam, Algol. 2010; 31(4):529-55.
17. Buchheim MA, Keller A, Koetschan C, Forster F, Merget B, Wolf M. Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life. PLoS One. 2011; 6(2):e16931. https://doi.org/10.1371/journal.pone.0016931
18. Caisová L, Marin B, Melkonian M. A close-up view on ITS2 evolution and speciation-a case study in the Ulvophyceae (Chlorophyta, Viridiplantae). BMC Evol Biol. 2011; 11: 262. https://doi.org/10.1186/1471-2148-11-262
19. Pawlowski J, Audic S, Adl S, Bass D, Belbahri L, Berney C, Bowser SS, Cepicka I, Decelle J, Dunthorn M, Fiore-Donno AM. CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol. 2012; 10: e1001419. https://doi.org/10.1371/journal.pbio.1001419
20. Lang AS, Kruijer JD, Stech M. DNA barcoding of Arctic bryophytes: an example from the moss genus Dicranum (Dicranaceae, Bryophyta). Polar Biol. 2014; 37: 1157-69. https://doi.org/10.1007/s00300-014-1509-7
21. Hofbauer WK, Forrest LL, Hollingsworth PM, Hart ML. Preliminary insights from DNA barcoding into the diversity of mosses colonising modern building surfaces. Bryophyte Diversity Evol. 2016; 38:1-22. https://doi.org/10.11646/bde.38.1.1
22. Liu Y, YAN HF, Cao T, GE XJ. Evaluation of 10 plant barcodes in bryophyta (Mosses). J Syst Evol. 2010; 48: 36-46. https://doi.org/10.1111/j.1759-6831.2009.00063.x
23. Ebihara A, Nitta JH, Ito M. Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan. PLoS One 2010; 5: e15136. https://doi.org/10.1371/journal.pone.0015136
24. Li F-W, Kuo L-Y, Rothfels CJ, Ebihara A, Chiou W-L, Windham MD, et al. rbcL and matK earn two thumbs up as the core DNA barcode for Ferns. PLoS One. 2011; 6: e26597. https://doi.org/10.1371/journal.pone.0026597
25. Ma XY, Xie CX, Liu C, Song JY, Yao H, Luo K, Zhu YJ, Gao T, Pang XH, Qian J, Chen SL. Species identification of medicinal pteridophytes by a DNA barcode marker, the chloroplast psbA-trnH intergenic region. Biol Pharm Bull. 2010; 33: 1919-24. https://doi.org/10.1248/bpb.33.1919
26. Gu W, Song J, Cao Y, Sun Q, Yao H, Wu Q, Chao J, Zhou J, Xue W, Duan J. Application of the ITS2 region for barcoding medicinal plants of Selaginellaceae in Pteridophyta. PloS one. 2013; 8(6): e67818. https://doi.org/10.1371/journal.pone.0067818
27. Wang AH, Wang FG, Zhang WW, Ma XD, Li XW, Yi QF, Li DL, Duan L, Yan YH, Xing FW. Revision of series Gravesiana (Adiantum L.) based on morphological characteristics, spores and phylogenetic analyses. PloS one. 2017; 12(4): e0172729. https://doi.org/10.1371/journal.pone.0172729
28. Christenhusz MJ, Byng JW. The number of known plants species in the world and its annual increase. Phytotaxa. 2016; 261:201-17. https://doi.org/10.11646/phytotaxa.261.3.1
29. Sass C, Little DP, Stevenson DW, Specht CD. DNA barcoding in the Cycadales: testing the potential of proposed barcoding markers for species identification of Cycads. PloS One 2007; 2: e1154. https://doi.org/10.1371/journal.pone.0001154
30. Li Y, Gao LM, Poudel RC, Li DZ, Forrest A. High universality of matK primers for barcoding gymnosperms. J Syst Evol. 2011; 49: 169-75. https://doi.org/10.1111/j.1759-6831.2011.00128.x
31. Vijayan K, Tsou CH. DNA barcoding in plants: taxonomy in a new perspective. Curr. Sci. 2010:1530-41.
32. Kress J, Erickson DL. 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. https://doi.org/10.1371/journal.pone.0000508
33. Newmaster SG, Fazekas AJ, Steeves RAD, Janovec J. Testing candidate plant barcode regions in the Myristicaceae. Mol Ecol Resour. 2008; 8: 480-490. https://doi.org/10.1111/j.1471-8286.2007.02002.x
34. Saddhe AA, Jamdade RA, Kumar K. Assessment of mangroves from Goa, west coast India using DNA barcode. SpringerPlus. 2016; 5:1554. https://doi.org/10.1186/s40064-016-3191-4
35. Saddhe AA, Jamdade RA, Kumar K. Evaluation of multilocus marker efficacy for delineating mangrove species of West Coast India. PLoS One. 2017; 12: e0183245. https://doi.org/10.1371/journal.pone.0183245
36. Awad M, Fahmy RM, Mosa KA, Helmy M, El-Feky FA. Identification of effective DNA barcodes for Triticum plants through chloroplast genome-wide analysis. Comput Biol Chem. 2017; 71: 20-31. https://doi.org/10.1016/j.compbiolchem.2017.09.003
2. Hebert PDN, Cywinska A, Ball SL, deWaard JR. Biological identifications through DNA barcodes. Proc R Soc Biol Sci SerB. 2003; 270: 313-321. https://doi.org/10.1098/rspb.2002.2218
3. CBOL Plant Working Group. A DNA barcode for land plants. Proc Natl Acad Sci USA. 2009; 106: 12794-12797. https://doi.org/10.1073/pnas.0905845106
4. China Plant BOL Group, Li DZ, Gao LM, Li HT, Wang H, Ge XJ, 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. 2011; 108: 19641-19646. https://doi.org/10.1073/pnas.1104551108
5. Chen S, Yao H, Han J, Liu C, Song J, et al. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. Plos One. 2010; 5: e8613. https://doi.org/10.1371/journal.pone.0008613
6. Mohammed Abubakar B, MohdSalleh F, Shamsir Omar MS, Wagiran A. DNA Barcoding and Chromatography Fingerprints for the Authentication of Botanicals in Herbal Medicinal Products. Evid Based Complement Alternat Med. 2017.1352948.
7. Li HQ, Chen JY, Wang S, Xiong SZ. Evaluation of six candidate DNA barcoding loci in Ficus (Moraceae) of China. Mol Ecol Resour. 2012; 12: 783-790. https://doi.org/10.1111/j.1755-0998.2012.03147.x
8. Chen J, Zhao J, Erickson DL, Xia N, Kress WJ. Testing DNA barcodes in closely related species of Curcuma (Zingiberaceae) from Myanmar and China. Mol Ecol Resour. 2015; 15: 337-348. https://doi.org/10.1111/1755-0998.12319
9. Xiang XG, Hu H, Wang W, Jin XH. DNA barcoding of the recently evolved genus Holcoglossum (Orchidaceae: Aeridinae): a test of DNA barcode candidates. Mol Ecol Resour. 2011; 11: 1012-1021. https://doi.org/10.1111/j.1755-0998.2011.03044.x
10. Zhang CY, Wang FY, Yan HF, Hao G, Hu CM, et al. Testing DNA barcoding in closely related groups of Lysimachia L. (Myrsinaceae). Mol Ecol Resour. 2012; 12: 98-108. https://doi.org/10.1111/j.1755-0998.2011.03076.x
11. Mishra P, Kumar A, Nagireddy A, Mani DN, Shukla AK, Tiwari R, Sundaresan V. DNA barcoding: an efficient tool to overcome authentication challenges in the herbal market. Plant biotechnol J. 2016; 14: 8-21. https://doi.org/10.1111/pbi.12419
12. Janjua S, Fakhar-I-Abbas, William K, Malik IU, Mehr J. DNA Mini-barcoding for wildlife trade control: a case study on identification of highly processed animal materials. Mitochondrial DNA. 2017; 28: 544-6. https://doi.org/10.3109/24701394.2016.1155051
13. Manoylov KM. Taxonomic identification of algae (morphological and molecular): species concepts, methodologies, and their implications for ecological bioassessment. J phycol. 2014; 50: 409-24. https://doi.org/10.1111/jpy.12183
14. Subhadra B. Algal biorefinery?based industry: an approach to address fuel and food insecurity for a carbon?smart world. J Sci Food Agric. 201; 91: 2-13. https://doi.org/10.1002/jsfa.4207
15. Hadi SIIA, Santana H, Brunale PPM, Gomes TG, Oliveira MD, Matthiensen A, et al. (2016) DNA barcoding green microalgae isolated from neotropical inland waters. Plos One 11(2): e0149284. https://doi.org/10.1371/journal.pone.0149284
16. Hall JD, Fucikova K, Lo C, Lewis LA, Karol KG. An assessment of proposed DNA barcodes in freshwater green algae. Cryptogam, Algol. 2010; 31(4):529-55.
17. Buchheim MA, Keller A, Koetschan C, Forster F, Merget B, Wolf M. Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics: towards an automated reconstruction of the green algal tree of life. PLoS One. 2011; 6(2):e16931. https://doi.org/10.1371/journal.pone.0016931
18. Caisová L, Marin B, Melkonian M. A close-up view on ITS2 evolution and speciation-a case study in the Ulvophyceae (Chlorophyta, Viridiplantae). BMC Evol Biol. 2011; 11: 262. https://doi.org/10.1186/1471-2148-11-262
19. Pawlowski J, Audic S, Adl S, Bass D, Belbahri L, Berney C, Bowser SS, Cepicka I, Decelle J, Dunthorn M, Fiore-Donno AM. CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms. PLoS Biol. 2012; 10: e1001419. https://doi.org/10.1371/journal.pbio.1001419
20. Lang AS, Kruijer JD, Stech M. DNA barcoding of Arctic bryophytes: an example from the moss genus Dicranum (Dicranaceae, Bryophyta). Polar Biol. 2014; 37: 1157-69. https://doi.org/10.1007/s00300-014-1509-7
21. Hofbauer WK, Forrest LL, Hollingsworth PM, Hart ML. Preliminary insights from DNA barcoding into the diversity of mosses colonising modern building surfaces. Bryophyte Diversity Evol. 2016; 38:1-22. https://doi.org/10.11646/bde.38.1.1
22. Liu Y, YAN HF, Cao T, GE XJ. Evaluation of 10 plant barcodes in bryophyta (Mosses). J Syst Evol. 2010; 48: 36-46. https://doi.org/10.1111/j.1759-6831.2009.00063.x
23. Ebihara A, Nitta JH, Ito M. Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan. PLoS One 2010; 5: e15136. https://doi.org/10.1371/journal.pone.0015136
24. Li F-W, Kuo L-Y, Rothfels CJ, Ebihara A, Chiou W-L, Windham MD, et al. rbcL and matK earn two thumbs up as the core DNA barcode for Ferns. PLoS One. 2011; 6: e26597. https://doi.org/10.1371/journal.pone.0026597
25. Ma XY, Xie CX, Liu C, Song JY, Yao H, Luo K, Zhu YJ, Gao T, Pang XH, Qian J, Chen SL. Species identification of medicinal pteridophytes by a DNA barcode marker, the chloroplast psbA-trnH intergenic region. Biol Pharm Bull. 2010; 33: 1919-24. https://doi.org/10.1248/bpb.33.1919
26. Gu W, Song J, Cao Y, Sun Q, Yao H, Wu Q, Chao J, Zhou J, Xue W, Duan J. Application of the ITS2 region for barcoding medicinal plants of Selaginellaceae in Pteridophyta. PloS one. 2013; 8(6): e67818. https://doi.org/10.1371/journal.pone.0067818
27. Wang AH, Wang FG, Zhang WW, Ma XD, Li XW, Yi QF, Li DL, Duan L, Yan YH, Xing FW. Revision of series Gravesiana (Adiantum L.) based on morphological characteristics, spores and phylogenetic analyses. PloS one. 2017; 12(4): e0172729. https://doi.org/10.1371/journal.pone.0172729
28. Christenhusz MJ, Byng JW. The number of known plants species in the world and its annual increase. Phytotaxa. 2016; 261:201-17. https://doi.org/10.11646/phytotaxa.261.3.1
29. Sass C, Little DP, Stevenson DW, Specht CD. DNA barcoding in the Cycadales: testing the potential of proposed barcoding markers for species identification of Cycads. PloS One 2007; 2: e1154. https://doi.org/10.1371/journal.pone.0001154
30. Li Y, Gao LM, Poudel RC, Li DZ, Forrest A. High universality of matK primers for barcoding gymnosperms. J Syst Evol. 2011; 49: 169-75. https://doi.org/10.1111/j.1759-6831.2011.00128.x
31. Vijayan K, Tsou CH. DNA barcoding in plants: taxonomy in a new perspective. Curr. Sci. 2010:1530-41.
32. Kress J, Erickson DL. 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. https://doi.org/10.1371/journal.pone.0000508
33. Newmaster SG, Fazekas AJ, Steeves RAD, Janovec J. Testing candidate plant barcode regions in the Myristicaceae. Mol Ecol Resour. 2008; 8: 480-490. https://doi.org/10.1111/j.1471-8286.2007.02002.x
34. Saddhe AA, Jamdade RA, Kumar K. Assessment of mangroves from Goa, west coast India using DNA barcode. SpringerPlus. 2016; 5:1554. https://doi.org/10.1186/s40064-016-3191-4
35. Saddhe AA, Jamdade RA, Kumar K. Evaluation of multilocus marker efficacy for delineating mangrove species of West Coast India. PLoS One. 2017; 12: e0183245. https://doi.org/10.1371/journal.pone.0183245
36. Awad M, Fahmy RM, Mosa KA, Helmy M, El-Feky FA. Identification of effective DNA barcodes for Triticum plants through chloroplast genome-wide analysis. Comput Biol Chem. 2017; 71: 20-31. https://doi.org/10.1016/j.compbiolchem.2017.09.003
Downloads
Published
25-12-2017
How to Cite
1.
Saddhe AA, Kumar K. DNA barcoding of plants: Selection of core markers for taxonomic groups. Plant Sci. Today [Internet]. 2017 Dec. 25 [cited 2024 Nov. 19];5(1):9-13. Available from: https://horizonepublishing.com/journals/index.php/PST/article/view/356
Issue
Section
Mini Reviews
License
Copyright and Licence details of published articles
Authors who publish with this journal agree to the following terms:
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Creative Commons Attribution License that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
Open Access Policy
Plant Science Today is an open access journal. There is no registration required to read any article. All published articles are distributed under the terms of the Creative Commons Attribution License (CC Attribution 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited (https://creativecommons.org/licenses/by/4.0/). Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
