Jump to ContentJump to Main Navigation
Show Summary Details
More options …

DNA Barcodes

Ed. by Mitchell, Andrew

1 Issue per year


Emerging Science

Open Access
Online
ISSN
2299-1077
See all formats and pricing
More options …

Towards a DNA barcode library for Egyptian flora, with a preliminary focus on ornamental trees and shrubs of two major gardens

Hosam O. Elansary
  • Molecular Biology Laboratory, Floriculture, Ornamental Horticulture and Garden Design Department, Faculty of Agriculture (El-Shatby), Alexandria University, Alexandria, Egypt
  • Biodiversity Institute of Ontario, University of Guelph, ON N1G 2W1, Canada
  • Email
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
Published Online: 2013-09-06 | DOI: https://doi.org/10.2478/dna-2013-0004

Abstract

The flora of Egypt comprises over 20 000 species which requires an accrued conservation effort. A successful preservation of such an impressive diversity requires the development of accurate identification tools. In this study, I provide the first attempt to reach this objective using molecular approach known as DNA barcoding, and reconstructing the first barcode library for Egyptian flora. Specifically, the use of matK and rbcLa genes as barcodes for trees and shrubs in two main gardens in Egypt was studied. 152 specimens (145 species) were collected mainly from Antoniades and Orman gardens and sequenced. Sequencing success was 93.46% in rbcLa whereas matK showed lower percentage (74.39%). Using matK sequences taxa were correctly assigned by 97.16, 86.79 and 49.05 % on the levels of family, genus and species respectively; also rbcLa revealed 99.27, 86.13 and 51.82% on the levels of family, genus and species respectively. Furthermore, both markers provided us with a species and occasionally subspecies level discrimination tool in many investigated cases and a DNA barcode library for 152 specimens of the 145 species of trees and shrubs common in two main historical gardens in Egypt.

Keywords: matK; rbcLa; Egypt; barcoding

  • [1] Khedr A, Cadotte MW, El-Keblawy A, Lovett-Doust J (2002) Phylogenetic diversity and ecological features in the Egyptian flora. Biodiversity and Conservation 11:1809-1824. CrossrefGoogle Scholar

  • [2] Packer L, Gibbs J, Sheffield C, Hanner R (2009) DNA barcoding and the mediocrity of morphology. Molecular Ecology Resources 9:42-50. CrossrefPubMedGoogle Scholar

  • [3] Pires AC, Marinoni L (2010) DNA barcoding and traditional taxonomy unified through Integrative Taxonomy: a view that challenges the debate questioning both methodologies. Biota Neotropica 10:339-346. Web of ScienceGoogle Scholar

  • [4] Van der Bank HF, Greenfield R, Daru BH, Yessoufou K (2012) DNA barcoding reveals micro-evolutionary changes and river system-level phylogeographic resolution of African silver catfish, Schilbe intermedius (Actinopterygii: Siluriformes: Schilbeidae) from seven populations across different African river systems. Acta Ichthyol. Piscat. 42 :307–320. Web of ScienceGoogle Scholar

  • [5] Kress J, Erickson DL (2007) A two-locus global DNA barcode for land plants: the coding rbcLa gene complements the noncoding trnH-psbA spacer region. PLoS One, 2:e508. Web of ScienceGoogle Scholar

  • [6] Janzen DH, Hallwachs W, Blandin P, Burns JM, Cadiou J, Chacon I, Dapkey T, et al (2009) Integration of DNA barcoding into an ongoing inventory of complex tropical biodiversity. Molecular Ecology Resources 9:1–26. PubMedCrossrefWeb of ScienceGoogle Scholar

  • [7] Casiraghi M, Labra M, Ferri E, Galimberti A, De Mattia F (2010) DNA barcoding: theoretical aspects and practical applications. Nimis P. L., Vignes Lebbe R. (eds.) Tools for Identifying Biodiversity: Progress and Problems – pp. 269-273. Google Scholar

  • [8] Nanney DL (1982) Genes and phenes in tetrahymena. BioScience 32:783–788. CrossrefGoogle Scholar

  • [9] Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society 270:313–321. Google Scholar

  • [10] Kress WJ, Wurdack KJ, Zimmer EA, Weigt LA, Janzen DH (2005) Use of DNA barcodes to identify flowering plants. Proceedings of the National Academy of Sciences of the U S A 102:8369-8374. Google Scholar

  • [11] CBOL plant working group (2009) A DNA barcode for all land plants. Proceedings of the National Academy of Sciences of the U S A 106:12794-12797. Google Scholar

  • [12] Egyptian ministry of agriculture (2007) Botanical groups in Orman. Egyptian Ministry of Agriculture and land Reclamation, Central Administration for Arboriculture and Environment, March 2007, Part I. Google Scholar

  • [13] Ministry of Agriculture and Land Reclamation (Arab Republic of Egypt) (2006). Antoniades garden. Google Scholar

  • [14] Elansary HO, Elansary DO (2013) Genetic diversity and biochemical activity of leaves and fruits of main Ficus Sp. grown in Egypt. Journal of Horticultural Science & Ornamental Plants 5:30-36. Google Scholar

  • [15] Younis RAA, Ismail OM, Soliman SS (2009) Identification of sex-specific DNA markers for Date Palm (Phoenix dactylifera L.) using RAPD and ISSR techniques. Research Journal of Agriculture and Biological Sciences 4:278-284. Google Scholar

  • [16] Elansary HO, Mostafa GG, Elansary DO, Hussein A (2011) Assessment of genetic diversity within the genus Acacia grown in Egypt and studying its relation to leaf tannin and phenolic contents. Seventh Pl. Breed. Conf. May 4-5, 2011, Alexandria, Egypt. Egyptian Journal of Plant Breeding 2:243- 250 Special issue. Google Scholar

  • [17] Mars M (2003) Fig (Ficus carica L.) genetic resources and breeding. Acta Horticulturae 605:19-27 Google Scholar

  • [18] Rout GR , Aparajita S (2009) Genetic Relationships among 23 Ficus Accessions Using Inter- Simple Sequence Repeat Markers. Journal of Crop Science and Biotechnology 12:91 -96. Google Scholar

  • [19] Johnson DV (2011) Introduction: Date Palm Biotechnology from Theory to Practice. In: Jain SM, Al-Khayri JM, Johnson DV, editors. Date Palm Biotechnology. (Netherlands: Springer ) p 1-11. Google Scholar

  • [20] Zaid A, Arias-Jiménez EJ (2001) Date palm cultivation. FAOSTAT (http://www.fao.org/DOCREP/006/Y4360E/ y4360e00.htm#Contents) Google Scholar

  • [21] FAOSTAT (2010) Dates production quantity. http:// en.wikipedia.org/wiki/UN_Food_%26_Agriculture_ Organisation Google Scholar

  • [22] Sedra MH, Lashermes P, Trouslot P, Combes MC, Hamon S (1998) Identification and genetic diversity analysis of Date palm (Phoenix dactylifera L.) varieties from Morocco using RAPD markers. Euphytica 103:75-82. CrossrefGoogle Scholar

  • [23] Trifi M, Rhouma A, Marrakchi M (2000) Phylogenetic relationships in Tunisian Date palm (Phoenix dactylifera L.) germplasm collection using DNA amplification fingerprinting. Agronomie 20:665-671. CrossrefGoogle Scholar

  • [24] Trifi M (2001) Polymorphisme et typage moléculaire de variétés tunisiennes de palmier dattier (Phoenix dactylifera L.): relation avec la résistance au bayoud. Thèse Doctorat d’Etat, Université Tunis-El Manar, Fac. Sc. Tunis, 141. Google Scholar

  • [25] El-Kishin DA, Adawy SS, Hussein EHA (2003) AFLP fingerprinting of some Egyptian date palm (Phoenix dactylifera L.) cultivars. Arab Journal of Biotechnology 2:223-234. Google Scholar

  • [26] Younis RAA, Ismail OM, Soliman SS (2009) Identification of sex-specific DNA markers for Date Palm (Phoenix dactylifera L.) using RAPD and ISSR techniques. Research Journal of Agriculture and Biological Sciences 4:278-284. Google Scholar

  • [27] Al-Qurainy F, Khan S, Al-Hemaid FM, Ali MA, Tarroum M, Ashraf M (2011) Assessing Molecular Signature for Some Potential Date(Phoenix dactylifera L.) Cultivars from Saudi Arabia, Based on Chloroplast DNA Sequences rpoB and psbA-trnH. Int. J. Mol. Sci. 2011, 12, 6871- 6880. CrossrefWeb of ScienceGoogle Scholar

  • [28] Levin RA, Wagner WL, Hoch PC, Nepokroeff M, Pires JC, Zimmer EA, Sytsma KJ (2003) Family-level relationships of Onagraceae based on chloroplast rbcLa and ndhF data. American Journal of Botany 90:107-115 CrossrefGoogle Scholar

  • [29] Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Molecular Biology and Evolution 28:2731-2739. Web of ScienceCrossrefGoogle Scholar

  • [30] Ratnasingham, S. & Hebert, P. D. N. (2007). BOLD: The Barcode of Life Data System (www.barcodinglife.org). Molecular Ecology Notes 7: 355-364. PubMedWeb of ScienceCrossrefGoogle Scholar

  • [31] Nei M (1987) Molecular Evolutionary Genetics. Columbia University Press, New York. Google Scholar

  • [32] Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19: 2496- 2497. PubMedCrossrefGoogle Scholar

  • [33] Cabrera LI, Salazar GA, Martínez E, Ramos C, Escalante P, Chiang F , Sousa M, Kuzmina M (2011) DNA Barcode of the Flora of Calakmul, Yucatan Peninsula, Mexico. Fourth International barcode of life conference, Adelaide, Australia 28 September -3 December. Google Scholar

  • [34] Mabberley, D J (1978) The plant-book. A portable dictionary of the higher plants. Pp. xii + 706 [reprints, with corrections, Pp. 707 - 1989, 1990, 1993 (twice), 1996]. (Cambridge University Press) Google Scholar

  • [35] Encyclopædia Britannica Online (2011) Fabaceae. Available at: http://original.search.eb.com/eb/article-9105203 [last accessed 26.10.2011]. Google Scholar

  • [36] Roy S, Tyagi A, Shukla V, Kumar A, Singh UM, et al. (2010) Universal Plant DNA Barcode Loci May Not Work in Complex Groups: A Case Study with Indian Berberis Species. PLoS ONE 5(10): e13674 Web of ScienceGoogle Scholar

  • [37] Manzanilla V & Bruneau A (2012) Phylogeny reconstruction in the Caesalpinieae grade (Leguminosae) based on duplicated copies of the sucrose synthase gene and plastid markers. Molecular Phylogenetics and Evolution 65:149–162. CrossrefWeb of ScienceGoogle Scholar

  • [38] El-Hadrami I, El-Hadrami A (2009) Breeding date palm. In: Jain SM. Priyadarshan PM (eds.) Breeding plantation tree crops. (Springer, New York) pp.191-216. Google Scholar

About the article


Received: 2013-03-30

Accepted: 2013-06-30

Published Online: 2013-09-06


Citation Information: DNA Barcodes, ISSN (Online) 2299-1077, DOI: https://doi.org/10.2478/dna-2013-0004.

Export Citation

©2013 Versita Sp. z o.o.. This content is open access.

Citing Articles

Here you can find all Crossref-listed publications in which this article is cited. If you would like to receive automatic email messages as soon as this article is cited in other publications, simply activate the “Citation Alert” on the top of this page.

[1]
Hosam O. Elansary, Muhammad Ashfaq, Hayssam M. Ali, Kowiyou Yessoufou, and Diego Breviario
PLOS ONE, 2017, Volume 12, Number 2, Page e0172170
[2]
Hosam O. Elansary and Eman A. Mahmoud
Journal of Essential Oil Research, 2015, Volume 27, Number 1, Page 82

Comments (0)

Please log in or register to comment.
Log in