Assessing the effectiveness of barcoding for conservation of rare plant species in the Republic of Uzbekistan

F.U. Mustafina ^a*, D.N. Jamalova ^a**, D.E. Turdiev ^a***, G.T. Kurbaniyazova ^a****, A.Dj. Gaziev ^a*****, N.Yu. Beshko ^a******, K.Sh. Tojibaev ^a*******, Z.Z. Ibragimov ^b********, K.T. Boboev ^c*********

^aInstitute of Botany, Academy of Sciences of the Republic of Uzbekistan, Tashkent, 100125 Republic of Uzbekistan

^bA.S. Sadykov Institute of Bioorganic Chemistry, Academy of Sciences of the Republic of Uzbekistan, Tashkent, 100143 Republic of Uzbekistan

^cResearch Institute of Hematology and Blood Transfusion of the Ministry of Health of the Republic of Uzbekistan, Tashkent, 100097 Uzbekistan

E-mail: ^*mustafinaferuza@yahoo.com, ^**dilafruz_jamalova.91@mail.ru, ^***doston.turdiyev.91@mail.ru, ^****kurbaniyazova94@list.ru, ^*****gazievalim644@gmail.com, ^******natalia_beshko@mail.ru, ^*******ktojibaev@mail.ru, ^*******z.ibragim@gmail.com, ^********saboboev@mail.ru

Received February 9, 2022

ORIGINAL ARTICLE

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DOI: 10.26907/2542-064X.2022.3.408-437

For citation: Mustafina F.U., Jamalova D.N., Turdiev D.E., Kurbaniyazova G.T., Gaziev A.Dj., Beshko N.Yu., Tojibaev K.Sh., Ibragimov Z.Z., Boboev K.T. Assessing the effectiveness of barcoding for conservation of rare plant species in the Republic of Uzbekistan. Uchenye Zapiski Kazanskogo Universiteta. Seriya Estestvennye Nauki, 2022, vol. 164, no. 3, pp. 408–437. doi: 10.26907/2542-064X.2022.3.408-437. (In Russian)

Abstract

This article presents, for the first time, a reference database of the nucleotide sequences for three DNA barcodes (ITS2, matK, and rbcL) of 65 rare and critically endangered plant species of the Republic of Uzbekistan (133 samples, two samples per species), including 23 monocots and 42 dicots. ITS2 region was proposed as the most variable, easily amplified and sequenced for both monocot and dicot species. Therefore, it was recommended as the main DNA barcode. The obtained reference database uploaded to the BOLD v4 platform should be useful for pharmaceutical companies, environmental and customs offices, as well as for phylogenetic research.

Keywords: barcoding, rare species, endemics, biodiversity conservation, BOLD

Acknowledgments. We thank our colleagues from the Research Institute of Hematology and Blood Transfusion of the Ministry of Health of the Republic of Uzbekistan for their kind cooperation and help. K.T. Babaeva and Z.Z. Ibragimov are specially acknowledged for their valuable contributions.

The study was performed as part of: project MRB-AN-2019-30 “Genetic inventory of rare and endangered plant species in Belarus and Uzbekistan using DNA barcoding technology”; 23/2020 agreement between the Institute of Botany and the State Committee of the Republic of Uzbekistan for Ecology and Nature Conservation; and state project “Tree of life: Monocots of Uzbekistan” (PFI-5) funded by the Institute of Botany, Academy of Sciences of the Republic of Uzbekistan.

Figure Captions

Fig. 1. Studied species: a) Iris orchioides Carrière; b) Iris magnifica Vved.; c) Tulipa butkovii Botschantz.; d) Tulipa dubia Vved.; e) Tulipa greigii Regel.; f) Tulipa ingens Hoog; g) Tulipa kaufmanniana Regel; h) Tulipa lehmanniana Merckl.; i) Tulipa vvedenskyi Botschantz.; j) Tulipa carinata Vved.; k) Tulipa kaufmanniana Regel; l) Astragalus pterocephalus Bunge; m) Astragalus xanthomeloides Korovin & Popov; n) Astragalus pterocephalus Bunge; o) Ferula tadshikorum Pimenov; p) Ferula foetida (Bunge) Regel; q) Hedysarum taschkendicum Popov; r) Ferula tadshikorum Pimenov.

Fig. 2. Visual assessment of the DNA quality in 1.2% agarose gel after the PCR product treatment with the ExoSAP-IT™ PCR Product Clean-up reagent for species of the following genera: Tulipa (a), Dracocephalum and Hedysarum (b) (primer rbcL).

Fig. 3. Visual assessment of the DNA quality in 1.2% agarose gel after the PCR product treatment with the ExoSAP-IT™ PCR Product Clean-up reagent for species of the following genera: Asrtragalus (a), Dracocephalum and Hedysarum D2-H41 (b) (primer rbcL-FP/rbcL-RP).

Fig. 4. Page on the BOLD platform with the herbarium specimen image of Hedysarum baldshuanicum B. Fedtsch (a) and its ITS2, matK, and rbcL sequences (b), as well as with the herbarium specimen image of Tulipa fosteriana W. Irving (c) and its ITS2, matK, and rbcL sequences (d).

References

1. Kress W.J., Erickson D.L. (Eds.) DNA Barcodes: Methods and Protocols. New York, Humana Totowa, 2012. 485 p. doi: 10.1007/978-1-61779-591-6.
2. Hebert P.D.N., Penton E.H., Burns J.M., Janzen D.H., Hallwachs W. Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator. Proc. Natl. Acad. Sci. U. S. A., 2004, vol. 101, no. 41, pp. 14812–14817. doi: 10.1073/pnas.0406166101.
3. Baraloto C., Hardy O.J., Paine C.E.T., Dexter K.G., Cruaud C., Dunning L.T., Gonzalez M.-A., Molino J.-F., Sabatier D., Savolainen V., Chave J. Using functional traits and phylogenetic trees to examine the assembly of tropical tree communities. J. Ecol., 2012, vol. 100, no. 3, pp. 690–701. doi: 10.1111/j.1365-2745.2012.01966.x.
4. Muellner A.N., Schaefer H., Lahaye R. Evaluation of candidate DNA Barcoding loci for economically important timber species of mahogany family (Meliaceae). Mol. Ecol. Resour., 2011, vol. 11, no. 3, pp. 450–460. doi: 10.1111/j.1755-0998.2011.02984.x.
5. CBOL Plant Working Group. A DNA barcode for land plants. Proc. Natl. Acad. Sci. U. S. A., 2009, vol. 106, no. 31, pp. 12794–12797. doi: 10.1073/pnas.0905845106.
6. Doyle J.J., Doyle J.L. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem. Bull., 1987, vol. 19, no. 1, pp. 11–15.
7. Kearse M., Moir R., Wilson A., Stones-Havas S., Cheung M., Sturrock S., Buxton S., Cooper A., Markowitz S., Duran C., Thierer T., Ashton B., Meintjes P., Drummond A. Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics, 2012, vol. 28, no. 12, pp. 1647–1649. doi: 10.1093/bioinformatics/bts199.
8. Edgar R.C. MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinf., 2004, vol. 5, art. 113, pp. 1–19. doi: 10.1186/1471-2105-5-113.
9. Ratnasingham S., Hebert P.D.N. BOLD: The Barcode of Life Data System (http://www.barcodinglife.org). Mol. Ecol. Notes, 2007, vol. 7, no. 3, pp. 355–364. doi: 10.1111/j.1471-8286.2007.01678.x.
10. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol., 1990, vol. 215, no. 3, pp. 403–410. doi: 10.1016/S0022-2836(05)80360-2.
11. Saitou N., Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 1987, vol. 4, no. 4, pp. 406–425. doi: 10.1093/oxfordjournals.molbev.a040454.
12. Haynes W. Maximum likelihood estimation. In: Dubitzky W., Wolkenhauer O., Cho K.H., Yokota H. (Eds.) Encyclopedia of Systems Biology. New York, Springer, 2013, pp. 1190–1191. doi: 10.1007/978-1-4419-9863-7_1235.
13. Nei M. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 1978, vol. 89, no. 3, pp. 583–590. doi: 10.1093/genetics/89.3.583.
14. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. MEGA6: Molecular Evolutionary    Genetics Analysis version 6.0. Mol. Biol. Evol., 2013, vol. 30, no. 12, pp. 2725–2729. doi: 10.1093/molbev/mst197.
15. Nylander J.A.A. MrModeltest Version 2. Program Distributed by the Author. Uppsala, Uppsala Univ., Evol. Biol. Cent., 2004.
16. Krasnaya kniga Respubliki Uzbekistan [Red Book of the Republic of Uzbekistan]. Vol. 1: Plants. Tashkent, Chinor ENK, 2019. 356 p. (In Russian)
17. Clement W.L., Donoghue M.J. Barcoding success as a function of phylogenetic relatedness in  Viburnum, a clade of woody angiosperms. BMC Evol. Biol., 2012, vol. 12, art. 73, pp. 1–13. doi: 10.1186/1471-2148-12-73.
18. Kim W.J., Ji Y., Choi G., Kang Y.M., Yang S., Moon B.C. Molecular identification and phylogenetic analysis of important medicinal plant species in genus Paeonia based on rDNA-ITS, matK, and rbcL DNA barcode sequences. Genet. Mol. Res.: GMR, 2016, vol. 55, no. 3, pp. 1–12. doi: 10.4238/gmr.15038472.

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