Botanica Pacifica. A journal of plant science and conservation 2024. 13(1):193-196
Article first published online: 01 APR 2024 | DOI: 10.17581/bp.2024.13113
DNA barcoding of some endangered plant species of the Altai Mountains based on five genetic markers
Natalia S. Nuzhdina1
,
Anna S. Erofeeva2 ,
Alexander A. Bondar3 &
Nataliya K. Kovtonyuk1 1 Central Siberian Botanical Garden SB RAS, Novosibirsk, Russia
2 Altai State Nature Biospheric Reserve, Gorno-Altaisk, Russia
3 Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia
The analysis of DNA nucleotide sequences is an important source of information in the identification of plant taxa or plant components in the composition of medicines. In this work, we studied the possibility of using universal molecular markers for DNA barcoding of rare plant species distributed in the Altai Biosphere Reserve, located in the Altai Republic (South Siberia, Russia). In order to identify commercially-used endangered species, universal markers recommended for DNA barcoding were applied: ITS (Internal Transcribed Spacers) region of nuclear ribosomal DNA and four regions of chloroplast DNA: trnL-F, trnH-psbA rpl32-trnL, and rpl16. Among 61 species of rare flowering plants protected in the Altai Biosphere Reserve, ten species belonging to eight families were studied. The results of sequencing showed that ITS, rpl32-trnL and trnH-psbA core plant barcodes are the most effective markers for discriminating rare species from the Altai Biosphere Reserve.
ДНК-штрихкодирование некоторых редких видов растений Алтая по данным анализа пяти генетических маркеров. Анализ нуклеотидных последовательностей ДНК является важным источником информации при идентификации таксонов у растений или растительных компонентов в составе медицинских препаратов. В настоящей работе нами исследована возможность применения молекулярных маркеров для ДНК-штрихкодирования редких краснокнижных видов растений, обитающих на территории Алтайского биосферного заповедника. Для идентификации видов были использованы маркерные локусы ITS ярДНК и trnL-F, trnH-psbA rpl32-trnL и rpl16 хлДНК. Результаты секвенирования показали, что наиболее эффективными для идентификации редких видов являются маркеры ITS, rpl32-trnL и trnH-psbA.
Keywords: DNA barcoding, endangered species, ITS, trnL-trnF, trnH-psbA, rpl32-trnL, rpl16-trnL, Altai Biosphere Reserve, ДНК-штрихкодирование, редкие виды, Алтайский биосферный заповедник
References
Amirahmadi, S., S. Kazempour Osaloo & A.A. Maassoumi 2010. Loss of chloroplast trnLUAA intron in two species of Hedysarum (Fabaceae): evolutionary implications. Iranian Journal of Biotechnology 8:150-155.
Artemov, I.A., A.Y. Korolyuk, N.N. Lashchinskiy & I.E. Smelyanskiy 2007. Criteria for choosing the key botanical territories within Altai-Sayan ecoregion. Siberian Ecologic Center, Novosibirsk, 102 pp.
Cowan, R.S., M.W. Chase, W.J. Kress & V. Savolainen 2006. 300,000 species to identify: problems, progress, and prospects in DNA barcoding of land plants. Taxon 55:611-616. CrossRef
Doyle, J.J. & J.L. Doyle 1987. A rapid DNA isolation of fresh leaf tissue. Phytochemical Bulletin 19:11-15.
Erst, A.S., A.Yu. Nikulin, V.Yu. Nikulin, A.L. Ebel, E.V. Zibzeev, M.T. Sharples, S. Baasanmunkh et al. 2022. Distribution analysis, updated checklist, and DNA barcodes of the endemic vascular flora of the Altai mountains, a Siberian biodiversity hotspot. Systematics and Biodiversity 20(1):1-30 CrossRef
Johnson, L.A. & D.E. Soltis 1994. matK DNA sequences and phylogenetic reconstruction in Saxifragaceae s. str. Systematics and Biodiversity 19:143-156. CrossRef
Jordan, W.C., M.W. Courtney & J.E. Neigel 1996. Low levels of intraspecific genetic variation at a rapidly evolving chloroplast DNA locus in North American duckweeds (Lemnaceae). American Journal of Botany 83:430-439. CrossRef
Kelchner, S.A. & L.G. Clark 1997. Molecular evolution and phylogenetic utility of the chloroplast rpl16 intron in Chusquea and the Bambusoideae (Poaceae). Molecular Phylogenetics and Evolution 8(3):385-397. CrossRef
Kress, W.J., K.J. Wurdack, E.A. Zimmer, L.A. Weigt & D.H. Janzen 2005. Use of DNA barcodes to identity flowering plants. PNAS 102:8369-8374. CrossRef
Kress, W.J. & D.L. Erickson 2007. A two-locus global DNA barcode for land plants: the coding rbcL gene complements the non-coding trnH-psbA spacer region. PLos ONE 6:e508. CrossRef
Maneev, A.G. (ed.) 2017. Red Book of the Altai Republic. Plants. GASU, Gorno-Altaisk, 267 pp. [Красная книга Республики Алтай (растения) 2017. (гл. ред. А.Г. Манеев). Горно-Алтайск: ГАГУ. 267с.].
Nuzhdina, N.S. & N.K. Kovtonyuk 2022. Genotyping NS and NSK herbaria specimens of Hedysarum (Fabaceae) using DNA sequencing. Botanica Pacifica 11(1):176-180. CrossRef
Okonechnikov, K., O. Golosova & M. Fursov 2012. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28:1166-1167. CrossRef
Saarela, J.M., P.C. Sokoloff, L.J. Gillespie, L.L. Consaul & R.D. Bull 2013. DNA barcoding the Canadian arctic flora: core plastid barcodes (rbcL + matK) for 490 vascular plant species. Plos ONE 8(10):e77982 CrossRef
Sang, T., D.J. Crawford & T.F. Stuessy 1997. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). American Journal of Botany 84:1120-1136. CrossRef
Shaw, J., E.B. Lickey, J.T. Beck, S.B. Farmer, W. Liu, J. Miller, K.C. Siripun, C.T. Winder, E.E. Schilling & R.L. Small 2005. The tortoise and the hare II: relative utility of 21 noncoding chloroplast DNA sequences for phylogenetic analysis. American Journal of Botany 92:142-166. CrossRef
Shaw, J., E.B. Lickey, E.E. Schilling & R.L. Small 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in Angiosperms: the tortoise and hare III. American Journal of Botany 94:275-288. CrossRef
Taberlet, P., L. Gielly, G. Pautou & J. Bouvet 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17:1105-1109. CrossRef
Tate, J.A. & B.B. Simpson 2003. Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploid species. Systematic Botany 28:723-737.
White, T. J., T. Bruns, S. Lee & J. Taylor 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR protocols: a guide to methods and applications (M.A. Innis, D.H. Gelfand, J.J. Sninsky & T.J. White, eds.), pp. 315-322, Academic Press, New York. CrossRef
Zolotukhin, N.I. & A.S. Erofeeva 2022. Chronicle of nature. Flora (vascular plants). Observation and study of phenomena and processes in the natural complex of the Altai Reserve (2015-2021). In: Scientific research in reserves and national parks of the Russian Federation (2015-2021), vol. 5 (D.M. Ochagov, ed.), pp. 38-40, Simferopol, Business-Inform. [Золотухин Н.И., Ерофеева А.С. 2022. Летопись природы. Флора (сосудистые растения). Наблюдение и изучение явлений и процессов в природном комплексе Алтайского заповедника (2015-2021 гг.) // Научные исследования в заповедниках и национальных парках Российской Федерации (2015-2021 гг.) / под ред. Д.М. Очагова). Симферополь: Бизнес-Информ. Вып. 5. С. 38-40].
|
|