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Investigation in the intergenic transcribed sequences to determination of genetic variation for Iranian species of salvia

By: Sedigheh Fabriki-Ourang

Key Words: Fingerprinting, ITS2, Ribosomal DNA, Salvia

J. Bio. Env. Sci. 11(6), 92-100, December 2017.

Certification: jbes 2017 0146 [Generate Certificate]

Abstract

The nuclear ribosomal DNA internal transcribed spacer (ITS) has been established as a suitable genomic region to clarify genomic and phylogenetic relationships of plant species. This study aimed to evaluate the performance of ITS2 DNA barcoding for distinguishing Salvia species and determine genetic relationships among Salvia species from different regions of Iran. The seeds of 12 Salvia species were provided and planted. Total genomic DNA was extracted and ITS2 regions were amplified by PCR with specific primers and were sequenced by Bioneer Company. Genetic distance between Salvia species was estimated according to the Kimura 2-Parameter (K2P) model. ITS2 secondary structures predicted based on ITS2 databases. Multiple sequences were aligned using ClustalW algorithm and phylogenetic analyses were conducted using maximum likelihood (ML). The lengths of ITS2 sequences ranged from 270 to 282 bp and the mean of GC content was 59.3%. The greatest variation in helix length (10 to 22 bp) in the secondary structure of ITS2 at different species of Salvia was related to the third helix. All of the Salvia species formed five major clades. The results showed that the species of Salvia genus in Iran can be clearly distinguished from each other using ITS2 DNA barcoding.

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Investigation in the intergenic transcribed sequences to determination of genetic variation for Iranian species of salvia

Aguilar C, Sanchez JA. 2007. Phylogenetic hypotheses of Gorgonii doctocorals according to ITS2 and their predicted RNA secondary structures. Molecular Phylogenetics and Evolution 43, 774–786.

Alvarez I, Wendel JF.  2003. Ribosomal ITS sequences and plant phylogenetic inference. Molecular Phylogenetics and Evolution 29(3), 417–434.

Alziar G. 1988. Catalogue synonymique des Salvia L. du monde (Lamiaceae) I-VI. Biocosme Mesogeen 5(3-4), 87-136.

Chen SL, Yao H, Han JP, Liu C, Song JY. 2010. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species. PLoS One 5(1), e8613.

http://dx.doi.org/10.1371/journal.pone.0008613.

Coleman AW. 2003. ITS2 is a double-edged tool for eukaryote evolutionary comparisons. Trends in Genetics 19, 370–375.

Coleman AW. 2007. Pan-eukaryote ITS2 homologies revealed by RNA secondary structure. Nucleic Acids Research 35, 3322-3329.

http://dx.doi.org/10.1093/nar/gkm233

Coleman AW. 2009. Is there a molecular key to the level of ‘‘biological species’’ in eukaryotes? Molecular Phylogenetics and Evolution 50, 197–203.

http://dx.doi.org/10.1016/j.ympev.2008.10.008

Epling CA. 1939. Revision of Salvia subgenus calosphace. Repertorium Specierum Novarum Regni Vegetabilis 110: 1-383.

Farka P, Holla M, Tekel J, Mellen S, Vaverkova S. 2005. Composition of the essential oils from the flowers and leaves of Salvia sclarea L. (Lamiaceae) cultivated in Slovak Republic. Journal of Essential Oil Research 17(2), 141–144.

Feliner GN, Rossello JA. 2007. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Molecular Phylogenetics and Evolution 44(2), 911–919.

http://dx.doi.org/10.1016/j.ympev.2007.01.013.

Keller A, Forster F, Muller T, Dandekar T, Schultz J. 2010. Including RNA secondary structures improves accuracy and robustness in reconstruction of phylogenetic trees. Biology Direct 5, 4.

Keller A, Schleicher T, Forster F, Ruderisch B, Dandekar T, Muller T, Wolf M. 2008. ITS2 data corroborate a monophyletic chlorophycean  group  (Sphaeropleales). Biomed Central Evolutionary Biology 8, 218.

http://www.biomedcentral.com/1471-2148/8/218.

Luo K, Chen SL, Chen KL, Song JY, Yao H. 2010. Assessment of candidate plant DNA barcodes using the Rutaceae family. China Life Sciences 40, 342–351.

Marshall E. 2005. Will DNA bar codes breathe life into classification. Science 307, 1037.

http://dx.doi.org/10.1126/science.307. 5712.1037.

Meyer CP, Paulay G. 2005. DNA Barcoding: error rates based on comprehensive sampling. PLoS biology 3, e422.

 http://dx.doi.org/10.1371/journal.pbio.0030422.

Piccolo SL, Alfonzo A, Conigliaro G, Moschetti G, Burruano S, Barone A. 2012. A simple and rapid DNA extraction method from leaves of grapevine suitable for polymerase chain reaction analysis. African Journal of Biotechnology 11(45), 10305-10309.

http://dx.doi.org/10.5897/AJB11.3023.

Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R. 2005. Towards writing the encyclopedia of life: an introduction to DNA barcoding. Philosophical Transactions of the Royal Society Biological Sciences 360, 1805–1811.

Schindel DE, Miller SE. 2005. DNA barcoding a useful tool for taxonomists. Nature 435, 17.

Schultz J, Maisel S, Gerlach D, Muller T, Wolf M. 2005. A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota. RNA 11, 361-364.

Schultz J, Muller T, Achtziger M, Seibel PN, Dandekar T, Wolf M. 2006. The internal transcribed spacer 2 database- a web server for (not only) low level phylogenetic analyses. Nucleic Acids Research 34, 704–707.

Schultz J, Wolf M. 2009. ITS2 sequence structure analysis in phylogenetics: a how- to manual for molecular systematics. Molecular Phylogenetics and Evolution 52, 520–523.

SepehryJavan Z, Rahmani F, Heidari R. 2012. Assessment of genetic variation of genus Salvia by RAPD and ISSR markers. Australian Journal of Crop Science 6(6), 1068-1073.

Steward AN. 1958. Manual of Vascular Plants of the Lower Yangtze Valley, China. Oregon State College. Corvallis, Oregon.

Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology Evolution 24, 1596–1599.

http://dx.doi.org/10.1093/molbev/msm092.

Thomas C. 2009. Plant bar code soon to become reality. Science 325, 526.

http://dx.doi.org/10.1126/science.325_526.

Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting positions-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673-4680.

Thornhill DJ, Lajeunesse TC, Santos SR. 2007. Measuring rDNA diversity in eukaryotic microbial systems: how intragenomic variation, pseudogenes, and PCR artifacts confound biodiversity estimates. Molecular Ecology 16, 5326–5340.

Walker JB, Sytsma KJ, Treutlein J. 2004. Salvia (Lamiaceae) is not monophyletic: implications for the systematic, radiation and ecological specializations of Salvia and tribe Mentheae. American Journal of Botany 91, 1115-1125.

http://dx.doi.org/10.3732/ajb.91.7.1115.

Wang M, Li J, Zhang L, Yang RW, Ding CB, Zhou YH, Yin ZQ. 2011. Genetic diversity among Salvia miltiorrhiza Bunge and related species using morphological traits and RAPD markers. Journal of Medicinal Plants Research 5(13), 2687-2694.

Wilson EO. 2003. The encyclopedia of life. Trends in Ecology and Evolution 18, 77-80.

Zhang Y, Li X, Wang Z. 2013. Diversity evaluation of Salvia miltiorrhiza using ISSR markers. Biochemical Genetics 51, 707-721.

Sedigheh Fabriki-Ourang.
Investigation in the intergenic transcribed sequences to determination of genetic variation for Iranian species of salvia.
J. Bio. Env. Sci. 11(6), 92-100, December 2017.
http://www.innspub.net/jbes/investigation-intergenic-transcribed-sequences-determination-genetic-variation-iranian-species-salvia/
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