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:: Volume 9, Issue 2 (2023) ::
pgr 2023, 9(2): 83-94 Back to browse issues page
Phylogenetic Analysis of Some Luffa Genotypes Based on the sequence of intergenic region of trnH-psbA
Halime Arbabi , Mojtaba Keykhasaber * , Leila Fahmideh , Valiollah Ghasemi Omran
Department of Plant Pathology, University of Zabol, Zabol, Iran , mkeikhasaber@uoz.ac.ir
Abstract:   (3656 Views)
Luffa (Luffa cylindrica) is a plant from the Cucurbitaceae family that grows mostly in tropical and subtropical regions, as well as in most regions of Iran. In this research, the genetic diversity of nine native and non-native genotypes of L. cylindrica was investigated through the evaluation of the chloroplast trnH-psbA intergenic region (IGS). After sampling the young leaves, DNA extraction was performed by using the Dellaporta method, and PCR was conducted by using IGS intergenic region primers. After sequencing of the amplified products, their quality was determined using Chromas software and then aligned using ClustalW method by BioEdit and MEGA7 softwares. Next, the dendrogram of phylogenic relationships was drawn and the matrix of the difference and similarity of the sequences were determined. In the present research, by analyzing the relationships between studied samples, based on the trnH-psbA (IGS) marker, a strong intraspecies variation was observed in native and non-native L. cylindrical genotypes. The genetic distance matrix between the samples examined in this research ranged from 0 to 6.865 with an overall average distance of 2.53. The average value of synonymous and non-synonymous substitutions (dN/dS) for the IGS sequence was ds/dn = 0.68, which indicates positive and pure line selections in the process of natural selection of studied genotypes. The results of this research showed that trnH-psbA is a suitable marker for evaluation of the intraspecific diversity of luffa species.
Keywords: Intraspecies genetic diversity, Chloroplast marker, DNA barcoding
Full-Text [PDF 650 kb]   (1202 Downloads)    
Type of Study: Research | Subject: Molecular genetics
References
1. Advai, M. (2012). Studying the kinship relationships between inverted tulip species (genus Fritillaria L.) in Iran using the synonymy of the chloroplastic trnH-psbA intergenic region and morphological traits. M.Sc. Thesis, Shahrekord University, Shahrekord, Iran (In persian).
2. Akinyinka Akinwumi, K., Olusoji Eleyowo, O. and Omowunmi Oladipo, O. (2022). A review on the ethnobotanical uses, phytochemistry and pharmacological effect of Luffa cylindrinca. Natural Drugs from Plants. doi: 10.5772/intechopen.98405. [DOI:10.5772/intechopen.98405]
3. Asadi, F., Dezhsetan, S., Ghahramanzadeh, R., Razmjou, J., Alebrahim, M.T. (2015). DNA barcoding of some medicinal plants. Journal of Crop Biotechnology, 4(10): 31-40 (In persian).
4. Asghari Mirak, A., Alaviakia, S.S. and Mohammadi, S.A. (2022). Investigating genetic diversity and relationships in some henbane (Hyoscyamus spp.) populations based on polymorphisms resulting from retrotransposon insertion. Plant Genetic Researches, 9(1): 117-134 (In Persian). [DOI:10.52547/pgr.9.1.9]
5. Bolson, M., Smidt, E.C., Brotto, M.L. and Silva-Pereira, V. (2015). ITS and trnH-psbA as efficient DNA barcodes to identify threatened commercial woody angiosperms from Southern Brazilian Atlantic rainforests. PLoS ONE, 10: e0143049. [DOI:10.1371/journal.pone.0143049] [PMID] [PMCID]
6. Chapolagh Paridari, I., Jalali, G., Sonboli, A. and Zarafshar, M. (2012). Revision of Iranian carpinus species using of molecular markers (nrDNA its and trnh-psba). Iranian Journal of Rangelands and Forests Plant Breeding and Genetic Research, 20(1): 1-13 (In Persian).
7. De Vere, N., Rich, T.C., Trinder, S.A. and Long, C. (2015). DNA barcoding for plants. Methods in Molecular Biology, 1245: 101-18. [DOI:10.1007/978-1-4939-1966-6_8] [PMID]
8. Dellaporta, S.L., Wood, J. and Hicks, J.B. (1993). A plant DNA minipreparation: version II. Plant Molecular Biology Reporter, 1: 19-22. [DOI:10.1007/BF02712670]
9. Fattahi Dehkordi, N., Ghaemi Ghehsareh, M., Shiran, B. and Siampoor, M. (2022). Comparison of the Efficacy of Two Chloroplast DNA Marker (psbA-trnH and trnL-F) in Determining the Phylogenetic Relationships among Honeysuckle Species in Iran. Iranian Journal of Horticultural Science and Technology, 23(1): 1-12 (In Persian).
10. Fox, G.E., Pechman, K.R. and Woese, C.R. (1977). Comparative cataloging of 16 S ribosomal ribonucleic acid: molecular approach to procaryotic systematics. International Journal of Systematic and Evolutionary Microbiology, 27(1): 44-57. [DOI:10.1099/00207713-27-1-44]
11. Ghahramanzadeh, R., Marashi, S.H., Van De Wiel, C., Malekzadeh, S., Shahriari, F. and Smulders, R. (2012). Discrimination of the invasive plant species, myriophyllum spp., from native relatives using DNA barcoding. Iranian Plant Protection Research, 26(1): 101-109 (In Persian).
12. Gholipour, A., Kazemitabar, S.K. and Sharifi Soltani, S. (2021). Study of genetic diversity of wild and regenerated accessions of Acorus calamus (Acoraceae) by ISSR markers. Plant Genetic Researches, 7(2): 109-118 (In Persian). [DOI:10.52547/pgr.7.2.9]
13. Haji Ahmadi, Z., Talebi, M. and Seyyed Tabatabai, B.E. (2013). Determining pomegranate phylogeny using psbA-trnH, rbcL, matK and ITS plant barcodes. 12th Congress of Iranian Genetics Society, Tehran, Iran (In Persian).
14. Hajibabaei, M., Janzen, D.H., Burns, J.M., Hallwachs, W. and Hebert, P.D.N. (2006). DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences, 103: 968-971. [DOI:10.1073/pnas.0510466103] [PMID] [PMCID]
15. Hebert, P.D.N., Cywinska, A., Ball, S.L. and de Waard, J.R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences, 270: 313-322. [DOI:10.1098/rspb.2002.2218] [PMID] [PMCID]
16. Hosseinzadeh Colagar, A., Akbarzadeh Roshan, F. and Yousefzadeh, H. (2013). Determination of taxonomic status of chestnut in northern Iran using psbA molecular markers and trnH-psbA intergenic region. 8th Biotechnology Conference of the Islamic Republic of Iran and 4th National Conference on Biosafety, Tehran, Iran (In Persian).
17. Kress, W.J. (2017). Plant DNA barcodes: applications today and in the future. Insect Systematics & Evolution, 55: 291-307. [DOI:10.1111/jse.12254]
18. Kress, W.J., Wurdack, K.J., Zimmer, E.A., Weigt, L.A. and Janzen, D.H. (2005). Use of DNA barcodes to identify flowering plants. Proceedings of the Royal Society B: Biological Sciences, 102: 8369-8374. [DOI:10.1073/pnas.0503123102] [PMID] [PMCID]
19. Li, J., Bi, H., Li, Z. and Feng, J. (2008). Genetic analysis of Ziziphus Jujube Huizao using ISSR markers. 1th International Jujube Symposium, Baoding, China. [DOI:10.17660/ActaHortic.2009.840.15]
20. Maheswaran, M. (2004). Molecular markers: history, features and applications. Advanced Biotechnology, 51: 373-8
21. Miller, S.E. (2007). DNA barcoding and the renaissance of taxonomy. Proceedings of the National Academy of Sciences, 104: 4775-4776. [DOI:10.1073/pnas.0700466104] [PMID] [PMCID]
22. Min, X.J. and Hickey, D.A. (2007). Assessing the effect of varying sequence length on DNA barcoding of fungi. Molecular Ecology Notes, 7: 365-373. [DOI:10.1111/j.1471-8286.2007.01698.x] [PMID] [PMCID]
23. Nei, M. and Gojobori, T. (1986). Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Molecular Biology and Evolution, 3(5): 418-426.
24. Oboh, I. and Aluyor, E. (2009). Luffa cylindrical-an emerging cash crop. African Journal of Agricultural Research, 4: 684-688.
25. Okusanya, O.T., Ola-Adams, B.A. and Bamidele, J.F. (198)1. Variations in size, leaf morphology, and fruit characters among 25 populations of Luffa aegyptiaca. Canadian Journal of Botany, 59(12): 2618-2627. [DOI:10.1139/b81-314]
26. Ota, T. and Nei, M. (1994). Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites. Journal of Molecular Evolution, 38: 642-643. [DOI:10.1007/BF00175885]
27. Pang, X., Luo, H. and Sun, C. (2012). Assessing the potential of candidate DNA barcodes for identifying non-flowering seed plants. Plant Biology, 14: 839-844. [DOI:10.1111/j.1438-8677.2011.00554.x] [PMID]
28. Ross, H.A., Murugan, S. and Li, W.L.S. (2008). Testing the reliability of genetic methods of species identification via simulation. Systematic Biology, 57: 216-230. [DOI:10.1080/10635150802032990] [PMID]
29. Sang, T, Crawford, D.J. and Stuessy, T.F. (1997). Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). American Journal of Botany, 84: 1120-1136. [DOI:10.2307/2446155] [PMID]
30. Schindel, D.E. and Miller, S.E. (2005). DNA barcoding a useful tool for taxonomists. Nature, 435: 17. [DOI:10.1038/435017b] [PMID]
31. Seifert, K.A., Samson, R.A., Dewaard, J.R., Houbraken, J., Lévesque, C.A., Moncalvo, J.M., Louis-Seize, G. and Hebert, P.D. (2007). Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proceedings of the National Academy of Sciences, 104(10): 3901-3906. [DOI:10.1073/pnas.0611691104] [PMID] [PMCID]
32. Shah, J.J., Thanki, Y.J. and Kothari, I.L. (1980). Skeletal fibrous net in fruits of Luffa cylindrica M. Roem, and Luffa acutangula Roxb. In: Nagaraj, M. and Malik, C.P., Eds., Current Trends in Botanical Research, p. 61-72. Kalyani Publishers, New Delhi, IN.
33. Shirzaie, A., Solouki, M. and Fahmideh L. (2021). Molecular analysis of some mango genotypes in southern Iran based on trnhH-psbA intergenic region. Iranian Journal of Horticultural Science and Technology, 22(4): 449-464 (In Persian).
34. Talebi, R., Fayaz, R., Mardi, M., Pirsyedi, S.M. and Naji, A.M. (2008). Genetic relationships among chickpea (Cicer arietinum) elite lines based on RAPD and agronomic markers. International Journal of Agriculture and Biology, 8: 301-305.
35. Tamura, K. and Nei, M. (1993). Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular Biology and Evolution, 10: 512-526.
36. Woese, C.R. (1987). Bacterial evolution. Microbiological Reviews, 51: 221-271. [DOI:10.1128/jb.169.12.5546-5555.1987] [PMID] [PMCID]
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Arbabi H, Keykhasaber M, Fahmideh L, Ghasemi Omran V. Phylogenetic Analysis of Some Luffa Genotypes Based on the sequence of intergenic region of trnH-psbA. pgr 2023; 9 (2) :83-94
URL: http://pgr.lu.ac.ir/article-1-256-en.html


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Volume 9, Issue 2 (2023) Back to browse issues page
پژوهش های ژنتیک گیاهی Plant Genetic Researches
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