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Evaluation of five genomic DNA extraction methods for downstream molecular applications in fresh and herbarium leaves of Astragalus fridae | ||
| Rostaniha | ||
| دوره 24، شماره 2 - شماره پیاپی 69، اسفند 2023، صفحه 89-98 اصل مقاله (367.66 K) | ||
| نوع مقاله: Research Paper | ||
| شناسه دیجیتال (DOI): 10.22092/bot.j.iran.2023.360969.1343 | ||
| نویسندگان | ||
| Zahra Alidoosty Shahraky1؛ Atefe Amirahmadi* 2؛ Parisa Farrokh3؛ Arezou Rezaei3؛ Javad Ghasemian4 | ||
| 1MSc Graduate in Biochemistry, School of Biology, Damghan University, Damghan, Iran | ||
| 2Assistant Prof., School of Biology and Institute of Biological Sciences, Damghan University, P.O. Box 36716-45667, Damghan, Iran | ||
| 3Assistant Prof., School of Biology and Institute of Biological Sciences, Damghan University, Damghan, Iran | ||
| 4Assistant Prof., School of Mathematics and Computer Sciences, Damghan University, Damghan, Iran | ||
| چکیده | ||
| The protection of genetic resources is crucial for safeguarding national assets as natural resources face various threats such as climate change and changing land use. To conserve endangered species such as Astragalus fridae, an endemic species of gypsum soils of Semnan province (Iran) which is on the brink of extinction due to limited distribution and habitat destruction, establishing a gene bank is essential. To ensure the survival of this species, it is necessary to extract high-quality and high-quantity DNA. The present survey, has evaluated five genome extraction methods including Protocol A (main CTAB), Protocol B (CTAB without β-mercaptoethanol), Protocol C (CTAB without ammonium acetate), Protocol D (the modified Murray & Thompson method), and Protocol E (GeneAll Plant Kit), to determine their ability to extract DNA from fresh and herbarium leaves of A. fridae. The quality and quantity of DNA were assessed using gel electrophoresis, spectrophotometry, and usability of the purified DNA tested by PCR of the ITS region of nuclear ribosomal DNA. Protocol D yielded the highest quality of the extracted genome from fresh leaves, and Protocol A, extracted the highest DNA concentration from fresh leaves. Although Protocols B and C extracted a reasonable amount of genome of acceptable quality with dry leaves, the ITS region was not amplified in these samples, rendering them unsuitable for DNA extraction of A. fridae. | ||
| کلیدواژه‌ها | ||
| climate change؛ CTAB؛ endangered species؛ endemic؛ threats | ||
| عنوان مقاله [English] | ||
| ارزیابی پنج روش استخراج DNA ژنومی برای کاربردهای مولکولی پایین دست در برگ‌های تازه و هرباریومی Astragalus fridae | ||
| نویسندگان [English] | ||
| زهرا علیدوستی شهرکی1؛ عاطفه امیراحمدی2؛ پریسا فرخ3؛ آرزو رضایی3؛ جواد قاسمیان4 | ||
| 1دانش‌آموخته کارشناسی ارشد بیوشیمی، دانشکده زیست شناسی، دانشگاه دامغان، دامغان، ایران | ||
| 2استادیار دانشکده زیست شناسی و پژوهشکده علوم زیستی، دانشگاه دامغان، کدپستی 45667-36716، دامغان، ایران | ||
| 3استادیار دانشکده زیست شناسی و پژوهشکده علوم زیستی، دانشگاه دامغان، دامغان، ایران | ||
| 4استادیار دانشکده ریاضی و علوم کامپیوتر، دانشگاه دامغان، دامغان، ایران | ||
| چکیده [English] | ||
| حفاظت از ذخایر ژنتیکی جزو حیاتی حفاظت از سرمایه ملی است. از آنجایی که منابع طبیعی توسط عوامل مختلفی از جمله تغییرات آب و هوایی و تغییر کاربری اراضی تهدید می‌شود، بنابراین ایجاد بانک ژن برای حفاظت از گونه‌های در خطر انقراض ضروری به نظر می‌رسد. Astragalus fridae Rech.f. (باقلاییان) گونه بومی خاک‌های گچی استان سمنان است که به دلیل پراکنش محدود و تخریب زیستگاه در حال انقراض می‌باشد. برای اطمینان از بقای این گونه، باید تلاش‌هایی برای استخراج DNA با کیفیت و کمیت بالا انجام شود. به این منظور، پنج روش استخراج ژنوم شامل پروتکل A (CTAB اصلی)، پروتکل B (CTAB بدون بتا-مرکاپتواتانول)، پروتکل C (CTAB بدون استات آمونیوم)، پروتکل D (روش اصلاح شده موری و تامسون) و پروتکل E (کیت گیاهی GeneAll)، از نظر توانایی آن‌ها در استخراج DNA از برگ‌های تازه و هرباریومی مورد ارزیابی قرار گرفتند. کیفیت و کمیت DNA توسط ژل الکتروفورز و اسپکتروفتومتری بررسی شد و قابلیت استفاده DNA خالص شده توسط PCR ناحیه ITS DNA ریبوزومی هسته‌ای مورد آزمایش قرار گرفت. بالاترین کیفیت ژنوم استخراج شده به پروتکل D با برگ‌های تازه اختصاص یافت. بیشترین غلظت DNA از برگ‌های تازه (پروتکل A) به دست آمد. اگرچه مقدار معقولی از ژنوم با کیفیت قابل قبول توسط پروتکل‌های B و C با برگ‌های خشک استخراج شد ولی منطقه ITS در این نمونه‌ها تکثیر نشد، بنابراین پروتکل‌های B و C برای استخراج ژنوم A. fridae مناسب نبودند. | ||
| کلیدواژه‌ها [English] | ||
| بومی, تغییرات آب و هوایی, تهدید, در معرض خطر انقراض, CTAB | ||
| مراجع | ||
|
Abdel-Latif, A. & Osman, G. 2017. Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize. Plant Methods 13: 1. Aboul-Maaty, N.A.F. & Oraby, H.A.S. 2019. Extraction of high-quality genomic DNA from different plant orders applying a modified CTAB-based method. Bulletin of the National Research Centre 43: 25–34. Alidoosty Shahraky, Z., Farrokh, P., Amirahmadi, A., Rezaei, A. & Ghasemian, J. 2023. Comparison of five genomic DNA extraction methods in Iranian Medicinal Plant, Echium amoenum. Journal of Plant Research (Iranian Journal of Biology) 36(3): 216–231 (In Persian). Amirahmadi, A., Kazempour-Osaloo, S., Moein, F., Kaveh, A. & Maassoumi, A.A. 2014. Molecular systematics of the tribe Hedysareae (Fabaceae) based on nrDNA ITS and plastid trnL-F and matK sequences. Plant Systematics and Evolution 300(4): 729–747. Azmat, M.A., Khan, I.A., Cheema, H.M.N., Rajwana, I.A., Sattar Khan, A. & Khanet, A.A. 2012. Extraction of DNA suitable for PCR applications from mature leaves of Mangifera indica L. Journal Zhejiang University Science B (Biomedicine and Biotechnology) 13(4): 239–243. Bedir, E., Pugh, N., Calis, I., Pasco, D.S. & Khan, I.A. 2000. Immunostimulatory effects of cycloartane-type triterpene glycosides from Astragalus species. Biological and Pharmaceutical Bulletin 23(7): 834–837. Castillo, C., Valencia, I., Reyes, G. & Hong, E. 1993. 3-Nitropropionic acid, obtained from Astragalus species, has vasodilator and antihypertensive properties. Drug Development Researches 28(2): 183–188. Costa, C.M. & Roberts, R.P. 2014. Techniques for improving the quality and quantity of DNA extracted from herbarium specimens. Phytoneuron 48(1): 1–8. Doyle, J.J. & Doyle, J.L. 1987. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin 19(1): 11–15. El-Sebakhy, N.A., Asaad, A.M., Abdallah, R.M., Toaima, S.M., Abdel-Kader, M.S. & Stermitz, F.R. 1994. Antimicrobial isoflavans from Astragalus species. Phytochemistry 36(6): 1387–1389. Farsi, M. & Zolala, J. 2003. Introduction to Plant Biotechnology. Ferdowsi University of Mashhad Publication, Mashhad. 495 pp. (In Persian). Fathiazad, F., Movafeghi, A. & Khosropanah, M. 2012. Flavonol glycosides from the leaves of Astragalus microcephalus. International Journal of Biosciences 2(7): 23–28. Ghahremaninejad, F., Nejad Falatoury, A. & Memariani, F. 2020. Typification and an emended description of Astragalus moussavii (Fabaceae, Papilionoideae). Phytotaxa 441(1): 60–68. Ghasemian-Yadegari, J., Nazemiyeh, H., Hamedeyazdan, H. & Fathiazad, F. 2017. Secondary metabolites from the roots of Astragalus maximus. Research Journal of Pharmacognosy 4(2): 31–38. Heikrujam, J., Kishor, R. & Mazumder, P.B. 2020. The Chemistry Behind Plant DNA Isolation Protocols. Pp. 131–142. In: Boldura, O-M., Baltă, C. & Awwad, N.S. (eds), Biochemical Analysis Tools-Methods for Bio-Molecules Studies. IntechOpen, UK. Hollingsworth, P.M. 2011. Refining the DNA barcode for land plants. Proceedings of the National Academy of Sciences of the United States of America 108(49): 19451–19452. Huang, X., Wang, D., Hu, Y., Lu,Y., Guo, Z., Kong, X. & Sun, J. 2008. Effect of sulfated Astragalus polysaccharide on cellular infectivity of infectious bursal disease virus. International Journal of Biological Macromolecules 42(2): 166–171. Jalali Roudsary, L., Jafari, A., Vaezi, J. & Karimi, E. 2022. A simple and efficient DNA extraction protocol for old herbarium leaves of Bellevalia (Asparagaceae, Scilloideae). Nova Biologica Reperta 9(2): 124–131. Jalili, A. & Jamzad, Z. 1999. Red Data Book of Iran. Research Institute of Forest and Rangelands Publication, Tehran. 748 pp. Jia, R., Cao, L., Xu, P., Jeney, G. & Yin, G. 2012. In vitro and in vivo hepatoprotective and antioxidant effects of Astragalus polysaccharides against carbon tetrachloride-induced hepatocyte damage in common carp (Cyprinus carpio). Fish Physiology and Biochemistry 38(3): 871–881. Kasem, S., Rice, N. & Henry, R. 2008. DNA Extraction from Plant Tissue. Pp. 219–271. In: Henry, R.J. (ed.), Plant Genotyping II: SNP Technology. CABI, Wallingford. Kates, H.R., Doby, J.R., Siniscalchi, C.M., LaFrance, R., Soltis, D.E., Soltis, P.S., Guralnick, R.P. & Folk, R.A. 2021. The effects of herbarium specimen characteristics on short-read NGS sequencing success in nearly 8000 specimens: old, degraded samples have lower DNA yields but consistent sequencing success. Frontiers in Plant Science 12: https://doi.org/10.3389/fpls.2021.669064. Kaveh, A., Kazempour-Osaloo, S., Amirahmadi, A., Maassoumi, A. & Schneeweiss, G. 2019. Systematics of Onobrychis sect. Heliobrychis (Fabaceae): morphology and molecular phylogeny revisited. Plant Systematics and Evolution 305(1): 33–48. Luo, Y., Qin, Z., Hong, Z., Zhang, X., Ding, D., Fu, J-H., Zhang, W-D. & Chen, J. 2004. Astragaloside IV protects against ischemic brain injury in a murine model of transient focal ischemia. Neuroscience Letters 363(3): 218–223. Manoj, K., Tushar, B. & Sushama, C. 2007. Isolation and purification of genomic DNA from black plum (Eugenia jambolana Lam.) for analytical applications. International Journal Biotechnology Biochemical 3(1): 49–55. Mozaffarian, V. 2003. A Dictionary of Iranian Plant Names. Farhang-e Moaser, Tehran. 762 pp. Petit, R.J. & Excoffier, L. 2009. Gene flow and species delimitation. Trends in Ecology & Evolution 24(7): 386–393. Pipan, B., Zupančič, M., Blatnik, E., Dolničar, P. & Meglič, V. 2018. Comparison of six genomic DNA extraction methods for molecular downstream applications of apple tree (Malus × domestica). Cogent Food & Agriculture 4(1): https://doi.org/10.1080/23311932.2018.1540094. Pistelli, L., Bertoli, A., Lepori, E., Morelli, I. & Panizzi, L. 2002. Antimicrobial and antifungal activity of crude extracts and isolated saponins from Astragalus verrucosus. Fitoterapia 73(4): 336–339. Riahi, M., Zarre, S. & Maassoumi, A.A. 2010. An inexpensive and rapid method for extracting papilionoid genomic DNA from herbarium specimens. Genetics and Molecular Research 9(3): 1334–1342. Rios, J. & Waterman, P. 1997. A review of the pharmacology and toxicology of Astragalus. Phototherapy Research 11(6): 411–418. Saboora, A., Rad, M.A., Asgarani, E. & Radjabian, T. 2019. Comparison study of three methods for genomic DNA extraction from fresh and herbarium leaf specimens of Achillea wilhelmsii C. Koch. Nova Biologica Reperta 5(4): 458–465 (In Persian). Sahu, S.K., Thangaraj, M. & Kathiresan, K. 2012. DNA extraction protocol for plants with high levels of secondary metabolites and polysaccharides without using liquid nitrogen and phenol. ISRN Molecular Biology 14: 205049. doi: 10.5402/2012/205049. Sang, T., Crawford, D.J. & Stuessy, T. 1995. Documentation of reticulate evolution in peonies (Paeonia) using internal transcribed spacer sequences of nuclear ribosomal DNA: Implications for biogeography and concerted evolution. Proceedings of the National Academy of Sciences 92(15): 6813–6817. Siwicka, D., Skopinska-Rozewska, E. & Bodera, P. 2011. Immunotropic and anti-tumor effects of plant adaptogens. III. Astragalus (Fabaceae). Central European Journal of Immunology 36(2): 104–107. Song, C., Zheng, Z., Liu, D. & Hu, Z. 1996. Antimicrobial isoflavans from Astragalus membranaceus (Fisch.) Bunge. Acta Botanica Sinica 39(5): 486–488. Souza, H.A.V., Mueller, L.A.C., Brandão, R.L. & Lovato, M.B. 2012. Isolation of high quality and polysaccharide-free DNA from leaves of Dimorphandra mollis (Leguminosae), a tree from the Brazilian Cerrado. Genetics and Molecular Research 11(1): 756–764. SPSS, 2016. IBM SPSS Statistics for Windows, Ver. 24.0. IBM Corp., Armonk, NY. Tsitrone, A., Kirkpatrick, M. & Levin, D.A. 2003. A model for chloroplast capture. Evolution 57(8): 1776–1782. Vinson, C.C., Mangaravite, E., Sebbenn, A.M. & Lander, T.A. 2018. Using molecular markers to investigate genetic diversity, mating system and gene flow of Neotropical trees. Brazilian Journal of Botany 41(2): 481–496. White, T.J., Bruns, T. & Taylor, J. 1990. Amplification and Direct Sequencing of Fungal Ribosomal RNA Genes for Phylogenetics. PCR - Protocols and Applications - A Laboratory Manual. Pp. 315–322. Yesilada, E., Bedir, E., Çalış, İ., Takaishi, Y. & Ohmoto, Y. 2005. Effects of triterpene saponins from Astragalus species on in vitro cytokine release. Journal of Ethnopharmacology 96(1): 71–77. Zamani, Z., Sarkhoush, A., Fatahi Moghadam, M.R. & Ebadi, A. 2005. Comparison of six genomic DNA extraction from pomegranate (Punica granatum L.). Iranian Journal of Horticultural Science and Technology 6(2): 99–110 (In Persian). Zhang, W.D., Chen, H., Zhang, C., Liu, R.H., Li, H.L. & Chen, H.Z. 2006. Astragaloside IV from Astragalus membranaceus shows cardioprotection during myocardial ischemia in vivo and in vitro. Planta Medica 72(1): 4–8. | ||
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