| تعداد نشریات | 286 |
| تعداد نشریات سازمان | 84 |
| تعداد شماره‌ها | 2,856 |
| تعداد مقالات | 32,385 |
| تعداد مشاهده مقاله | 41,499,323 |
| تعداد دریافت فایل اصل مقاله | 18,697,875 |
شناسایی ژن‌های مسیر بیوسنتزی اسکلت ترپنوئید در میوه گیاه دارویی هندوانه ابوجهل (Citrullus colocynthis (L.) Schrad.) با استفاده از تکنیک توالی‌یابی RNA | ||
| تحقیقات گیاهان دارویی و معطر ایران | ||
| مقاله 13، دوره 35، شماره 4 - شماره پیاپی 96، مهر و آبان 1398، صفحه 691-702 اصل مقاله (954.75 K) | ||
| نوع مقاله: مقاله پژوهشی | ||
| شناسه دیجیتال (DOI): 10.22092/ijmapr.2019.125294.2510 | ||
| نویسندگان | ||
| معصومه درافشان1؛ مهدی سلطانی حویزه* 2؛ وحید شریعتی3 | ||
| 1دانشجوی کارشناسی ارشد، گروه ژنتیک و به‌نژادی گیاهی، واحد اهواز، دانشگاه آزاد اسلامی، اهواز، ایران | ||
| 2مربی، گروه ژنتیک و به‌نژادی گیاهی، واحد اهواز، دانشگاه آزاد اسلامی، اهواز، ایران | ||
| 3استادیار، پژوهشگاه ملی مهندسی ژنتیک و زیست‌فناوری، تهران، ایران | ||
| چکیده | ||
| شناسه دیجیتال (DOR): 98.1000/1735-0905.1398.35.691.96.4.1588.65 توالی‌یابی RNA در حال حاضر یک انتخاب مؤثر و پرسرعت برای مطالعه ترانسکریپتوم گونه‌های گیاهی غیر مدل است که برای شناسایی شبکه‌های ژنی و الگوهای بیان ژن‌های تولیدکننده متابولیت‌های ثانویه در اندام‌های مختلف گیاهان استفاده می‌شود. اصلی‌ترین ترکیب‌ها در بافت‌های میوه و برگ گیاه دارویی هندوانه ابوجهل (Citrullus colocynthis (L.) Schrad.) را ترپنوئیدها، فلاونوئیدها و آلکالوئیدها تشکیل می‌دهند. در این مطالعه، ترانسکریپتوم میوه گیاه هندوانه ابوجهل با استفاده از تکنیک توالی‌یابی RNA، بن‌سازه Iluumina HiSeq2500 اجرا گردید. بعد از کنترل کیفیت با استفاده از نرم‌افزارهای FastQC و Trimmomatic تعداد 21، 952 و 885 خوانش دارای کیفیت بالا تولید شد و با استفاده از برنامه Evidential-gene به‌صورت نوپدید یکپارچه‌سازی شد که منتهی به تولید 55 و 311 تک‌ژن دارای N50 برابر 927 جفت باز گردید. توالی تک‌ژن‌های یکپارچه شده در پایگاه KAAS بارگذاری شد. در مجموع 13، 657 تک‌ژن تفسیر شد که این تعداد در 134 مسیر زیستی قرار گرفتند. مسیر "اسکلت ترپنوئید" با تعداد 93 تک‌ژن از پرتعدادترین مسیرهای شناسایی شده از میان 1، 552 تک‌ژن مسیر بیوسنتز متابولیت ثانویه بود. با بررسی تک‌ژن‌های مرتبط با مسیر بیوسنتزی اسکلت ترپنوئید، 29 شناسه ژنی (K) شناسایی شد که تمام ژن‌های دو مسیر اصلی بیوسنتزی اسکلت ترپنوئیدی: مسیر سیتوزولی موالونیک اسید (MVA) و پلاستیدی متیل-ارتریتول-فسفات (MEP) از ابتدای مسیر تا تولید ایزوپنیل دی‌فسفات (IPP) را شامل می‌شود. شناسایی ژن‌های مسیر بیوسنتزی اسکلت ترپنوئید امکان تحقق توسعه تجاری محصول گیاه دارویی که پایه‌ای برای پژوهش‌های آینده مربوط به شناسایی مسیرهای بیوسنتزی سایر متابولیت‌های اختصاصی، مهندسی متابولیت، اصلاح مولکولی و به‌نژادی گیاهان دارویی است را فراهم می‌کند. | ||
| کلیدواژه‌ها | ||
| گیاه دارویی؛ توالی‌یابی نسل آینده؛ ترانسکریپتوم؛ یکپارچه‌سازی نوپدید؛ پایگاه اطلاعاتی | ||
| عنوان مقاله [English] | ||
| Identification of terpenoid backbone biosynthetic pathway genes in fruit of Citrullus colocynthis (L.) Schrad. medical plant by RNA sequencing | ||
| نویسندگان [English] | ||
| M. Dorafshan1؛ M. Soltani Howyzeh2؛ V. Shariati3 | ||
| 1M.Sc. student, Genetic and Plant Breeding Departemant, Ahvaz Branch, Islamic Azad University, Ahvaz, Iran | ||
| 2Genetic and Plant Breeding Departemant, Ahvaz Branch, Islamic Azad University, Ahvaz, Iran | ||
| 3National Institute of Genetic Engineering and Biotechnology, Tehran, Iran | ||
| چکیده [English] | ||
| Nowadays, RNA sequencing is an effective and fast choice to study the transcripts of non-model plant species used to identify gene networks and patterns of gene expression producing secondary metabolites in different plant organs. Terpenoids, flavonoids, and alkaloids are the main compounds in fruits and leaves of Citrullus colocynthis (L.) Schrad. In this study, the transcriptome of C. colocynthis fruit was performed using RNA-Seq technique, Iluumina HiSeq2500 platform. After quality control using FastQC and Trimmomatic software, 21,952,885 high-quality reads were produced and the de novo assembly with the Evidential-gene program resulted in the production of 55,311unigenes with an N50 equal to 927 base pairs. The sequence of assembled unigenes was loaded on the KAAS database. A total of 13,657 unigenes were annotated, matched into 134 biosynthetic pathways. The "terpenoid backbone" biosynthetic pathway with 93 unigenes was one of the most numerous identified pathways among 1,552 unigenes of secondary metabolites biosynthetic pathway. By examining the unigenes associated with the biosynthetic pathway of the terpenoid backbone, 29 gene identifiers (K number) of the pathway were detected, which contained all identified genes of the two main biosynthetic pathways, Mevalonic Acid (MVA) and Methylerythritol Phosphate (MEP) pathways, from the beginning of the path to the production of isoprenyl diphosphate (IPP). Identification of the genes in the biosynthetic pathway of the terpenoid backbone makes it possible to realize the commercial development of the medicinal plant products, providing the basis for further research on the identification of biosynthetic pathways of other specific metabolites, metabolite engineering, molecular breeding, and medical plants breeding. | ||
| کلیدواژه‌ها [English] | ||
| Medicinal plant, next generation sequencing, transcriptome, de novo assembly, database | ||
| مراجع | ||
|
- Ali, M., Hussain, R.M., Rehman, N.U., She, G., Li, P., Wan, X., Guo, L. and Zhao, J., 2018. De novo transcriptome sequencing and metabolite profiling analyses reveal the complex metabolic genes involved in the terpenoid biosynthesis in Blue Anise Sage (Salvia guaranitica L.). DNA Research, 25(6): 597-617. - Amiripour, M., Sadat Nouri, S.A., Shariati, V. and Soltani Howyzeh, M., 2018. Identification of terpenoid backbone biosynthetic pathway genes in Ajowan (Trachyspermum ammi L.) by RNA-Seq. Journal of Novin Genetic, 13(1): 133-141. - Bhat, S.V., Nagasampagi, B.A. and Sivakumar, M., 2007. Chemistry of Natural products. New York: Springer Berlin Heidelberg, 830p. - Cárdenas-Conejo, Y., Carballo-Uicab, V., Lieberman, M., Aguilar-Espinosa, M., Comai, L. and Rivera-Madrid, R., 2015. De novo transcriptome sequencing in Bixa orellana to identify genes involved in methylerythritol phosphate, carotenoid and bixin biosynthesis. BMC Genomics, 16(1): 877. - Carretero-Paulet, L., Ahumada, I., Cunillera, N., Rodrıguez-Concepción, M., Ferrer, A., Boronat, A. and Campos, N., 2002. Expression and molecular analysis of the Arabidopsis DXR gene encoding 1-deoxy-d-xylulose 5-phosphate reductoisomerase, the first committed enzyme of the 2-c-methyl-d-erythritol 4-phosphate pathway. Plant physiology, 129(4): 1581-1591. - Chen, J.C., Chiu, M.H., Nie, R.L., Cordell, G.A. and Qiu, S.X., 2005. Cucurbitacins and cucurbitane glycosides: structures and biological activities. Natural product reports, 22(3): 386-399. - Chen, Q., Ma, C., Qian, J., Lan, X., Chao, N., Sun, J. and Wu, Y., 2016. Transcriptome sequencing of Gynostemma pentaphyllum to identify genes and enzymes involved in triterpenoid biosynthesis. International Journal of Genomics, 2016(10): 1-10. - Croteau, R., Kutchan, T.M. and Lewis, N.G., 2000. Natural products (secondary metabolites). Biochemistry and Molecular Biology of Plants, 24: 1250-1319. - Cuong, D.M., Jeon, J., Morgan, A.M., Kim, C., Kim, J.K., Lee, S.Y. and Park, S.U., 2017. Accumulation of charantin and expression of triterpenoid biosynthesis genes in bitter melon (Momordica charantia). Journal of Agricultural and Food Chemistry, 65(33): 7240-7249. - Dane, F., Liu, J. and Zhang, C., 2007. Phylogeography of the bitter apple, Citrullus colocynthis. Genetic Resources and Crop Evolution, 54(2): 327-336. - Dhar, M.K., Koul, A. and Kaul, S., 2013. Farnesyl pyrophosphate synthase: a key enzyme in isoprenoid biosynthetic pathway and potential molecular target for drug development. New Biotechnology, 30(2): 114-123. - Dillies, M.A., Rau, A., Aubert, J., Hennequet-Antier, C., Jeanmougin, M., Servant, N., Keime, C., Marot, G., Castel, D., Estelle, J. and Guernec, G., 2013. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Briefings in Bioinformatics, 14(6): 671-683. - Drew, D.P., Dueholm, B., Weitzel, C., Zhang, Y., Sensen, C.W. and Simonsen, H.T., 2013. Transcriptome analysis of Thapsia laciniata Rouy provides insights into terpenoid biosynthesis and diversity in Apiaceae. International Journal of Molecular Sciences, 14(5): 9080-9098. - Fang, X., Yang, C.Q., Wei, Y.K., Ma, Q.X., Yang, L. and Chen, X.Y., 2011. Genomics grand for diversified plant secondary metabolites. Plant Diversity and Resources, 33(1): 53-64. - Fang, Y., Huang, J., Huang, X., Chen, S.H., Zou, P.C., Li, W.S., Yu, K. and Liu, Y.W., 2015. Generation of expressed sequence tags from a cDNA library of Coleus forskohlii for identification of genes involved in terpene biosynthesis. Biologia Plantarum, 59(3): 463-468. - Guo, Q., Ma, X., Wei, S., Qiu, D., Wilson, I.W., Wu, P., Tang, Q., Liu, L., Dong, S. and Zu, W., 2014. De novo transcriptome sequencing and digital gene expression analysis predict biosynthetic pathway of rhynchophylline and isorhynchophylline from Uncaria rhynchophylla, a non-model plant with potent anti-alzheimer’s properties. BMC Genomics, 15(1): 676. - Han, X.J., Wang, Y.D., Chen, Y.C., Lin, L.Y. and Wu, Q.K., 2013. Transcriptome sequencing and expression analysis of terpenoid biosynthesis genes in Litsea cubeba. PloS one, 8(10): e76890. - Harvey, A.L., Edrada-Ebel, R. and Quinn, R.J., 2015. The re-emergence of natural products for drug discovery in the genomics era. Nature Reviews Drug Discovery, 14(2): 111-129. - Hussain, A.I., Rathore, H.A., Sattar, M.Z., Chatha, S.A., Sarker, S.D. and Gilani, A.H., 2014. Citrullus colocynthis (L.) Schrad. (bitter apple fruit): A review of its phytochemistry, pharmacology, traditional uses and nutritional potential. Journal of Ethnopharmacology, 155(1): 54-66. - Hyun, T.K., Rim, Y., Jang, H.J., Kim, C.H., Park, J., Kumar, R., Lee, S., Kim, B.C., Bhak, J., Nguyen-Quoc, B. and Kim, S.W., 2012. De novo transcriptome sequencing of Momordica cochinchinensis to identify genes involved in the carotenoid biosynthesis. Plant Molecular Biology, 79(4-5): 413-427. - Jayakodi, M., Lee, S.C., Lee, Y.S., Park, H.S., Kim, N.H., Jang, W., Lee, H.O., Joh, H.J. and Yang, T.J., 2015. Comprehensive analysis of Panax ginseng root transcriptomes. BMC Plant Biology, 15(1): 138. - Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. and Tanabe, M., 2015. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Research, 44(D1): 457-462. - Kaushik, U., Aeri, V. and Mir, S.R., 2015. Cucurbitacins-an insight into medicinal leads from nature. Pharmacognosy reviews, 9(17): 12. - King, A.J., Brown, G.D., Gilday, A.D., Larson, T.R. and Graham, I.A., 2014. Production of bioactive diterpenoids in the Euphorbiaceae depends on evolutionarily conserved gene clusters. The Plant Cell, 26(8): 3286-3298. - Langenheim, J.H., 1994. Higher plant terpenoids: a phytocentric overview of their ecological roles. Journal of Chemical Ecology, 20(6): 1223-1280. - Lau, W. and Sattely, E.S., 2015. Six enzymes from mayapple that complete the biosynthetic pathway to the etoposide aglycone. Science, 349(6253): 1224-1228. - Li, H., Dong, Y., Yang, J., Liu, X., Wang, Y., Yao, N., Guan, L., Wang, N., Wu, J. and Li, X., 2012. De novo transcriptome of safflower and the identification of putative genes for oleosin and the biosynthesis of flavonoids. PloS one, 7(2): e30987. - Li, J., Liang, Q., Li, C., Liu, M. and Zhang, Y., 2018. Comparative transcriptome analysis identifies putative genes involved in dioscin biosynthesis in Dioscorea zingiberensis. Molecules, 23(2): E454. - Luo, H., Sun, C., Sun, Y., Wu, Q., Li, Y., Song, J., Niu, Y., Cheng, X., Xu, H., Li, C. and Liu, J., 2011. Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers. BMC Genomics, 12(5): S5. - Moore, B.D., Andrew, R.L., Külheim, C. and Foley, W.J., 2014. Explaining intraspecific diversity in plant secondary metabolites in an ecological context. New Phytologist, 201(3): 733-750. - Qiao, W., Li, C., Mosongo, I., Liang, Q., Liu, M. and Wang, X., 2018. Comparative transcriptome analysis identifies putative genes involved in steroid biosynthesis in Euphorbia tirucalli. Genes, 9(1): E38. - Rai, A., Yamazaki, M., Takahashi, H., Nakamura, M., Kojoma, M., Suzuki, H. and Saito, K., 2016. RNA-seq transcriptome analysis of Panax japonicus, and its comparison with other Panax species to identify potential genes involved in the saponins biosynthesis. Frontiers in Plant Science, 7: 481. - Rasulov, B., Talts, E., Kannaste, A. and Niinemets, U., 2015. Bisphosphonate inhibitors reveal a large elasticity of plastidic isoprenoid synthesis pathway in isoprene-emitting hybrid aspen. Plant Physiology, 168(2): 532-548. - Rodrıguez-Concepción, M. and Boronat, A., 2002. Elucidation of the methylerythritol phosphate pathway for isoprenoid biosynthesis in bacteria and plastids. a metabolic milestone achieved through genomics. Plant Physiology, 130(3):1079-1089. - Sando, T., Takaoka, C., Mukai, Y., Yamashita, A., Hattori, M., Ogasawara, N., Fukusaki, E. and Kobayashi, A., 2008. Cloning and characterization of mevalonate pathway genes in a natural rubber producing plant, Hevea brasiliensis. Bioscience, Biotechnology, and Biochemistry, 72(8): 2049-2060. - Soltani Howyzeh, M., Sadat Nouri, S.A., Shariati, V. and Amiripour, M., 2018. Comparative transcriptome analysis to identify putative genes involved in thymol biosynthesis pathway in medicinal plant Trachyspermum ammi L. Scientific Reports, 8(1): 13405. - Spyropoulou, E.A., Haring, M.A. and Schuurink, R.C., 2014. RNA sequencing on Solanum lycopersicum trichomes identifies transcription factors that activate terpene synthase promoters. BMC Genomics, 15(1): 402. - Steele, C.L., Katoh, S., Bohlmann, J. and Croteau, R., 1998. Regulation of oleoresinosis in grand fir (Abies grandis): differential transcriptional control of monoterpene, sesquiterpene, and diterpene synthase genes in response to wounding. Plant Physiology, 116(4): 1497-1504. - Sun, H., Li, F., Xu, Z., Sun, M., Cong, H., Qiao, F. and Zhong, X., 2017. De novo leaf and root transcriptome analysis to identify putative genes involved in triterpenoid saponins biosynthesis in Hedera helix L. PloS One, 12(8): e0182243. - Tang, Q., Ma, X., Mo, C., Wilson, I.W., Song, C., Zhao, H., Yang, Y., Fu, W. and Qiu, D., 2011. An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis. BMC Genomics, 12(1): 343. - Wang, Y., Pan, Y., Liu, Z., Zhu, X., Zhai, L., Xu, L., Yu, R., Gong, Y. and Liu, L., 2013. De novo transcriptome sequencing of radish (Raphanus sativus L.) and analysis of major genes involved in glucosinolate metabolism. BMC Genomics, 14(1): 836. - Wang, Z., Hu, H., Goertzen, L.R., McElroy, J.S. and Dane, F., 2014. Analysis of the Citrullus colocynthis transcriptome during water deficit stress. PLoS One, 9(8): e104657. - Yahyaa, M., Tholl, D., Cormier, G., Jensen, R., Simon, P.W. and Ibdah, M., 2015. Identification and characterization of terpene synthases potentially involved in the formation of volatile terpenes in carrot (Daucus carota L.) roots. Journal of agricultural and food chemistry, 63(19): 4870-4878. - Zhang, W., Tao, T., Liu, X., Xu, F., Chang, J. and Liao, Y., 2018. De novo assembly and comparative transcriptome analysis: novel insights into sesquiterpenoid biosynthesis in Matricaria chamomilla L. Acta Physiologiae Plantarum, 40(7): 129. | ||
|
آمار تعداد مشاهده مقاله: 1,152 تعداد دریافت فایل اصل مقاله: 1,101 |
||