| تعداد نشریات | 282 |
| تعداد نشریات سازمان | 80 |
| تعداد شمارهها | 3,208 |
| تعداد مقالات | 35,560 |
| تعداد مشاهده مقاله | 53,002,129 |
| تعداد دریافت فایل اصل مقاله | 92,287,709 |
شناسایی ریز RNAها و ژنهای هدف مرتبط در گیاه دارویی مرزه خوزستانی | ||
| تحقیقات ژنتیک و اصلاح گیاهان مرتعی و جنگلی ایران | ||
| مقاله 3، دوره 29، شماره 2 - شماره پیاپی 58، اسفند 1400، صفحه 182-195 اصل مقاله (888.65 K) | ||
| نوع مقاله: مقاله علمی - پژوهشی | ||
| شناسه دیجیتال (DOI): 10.22092/ijrfpbgr.2021.354879.1386 | ||
| نویسندگان | ||
| سمیه شمس1؛ احمد اسماعیلی* 2؛ فرهاد نظریان فیروز آبادی3؛ حسین مومیوند4 | ||
| 1دانشآموخته دکتری، گروه مهندسی تولید و ژنتیک گیاهی، دانشکده کشاورزی، دانشگاه لرستان، خرمآباد | ||
| 2نویسنده مسئول مکاتبات، استاد، گروه مهندسی تولید و ژنتیک گیاهی، دانشکده کشاورزی، دانشگاه لرستان، خرمآباد | ||
| 3استاد، گروه مهندسی تولید و ژنتیک گیاهی، دانشکده کشاورزی، دانشگاه لرستان، خرمآباد | ||
| 4استادیار، گروه علوم باغبانی، دانشکده کشاورزی، دانشگاه لرستان، خرمآباد | ||
| چکیده | ||
| میرناها (microRNAها)، دسته ای از مولکول های تنظیمکننده کوچک و غیر کدکننده هستند که بیان ژن را از طریق تخریب رونویسی یا سرکوب ترجمه تنظیم می کنند. میرناها، در تنظیم گستره وسیعی از فرایندهای متابولیکی و فیزیولوژیکی در گیاهان مشارکت دارند. خانواده نعناع بهویژه مرزه خوزستانی، گیاهان شناخته شده ای از نظر طعم، عطر و خواص دارویی هستند. تاکنون هیچگونه گزارشی از شناسایی میرنا برای گیاه دارویی مرزه خوزستانی (Jamzad khuzistanica Satureja) ثبت نشده است. ازاینرو، در این مطالعه برای پیشبینی میرنا و ژنهای هدفشان در مرزه خوزستانی، از رویکرد محاسباتی مبتنی بر جستجوی همسانی استفاده شد. یونیژن های غیر کدکننده بهعنوان توالی های کاندید پیشساز میرنا در نظر گرفته شدند. در نهایت پس از ارزیابی پارامترهای عمومی درصد باز GC، حداقل انرژی آزاد تاخوردگی (MFE)، شاخص حداقل انرژی آزاد تاخوردگی (MFEI) و ساختار ثانویه 58 میرنا شناسایی شد که از بین آنها با اعمال معیارهای شناسایی اختصاصی گیاهان و پالایش میرناهای پیشبینی شده از چند رونوشت، در نهایت 10 میرنا شناسایی شد. سپس 930 رونوشت هدف با استفاده از وبسایت psRNATarget برای آنها پیشبینی و با استفاده از ابزار BLASTx نرمافزار (v2.6.0) Blast+ NCBI تفسیر کارکردی شد. بررسی ژنهای هدف نشان داد که ژنهای پاسخدهنده اکسین، ژنهای GRAS ((Gibberlic-acid insensitive (GAI), Rspressor of GAI (RGA) and Scarerow (SCR))، ژن AGO2 ( 2 Argonaute) و ژنهای خانواده LAC (Laccase) از اهداف عمده میرناهای شناسایی شده در مرزه خوزستانی هستند. تجزیهوتحلیل غنیسازی مسیر در ژن های هدف نشان داد که مسیر بیوسنتز متابولیتهای ثانویه بهطور معنی داری جزء اهداف میرناهای شناسایی شده هستند. این مطالعه، اولین گزارش از شناسایی میرنا در مرزه خوزستانی بوده که نقش آنها را در تنظیم ژنهای هدف توصیف می کند. | ||
| کلیدواژهها | ||
| تجزیه محاسباتی؛ مرزه خوزستانی؛ میرنا؛ غیر کدکننده | ||
| عنوان مقاله [English] | ||
| Identification of miRNAs and target genes in Satureja khuzistanica Jamzad | ||
| نویسندگان [English] | ||
| S. Shams1؛ A. Ismaili2؛ F. Nazarian Firouz-Abadi3؛ H. Mumivand4 | ||
| 1PhD graduated, Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Lorestan University, Khorramabad, I.R. Iran. | ||
| 2Corresponding author, Prof., Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Lorestan University, Khorramabad, I.R. Iran | ||
| 3Prof., Department of Production Engineering and Plant Genetics, Faculty of Agriculture, Lorestan University, Khorramabad, I.R. Iran. | ||
| 4Assist. Prof., Department of Horticultural Sciences, Faculty of Agriculture, Lorestan University, Khorramabad, I.R. Iran | ||
| چکیده [English] | ||
| MicroRNAs (miRNAs) are one of the small and non-coding regulatory molecules, which regulate gene expression by transcriptional cleavage or translational suppression. miRNAs are involved in regulating a wide range of metabolic and physiological processes in plants.The mint family plants, especially Satureja khuzistanica, are well known herbs for its flavor, fragrance and medicinal properties. To date, no miRNAs have been identified in Satureja species. In present study, a computational approach based on homology search was used to identify miRNAs and their targets of Satureja khuzistanica. Non-coding unigenes were identified and considered for candidates of miRNAs precursor. After evaluating the general parameters such as GC percentage, minimum folding free energy (MFE), minimum free energy index (MFEI) and secondary structure, 58 miRNAs were identified, which among them, by applying plant specific parameters and filtring the miRNAs from several transcripts, overall ten miRNAs were identified. Then, 930 target transcripts were predicted using psRNATarget website and the annotation of them was performed by using BLASTx tools of NCBI Blast+ software (v2.6.0). Examination of target genes showed that auxin-responsive genes, GRAS, AGO2 and LAC family genes are the main targets of the identified miRNAs in S. khuzistanica. Pathway enrichment analysis of the target genes revealed that the secondary metabolic pathway is significantly among the targets of the identified miRNAs. This is the first study describing miRNAs and their role in the regulation of target genes in S. khuzistanica. | ||
| کلیدواژهها [English] | ||
| Computational analysis, Satureja khuzistanica, microRNA, Non-coding | ||
| مراجع | ||
|
Axtell, MJ., Westholm, JO. and Lai, EC. 2011. Vive la différence: biogenesis and evolution of microRNAs in plants and animals. Genome Biology. 12: 1-13. Bonnet, E., Wuyts, J., Rouzé, P. and Van de Peer, Y. 2004. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics. 20: 2911-2917. Castel, SE., Martienssen, RA., 2013. RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nature Reviews Genetics, 14: 100-112. Dai, X. and Zhao, PX. 2011. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Research. 39: W155-W159. Dhandapani, V., Ramchiary, N., Paul, P., Kim, J., Choi, SH., Lee, J., Hur, Y. and Lim, YP. 2011. Identification of potential microRNAs and their targets in Brassica rapa L. Molecules and Cells. 32: 21-37. Dudareva, N., Negre, F., Nagegowda, DA. and Orlova, I. 2006. Plant volatiles: recent advances and future perspectives. Critical Reviews in Plant Sciences. 25: 417-440. Fan, R., Li, Y., Li, C. and Zhang, Y. 2015. Differential microRNA analysis of glandular trichomes and young leaves in Xanthium strumarium L. reveals their putative roles in regulating terpenoid biosynthesis. PLoS One. 10(9), p.e0139002. Goossens, A., Häkkinen, ST., Laakso, I., Seppänen-Laakso, T., Biondi, S., De Sutter, V., Lammertyn, F., Nuutila, AM., Söderlund, H. and Zabeau, M. 2003. A functional genomics approach toward the understanding of secondary metabolism in plant cells. Proceedings of the National Academy of Sciences. 100 (14): 8595-8600. Guigon, I., Legrand, S., Berthelot, JF., Bini, S., Lanselle, D., Benmounah, M. and Touzet, H. 2019. miRkwood: a tool for the reliable identification of microRNAs in plant genomes. BMC Genomics. 20: 1-9. Gupta, O., Sharma, P., Gupta, R. and Sharma, I. 2014. MicroRNA mediated regulation of metal toxicity in plants: present status and future perspectives. Plant Molecular Biology. 84: 1-18. Gupta, OP., Karkute, SG., Banerjee, S., Meena, NL. and Dahuja, A. 2017. Contemporary understanding of miRNA-based regulation of secondary metabolites biosynthesis in plants. Frontiers in Plant Science. 8: 374. Haas, BJ., Papanicolaou, A., Yassour, M., Grabherr, M., Blood, PD., Bowden, J., Couger, MB., Eccles, D., Li, B. and Lieber, M. 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols. 8: 1494-1512. Hao, DC., Chen, SL., Xiao, PG. and Liu, M. 2012. Application of high‐throughput sequencing in medicinal plant transcriptome studies. Drug Development Research. 73: 487-498. Harvey, JJ., Lewsey, MG., Patel, K., Westwood, J., Heimstädt, S., Carr, JP. and Baulcombe, DC. 2011. An antiviral defense role of AGO2 in plants. PloS one. 6: e14639. Huang, W., Peng, S., Xian, Z., Lin, D., Hu, G., Yang, L., Ren, M. and Li, Z. 2017. Overexpression of a tomato miR171 target gene Sl GRAS 24 impacts multiple agronomical traits via regulating gibberellin and auxin homeostasis. Plant Biotechnology Journal. 15: 472-488. Jamzad, Z. 1994. A new species of the genus Satureja (Labiatae) from Iran. Iranian Journal of Botany. 6: 215-8. Lan Thi Hoang, X., Du Nhi, NH., Binh Anh Thu, N., Phuong Thao, N. and Phan Tran, LS. 2017. Transcription factors and their roles in signal transduction in plants under abiotic stresses. Current genomics. 18: 483-497. Li, L., Xu, J., Yang, D., Tan, X. and Wang, H. 2010. Computational approaches for microRNA studies: a review. Mammalian Genome. 21: 1-12. Liang. PH., Ko, TP. and Wang, AHJ. 2002. Structure, mechanism and function of prenyltransferases. European Journal of Biochemistry. 269(14): 3339–54. Mehta, A., Gupta, H., Rawal, R., Mankad, A., Tiwari, T., Patel, M. and Ghosh, A. 2016. In silico microRNA identification from stevia rebaudiana transcriptome assembly. European Journal of Medicinal Plants. 1-14. Meadows, CW., Mingardon, F., Garabedian, BM., Baidoo, EEK., Benites, VT., Rodrigues, AV., Abourjeily, R., Chanal, A. and Lee, TS. 2018. Discovery of novel geranylgeranyl reductases and characterization of their substrate promiscuity. Biotechnology for Biofuels. 11: 340. Mirjani, L., Salimi, A., Matinizadeh, M., Razavi, K. and Shahbazi, M. 2018. Effective factors on micropropagation of medicinal plant of Satureja khuzistanica. Iranian Journal of Rangelands and Forests Plant Breeding and Genetic Research. 26 (1): 53-62. (In Persian). Mishra, AK., Duraisamy, GS., Týcová, A. and Matoušek, J. 2015. Computational exploration of microRNAs from expressed sequence tags of Humulus lupulus, target predictions and expression analysis. Computational Biology and Chemistry. 59: 131-141. Naghavi, MR. and Karimi, AA. 2018. Identification of miRNAs and their target genes in red clover (Trifolium pretense). Iranian Journal of Rangelands and Forests Plant Breeding and Genetic Research. 26(2): 156-164. (In Persian). Patanun, O., Lertpanyasampatha, M., Sojikul, P., Viboonjun, U. and Narangajavana, J. 2013. Computational identification of microRNAs and their targets in cassava (Manihot esculenta Crantz.). Molecular Biotechnology. 53: 257-269. Reimand, J., Arak, T., Adler, P., Kolberg, L., Reisberg, S., Peterson, H. and Vilo, J. 2016. g: Profiler—a web server for functional interpretation of gene lists (2016 update). Nucleic acids research. 44: W83-W89. Sefidkon, F., Jamzad, Z. and Mirza, M. 2004. Chemical variation in the essential oil of Satureja sahendica from Iran. Food chemistry. 88: 325-328. Shariat, A., Karimzadeh, G., Assareh, MH. and Hadian, J. 2017. Variations of physiological indices and metabolite profiling in Satureja khuzistanica in response to drought stress. Iranian Journal of Rangelands and Forests Plant Breeding and Genetic Research. 25(2): 232-246. (In Persian). Shen, E., Singh, S., Ghosh, J., Patra, B., Paul, P., Yuan, L. and Pattanaik, S. 2017. The miRNAome of Catharanthus roseus: identification, expression analysis, and potential roles of microRNAs in regulation of terpenoid indole alkaloid biosynthesis. Scientific reports. 7, 43027. Shriram, V., Kumar, V., Devarumath, RM., Khare, TS. and Wani, SH. 2016. MicroRNAs as potential targets for abiotic stress tolerance in plants. Frontiers in Plant Science, 7: 817. Singh, N., Srivastava, S., Shasany, A.K. and Sharma, A. 2016. Identification of miRNAs and their targets involved in the secondary metabolic pathways of Mentha spp. Computational Biology and Chemistry, 64, pp.154-162. Sohrabi, S., Ismaili, A., Nazarian firouz abadi, F. and Fallahi, H. 2019. Identification and characterization of conserved miRNAs in lentil. Journal of Molecular and Cellular Research (Iranian Journal of Biology), 32(4): 606-616. (In Persian). Wang, CY., Zhang, S., Yu, Y., Luo, YC., Liu, Q., Ju, C., Zhang, YC., Qu, LH., Lucas, WJ. and Wang, X. 2014. MiR397b regulates both lignin content and seed number in Arabidopsis via modulating a laccase involved in lignin biosynthesis. Plant Biotechnology Journal. 12: 1132-1142. Wang, M., Wang, Q. and Wang, B. 2012. Identification and characterization of microRNAs in Asiatic cotton (Gossypium arboreum L.). PLoS One. 7: e33696. Yoon, EK., Yang, JH., Lim, J., Kim, SH., Kim, SK. and Lee, WS. 2010. Auxin regulation of the microRNA390-dependent transacting small interfering RNA pathway in Arabidopsis lateral root development. Nucleic Acids Research. 38: 1382-1391. Zhang, B., Pan, X., Cannon, CH., Cobb, GP. and Anderson, TA. 2006a. Conservation and divergence of plant microRNA genes. The Plant Journal. 46: 243-259. Zhang, B., Pan, X., Cobb, GP. and Anderson, TA. 2006b. Plant microRNA: a small regulatory molecule with big impact. Developmental Biology. 289: 3-16. Zhang, B., Pan, X., Cox, S., Cobb, G. and Anderson, T. 2006c. Evidence that miRNAs are different from other RNAs. Cellular and Molecular Life Sciences CMLS. 63: 246-254. | ||
|
آمار تعداد مشاهده مقاله: 657 تعداد دریافت فایل اصل مقاله: 515 |
||