با همکاری مشترک دانشگاه پیام نور و انجمن بیوتکنولوژی جمهوری اسلامی ایران

نوع مقاله : علمی پژوهشی

نویسندگان

1 استادیار، گروه زراعت و اصلاح نباتات، واحد خرم‌آباد، دانشگاه آزاد اسلامی ، خرم‌آباد، ایران

2 محقق، باشگاه پژوهشگران جوان و نخبگان، دانشگاه آزاد اسلامی، خرم آباد، ایران

3 استادیار، گروه کشاورزی، دانشگاه آزاد اسلامی واحد کنگاور، کنگاور، ایران

چکیده

میکرو RNA‌ها (miRNAs) گروهی از مولکول‌های RNA کوچک و غیر کدکننده‌ با طولی حدود 24-18 نوکلئوتید هستند که بیان ژن‌های هدف خود را در سطوح مختلف رونویسی و پس از رونویسی در گیاهان کنترل می‌کنند. میکرو RNA‌ها در فرآیندهای مختلفی مانند رشد و نمو، فرآیندهای زیستی، تکثیر سلولی و پاسخ به تنش‌ها در گیاهان نقش مهمی بازی می‌کنند. گشنیز زراعی با نام علمی (Coriandrum sativum L.) گیاهی از خانواده چتریان (Apiaceae) است که دارای کاربردهای غذایی و دارویی مختلفی است. ژنوم این گیاه تاکنون توالی‌یابی نشده است و هیچ‌گونه گزارشی از شناسایی میکرو RNA‌ها برای آن ثبت نشده است. مطالعه حاضر به‌منظور شناسایی میکرو RNA‌های محافظت شده بالقوه و ژن‌های هدف آن‌ها در ترنسکریپتوم گیاه گشنیز صورت گرفت. ابتدا ترنسکریپتوم بافت‌های بذر و برگ این گیاه سرهم‌بندی شد و رونوشت‌های غیر کد‌کننده به پروتئین شناسایی و به‌عنوان توالی‌های کاندید پیش‌ساز میکرو RNA در نظر گرفته شدند. در نهایت از بین توالی‌های کاندید سه میکرو RNA با نام‌های csa-miR162، csa-miR169 و csa-miR399 متعلق به سه خانواده محافظت شده میکرو RNA پس از اعمال فیلترهای سخت‌گیرانه شناسایی شد. میکرو RNAهای شناسایی شده دارای بیان متفاوتی در بافت‌های بذر و برگ بودند و نقش ژن‌های هدفشان در فرآیندهای مختلف زیستی نیز مورد تأیید قرار گرفت. در مجموع با توجه به اینکه میکرو RNAهای شناسایی شده در مطالعه حاضر دارای نقش تنظیمی بر طیف وسیعی از شبکه‌های ژنی و فرآیندهای زیستی مختلف در گیاه گشنیز هستند، می‌توان از آن‌ها به‌عنوان ژن‌های کاندید در بهبود عملکرد کمی و کیفی و همچنین مقاومت به تنش‌های مختلف در این گیاه بهره برد.

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

Identification and characterization of conserved miRNAs of Coriandrum sativum L. using next-generation sequencing data

نویسندگان [English]

  • Reza Mir Drikvand 1
  • Seyyed sajad Sohrabi 2
  • Seyyed Mohsen ُSohrabi 2
  • Kamran Samiei 3

1 Assistant Professor, Department of Agronomy and Plant Breeding, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran

2 Researcher, Young Researchers and Elite Club, Khorramabad branch, Islamic Azad University, Khorramabad, Iran

3 Assistant Professor, Department of Agronomy and Plant Breeding, Kangavar Branch, Islamic Azad University, Iran

چکیده [English]

MicroRNAs (miRNAs) are a class of small and noncoding RNAs with length of 18-24 nucleotides that control the expression of target genes at the transcriptional and post-transcriptional levels in plants. The miRNAs play an important role in different processes such as growth and development, cell proliferation and response to stresses in plants. Coriander or Coriandrum sativum L. is a plant of Apiaceae family with different nutritional and pharmaceutical applications. Up to now, the genome of this plant has not been sequenced and there is no report of miRNAs identification has been recorded for it. The present study was performed to identify the conserved miRNAs and their target genes in transcriptome of coriander plant. Firstly, Transcriptome of seed and leaf tissues was assembled and non-coding transcripts were identified and considered as miRNA precursor. Finally, among candidate sequences, three miRNAs named csa-miR162, csa-miR169 and csa-miR399 belong to three conserved families were identified after strict filtering. Identified miRNAs showed differential expression between seed and leaf tissues and also role of their target genes in different biological processes was confirmed. In general, given the regulatory roles of identified miRNAs on broad spectrum of gene networks and biological processes of coriander plant in the present study, these miRNAs can be used as candidate genes to improve qualitative and quantitative yield and resistance to different stresses in this plant.

کلیدواژه‌ها [English]

  • Coriander plant
  • miRBase
  • miRNA
  • Secondary Structure
  • Transcriptome
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of Molecular Biology. 215 (3): 403-410.
Baldrich P, Beric A, Meyers BC (2018) Despacito: the slow evolutionary changes in plant microRNAs. Current Opinion in Plant Biology. 42: 16-22.
Barciszewska-Pacak M, Knop K, Jarmołowski A, Szweykowska-Kulińska Z (2016) Arabidopsis thaliana microRNA162 level is posttranscriptionally regulated via splicing and polyadenylation site selection. Acta Biochimica Polonica. 63 (4): 811-816.
Bari R, Pant BD, Stitt M, Scheible WR (2006) PHO2, microRNA399, and PHR1 define a phosphate-signaling pathway in plants. Plant Physiology. 141 (3): 988-999.
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30 (15): 2114-2120.
Bonnet E, Wuyts J, Rouzé P, Van de Peer Y (2004) Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics. 20 (17): 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 (2): 100-112.
Chen X (2005) microRNA biogenesis and function in plants. FEBS Letters. 579 (26): 5923-5931.
Chiou TJ, Aung K, Lin SI, Wu CC, Chiang SF, Su CL (2006) Regulation of phosphate homeostasis by microRNA in Arabidopsis. Plant Cell. 18(2): 412-421.
Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Research. 39 (s2): 155-159.
Darughe F, Barzegar M, Sahari M (2012) Antioxidant and antifungal activity of Coriander (Coriandrum sativum L.) essential oil in cake. International Food Research Journal. 19 (3): 1253-1260.
de Almeida Freires I, Murata RM, Furletti VF, Sartoratto A, de Alencar SM, Figueira GM, de Oliveira Rodrigues JA, Duarte MCT, Rosalen PL (2014) Coriandrum sativum L.(coriander) essential oil: antifungal activity and mode of action on Candida spp., and molecular targets affected in human whole-genome expression. PLoS One. 9 (6): e99086.
Diederichsen A (1996) Coriander (Coriandrum sativum L.). Promoting the conservation and use of underutilized and neglected crops. International Potato Center, Lima,Peru/International Plant Genetic Resources Institute, Rome, Italy.
Duan J, Xia C, Zhao G, Jia J, Kong X (2012) Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data. BMC Genomics. 13 (1): 392.
Frazier TP, Xie F, Freistaedter A, Burklew CE, Zhang B (2010) Identification and characterization of microRNAs and their target genes in tobacco (Nicotiana tabacum). Planta. 232 (6): 1289-1308.
Galata M, Sarker LS, Mahmoud SS (2014) Transcriptome profiling, and cloning and characterization of the main monoterpene synthases of Coriandrum sativum L. Phytochemistry. 102: 64-73.
Gilbert D (2016) Accurate and complete gene construction with EvidentialGene. F1000Res. 5.
Gilbert DG (2018) Genes of the Pig, Sus scrofa, reconstructed with Evidential Gene. doi.org/10.110 1/412130
Gleave AP, Ampomah-Dwamena C, Berthold S, Dejnoprat S, Karunairetnam S, Nain B, Wang YY, Crowhurst RN, MacDiarmid RM (2008) Identification and characterisation of primary microRNAs from apple (Malus domestica cv. Royal Gala) expressed sequence tags. Tree Genetics & Genomes. 4 (2): 343-358.
Gomez-Flores R, Hernández-Martínez H, Tamez-Guerra P, Tamez-Guerra R, Quintanilla-Licea R, Monreal-Cuevas E, Rodríguez-Padilla C (2010) Antitumor and immunomodulating potential of Coriandrum sativum. Journal of Natural Products. 3:54-63.
Goossens A, Häkkinen ST, Laakso I, Seppänen-Laakso T, Biondi S, De Sutter V, Lammertyn F, Nuutila AM, Söderlund H, 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.
Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology. 29: 644-652.
Hammond SM (2015) An overview of microRNAs. Advanced Drug Delivery Reviews. 87: 3-14.
Hao DC, Chen SL, Xiao PG, Liu M (2012) Application of high‐throughput sequencing in medicinal plant transcriptome studies. Drug Development Research. 73 (8): 487-498.
Hedge I, Lamond J (1972) Coriandrum L. Flora of Turkey. 4: 330-331.
 
Jung HJ, Park SJ, Kang H (2013) Regulation of RNA metabolism in plant development and stress responses. Journal of Plant Biology. 56: 123-129.
Jung JH, Seo PJ, Park CM (2009) MicroRNA biogenesis and function in higher plants. Plant Biotechnology Reports. 3 (2): 111-126.
Kim W, Ahn HJ, Chiou TJ, Ahn JH (2011) The role of the miR399-PHO2 module in the regulation of flowering time in response to different ambient temperatures in Arabidopsis thaliana. Molecules and Cells. 32 (1): 83-88.
Laribi B, Kouki K, M'Hamdi M, Bettaieb T (2015) Coriander (Coriandrum sativum L.) and its bioactive constituents. Fitoterapia. 103: 9-26.
Lee H, Yoo SJ, Lee JH, Kim W, Yoo SK, Fitzgerald H, Carrington JC, Ahn JH (2010) Genetic framework for flowering-time regulation by ambient temperature-responsive miRNAs in Arabidopsis. Nucleic Acids Research. 38 (9): 3081-3093.
Li L, Xu J, Yang D, Tan X, Wang H (2010) Computational approaches for microRNA studies: a review. Mammalian Genome. 21 (1-2): 1-12.
Li X, Hou Y, Zhang L, Zhang W, Quan C, Cui Y, Bian S (2014) Computational identification of conserved microRNAs and their targets from expression sequence tags of blueberry (Vaccinium corybosum). Plant Signaling & Behavior. 9 (9): e29462.
Li Y, Zhao SL, Li JL, Hu XH, Wang H, Cao XL, Xu YJ, Zhao ZX, Xiao ZY, Yang N, Fan J, Huang F, Wang WM (2017) Osa-miR169 negatively regulates rice immunity against the blast fungus magnaporthe oryzae. Frontiers in Plant Science. 8: 2.
Lo Cantore P, Iacobellis NS, De Marco A, Capasso F, Senatore F (2004) Antibacterial activity of Coriandrum sativum L. and Foeniculum vulgare Miller var. vulgare (Miller) essential oils. Journal of Agricultural and Food Chemistry. 52 (26): 7862-7866.
López PA, Widrlechner MP, Simon PW, Rai S, Boylston TD, Isbell TA, Bailey TB, Gardner CA, Wilson LA (2008) Assessing phenotypic, biochemical, and molecular diversity in coriander (Coriandrum sativum L.) germplasm. Genetic Resources and Crop Evolution. 55 (2): 247-275.
Mandal S, Mandal M (2015) Coriander (Coriandrum sativum L.) essential oil: Chemistry and biological activity. Asian Pacific Journal of Tropical Biomedicine. 5 (6): 421-428.
Mandhan V, Kaur J, Singh K (2012) smRNAome profiling to identify conserved and novel microRNAs in Stevia rebaudiana Bertoni. BMC Plant Biology. 12 (1): 197.
Marangoni C, Moura NFd (2011) Sensory profile of Italian salami with coriander (Coriandrum sativum L.) essential oil. Food Science and Technology. 31 (1): 119-123.
Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet journal. 17(1): 10-12.
Mathiyalagan R, Subramaniyam S, Natarajan S, Kim YJ, Sun MS, Kim SY, Kim YJ, Yang DC (2013) Insilico profiling of microRNAs in korean ginseng (Panax ginseng Meyer). Journal of Ginseng Research. 37(2): 227-247.
Matvienko M (2015) CLC Genomics Workbench. Plant and Animal Genome Conference. Qiagen Bioinformatics Workshop at PAG 2015.
Mehta A, Gupta H, Rawal R, Mankad A, Tiwari T, Patel M, Ghosh A (2016) In Silico MicroRNA Identification from Stevia rebaudiana Transcriptome Assembly. European Journal of Medicinal Plants. 15 (2): 1-14.
Nakano T, Suzuki K, Fujimura T, Shinshi H (2006) Genome-Wide Analysis of the ERF Gene Family in Arabidopsis and Rice. Plant Physiology. 140 (2): 411-432.
Ono H, Ishii K, Kozaki T, Ogiwara I, Kanekatsu M, Yamada T (2015) Removal of redundant contigs from de novo RNA-Seq assemblies via homology search improves accurate detection of differentially expressed genes. BMC Genomics. 16: 1031.
Padmashree D, Ramachandraswamy N (2016) Identification and characterization of conserved miRNAs with its targets mRNA in Trichinella Spiralis. Bioinformation. 12 (5): 279.
Pant BD, Buhtz A., Kehr J, Scheible, WR (2008) MicroRNA399 is a long-distance signal for the regulation of plant phosphate homeostasis. The Plant Journal, 53: 731-738.
Park W, Li J, Song R, Messing J, Chen X (2002) CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Current Biology. 12 (17): 1484-1495.
Purswglove J, Brown E, Green C, Robbins S (1981) Spices. CABI, Wallingford, Oxfordshire.
Quinlan AR (2014) BEDTools: the Swiss‐army tool for genome feature analysis. Current Protocols in Bioinformatics. 47 (1): 11.12. 11-11.12. 34.
Rajeshwari U, Andallu B (2011) Medicinal benefits of coriander (Coriandrum sativum L). Spatula DD. 1 (1): 51-58.
Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP (2002) Prediction of Plant MicroRNA Targets. Cell. 110 (4): 513-520.
Silva F, Ferreira S, Queiroz JA, Domingues FC (2011) Coriander (Coriandrum sativum L.) essential oil: its antibacterial activity and mode of action evaluated by flow cytometry. Journal of Medical Microbiology. 60: 1479-1486.
Simon J (1990) Essential oils and culinary herbs. Indianapolis, Indiana, USA.
Singh VK, Singh AK, Singh S, Singh BD (2015) Next-Generation Sequencing (NGS) Tools and Impact in Plant Breeding. In: Al-Khayri JM, Jain SM, Johnson DV (eds) Advances in Plant Breeding Strategies: Breeding, Biotechnology and Molecular Tools. Springer International Publishing, Cham, pp 563-612.
Smith-Unna R, Boursnell C, Patro R, Hibberd JM, Kelly S (2016) TransRate: reference-free quality assessment of de novo transcriptome assemblies. Genome Research. 26 (8): 1134-1144.
Song L, Florea L (2015) Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads. GigaScience. 4 (1): 48.
Tian T, Wang J, Zhou X (2015) A review: microRNA detection methods. Organic & Biomolecular Chemistry. 13 (8): 2226-2238.
Unamba CIN, Nag A, Sharma RK (2015) Next Generation Sequencing Technologies: The Doorway to the Unexplored Genomics of Non-Model Plants. Frontiers in Plant Science. 6: 1074.
Wang M, Wang Q, Wang B (2012) Identification and characterization of microRNAs in Asiatic cotton (Gossypium arboreum L.). PLoS One. 7 (4): e33696.
Weiss EA (2002) Spice crops. CABI, Wallingford, Oxfordshire.
Xie F, Frazier TP, Zhang B (2010) Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). Planta. 232 (2): 417-434.
Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC (2005) Expression of Arabidopsis miRNA genes. Plant Physiology. 138 (4): 2145-2154.
Xu MY, Zhang L, Li WW, Hu XL, Wang MB, Fan YL, Zhang CY, Wang L (2014) Stress-induced early flowering is mediated by miR169 in Arabidopsis thaliana. Journal of Experimental Botany. 65 (1): 89-101.
Zhang B, Pan X, Cannon CH, Cobb GP, Anderson TA (2006a) Conservation and divergence of plant microRNA genes. The Plant Journal. 46 (2): 243-259.
Zhang B, Pan X, Cox S, Cobb GP, Anderson TA (2006b) Evidence that miRNAs are different from other RNAs. Cellular and Molecular Life Sciences CMLS. 63 (2): 246-254.
Zhang X, Zou Z, Gong P, Zhang J, Ziaf K, Li H, Xiao F, Ye Z (2011) Over-expression of microRNA169 confers enhanced drought tolerance to tomato. Biotechnology Letters. 33 (2): 403-409.
Zhao B, Ge L, Liang R, Li W, Ruan K, Lin H, Jin Y (2009) Members of miR-169 family are induced by high salinity and transiently inhibit the NF-YA transcription factor. BMC Molecular Biology. 10 (1): 10-29.
Zhao M, Ding H, Zhu JK, Zhang F, Li WX (2011) Involvement of miR169 in the nitrogen‐starvation responses in Arabidopsis. New Phytologist.190 (4): 906-915.
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research. 31 (13): 3406-3415.