[Home ] [Archive]   [ فارسی ]  
:: About :: Main :: Current Issue :: Archive :: Search :: Submit :: Contact ::
Main Menu
Home::
Journal Information::
Articles archive::
For Authors::
For Reviewers::
Registration::
Contact us::
Site Facilities::
::
Search in website

Advanced Search
..
Receive site information
Enter your Email in the following box to receive the site news and information.
..



 
..
:: Volume 9, Issue 2 (2023) ::
pgr 2023, 9(2): 55-70 Back to browse issues page
Identification and Functional Prediction of Long Non-Coding RNAs Responsive to Drought Stress in Lens culinaris L.
Razieh Khadivar , Ahmad Ismaili * , Seyed Sajad Sohrabi , Hasan Torabi Podeh
Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran , ismaili.a@lu.ac.ir
Abstract:   (4792 Views)
Drought stress is one of the main environmental factors that affects growth and productivity of crop plants, including lentil. In the course of evolution evolution, crucial genetic regulations mediated by non-coding RNAs (ncRNAs) have emerged in plant in response to drought and other abiotic stresses. In the present study, after identifying lncRNAs within the expression profile of lentil, RNA-seq data and real-time PCR analyses were employed to examine the expression pattern of some of the identified lncRNAs under drought stress. Additionally, psych R package was used to generate the lncRNAs-DEGs co-expression network. A total of 3590 lncRNA sequences were identified in lentils transcriptome. Numerous lncRNAs were co-expressed with genes involved in circadian rhythm regulation, zinc ion response, photosynthetic photoreaction, and ion homeostasis. The LCUL_evgLocus_104392, LCUL_evgLocus_99066 and LCUL_evgLocus_61876 sequences were differentially expressed in response to drought stress. Examining the co-expression of these sequences with differentially expressed genes in response to drought stress, led to the identification of metabolic pathways associated with these sequences. In this study, lncRNA sequences were identified for the first time in lentil, and provided useful insights into the function of lncRNA in plant resistance to drought stress. The lncRNAs-DEGs co-expression network can lead to a better understanding of drought response mechanisms in lentil.
Keywords: Drought stress, Lentil, LncRNA, PLncPRO
Full-Text [PDF 1421 kb]   (1009 Downloads)    
Type of Study: Research | Subject: Bioinformatics
References
1. Arumuganathan, K. and Earle, E.D. (1991). Nuclear DNA content of some important plant species. Plant Molecular Biology Reporter, 9: 208-218. [DOI:10.1007/BF02672069]
2. Au, P.C.K., Zhu, Q.H., Dennis, E.S. and Wang, M.B. (2011). Long non-coding RNA-mediated mechanisms independent of the RNAi pathway in animals and plants. RNA Biology, 8: 404-414. [DOI:10.4161/rna.8.3.14382] [PMID]
3. Bindea, G., Mlecnik, B., Hackl, H., Charoentong, P., Tosolini, M., Kirilovsky, A., Fridman, W.H., Pagès, F., Trajanoski, Z. and Galon, J. (2009). ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics, 25: 1091-1093. [DOI:10.1093/bioinformatics/btp101] [PMID] [PMCID]
4. Chen, L., Zhu, Q.H. and Kaufmann, K. (2020). Long non-coding RNAs in plants: emerging modulators of gene activity in development and stress responses. Planta, 252: 92. https://doi.org/10.1016/j.ncrna.2020.09.003 [DOI:10.3390/ncrna6020024] [PMID] [PMCID]
5. Chen, L.L. and Carmichael, G.G. (2010). Decoding the function of nuclear long non-coding RNAs. Current Opinion in Cell Biology, 22: 357-364. [DOI:10.1016/j.ceb.2010.03.003] [PMID] [PMCID]
6. Dong, S.M., Liang, X., LI, Z.B., Jie, S., Yan, H.B., LI, S.X., Liao, W.B. and Ming, P. (2022). A novel long non-coding RNA, DIR, increases drought tolerance in cassava by modifying stress-related gene expression. Journal of Integrative Agriculture, 21: 2588-2602. [DOI:10.1016/j.jia.2022.07.022]
7. Fukuda, M., Nishida, S., Kakei, Y., Shimada, Y. and Fujiwara, T. (2019). Genome-wide analysis of long intergenic noncoding RNAs responding to low-nutrient conditions in Arabidopsis thaliana: possible involvement of trans-acting siRNA3 in response to low nitrogen. Plant and Cell Physiology, 60: 1961-1973. [DOI:10.1093/pcp/pcz048] [PMID]
8. He, M., He, C.Q. and Ding, N.Z. (2018). Abiotic stresses: general defenses of land plants and chances for engineering multistress tolerance. Frontiers In Plant Science, 9: 1771. [DOI:10.3389/fpls.2018.01771] [PMID] [PMCID]
9. Hosseini, S.Z., Ismaili, A., Nazarian-Firouzabadi, F., Fallahi, H., Rezaei Nejad, A. and Sohrabi, S.S. (2021). Dissecting the molecular responses of lentil to individual and combined drought and heat stresses by comparative transcriptomic analysis. Genomics, 113: 693-705. [DOI:10.1016/j.ygeno.2020.12.038] [PMID]
10. Jarroux, J., Morillon, A. and Pinskaya, M. (2017). History, discovery, and classification of lncRNAs. Advances in Experimental Medicine and Biology, 1008:1-46 [DOI:10.1007/978-981-10-5203-3_1] [PMID]
11. Jha, U.C., Nayyar, H., Jha, R., Khurshid, M., Zhou, M., Mantri, N. and Siddique, K.H. (2020). Long non-coding RNAs: Emerging players regulating plant abiotic stress response and adaptation. BMC Plant Biology, 20: 1-20. [DOI:10.1186/s12870-020-02595-x] [PMID] [PMCID]
12. Khazaei, H., Caron, C.T., Fedoruk, M., Diapari, M., Vandenberg, A., Coyne, C.J., Mcgee, R. and Bett, K.E. (2016). genetic diversity of cultivated lentil (Lens culinaris Medik.) and its relation to the world's agro-ecological zones. Frontiers in Plant Science, 3901: 7. [DOI:10.3389/fpls.2016.01093] [PMID] [PMCID]
13. Kollist, H., Zandalinas, S.I., Sengupta, S., Nuhkat, M., Kangasjärvi, J. and Mittler, R. (2019). Rapid responses to abiotic stress: priming the landscape for the signal transduction network. Trends in Plant Science, 24: 25-37. [DOI:10.1016/j.tplants.2018.10.003] [PMID]
14. Kumar, B., Kumar, A., Jaiswal, S., Iquebal, M.A., Angadi, U.B., Tomar, R.S., Rai, A. and Kumar, D. (2022). Genome-wide identification of long non-coding RNAs in pearl millet (Pennisetum glaucum (L.)) genotype subjected to drought stress. Agronomy, 12(8): 1976. [DOI:10.3390/agronomy12081976]
15. Kumar, K. and Chakraborty, S. (2021). Roles of long non-coding RNAs in plant virus interactions. Journal of Plant Biochemistry and Biotechnology, 30: 684-697. [DOI:10.1007/s13562-021-00697-7]
16. Kumar, S., Barpete, S., Kumar, J., Gupta, P. and Sarker, A. (2013). Global lentil production: constraints and strategies. SATSA Mukhapatra-Annu Tech Issue, 17: 1-13.
17. Kumar, S., Hamwieh, A., Manickavelu, A., Kumar, J., Sharma, T. and Baum, M. (2014) Advances in Lentil Genomics. In: Gupta, S., Nadarajan, N. and Gupta, D.S., Eds., Legumes. in the Omic Era. pp. 111-130, Springer New York, USA. [DOI:10.1007/978-1-4614-8370-0_6]
18. Lamin-Samu, A.T., Zhuo, S., Ali, M. and Lu, G. (2022). Long non-coding RNA transcriptome landscape of anthers at different developmental stages in response to drought stress in tomato. Genomics, 114(4): 110383. [DOI:10.1016/j.ygeno.2022.110383] [PMID]
19. Livak, K.J. and Schmittgen, T.D. (2001). Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods, 25: 402-408. [DOI:10.1006/meth.2001.1262] [PMID]
20. Lu, X., Wang, X., Chen, X., Shu, N., Wang, J., Wang, D., Wang, S., Fan, W., Guo, L., Guo, X. and Ye, W. (2017). Single-base resolution methylomes of upland cotton (Gossypium hirsutum L.) reveal epigenome modifications in response to drought stress. BMC Genomics, 18: 297. [DOI:10.1186/s12864-017-3681-y] [PMID] [PMCID]
21. Ma, L., Bajic, V.B. and Zhang, Z. (2013). On the classification of long non-coding RNAs. RNA Biology, 10: 924-933. [DOI:10.4161/rna.24604] [PMID] [PMCID]
22. Muthusamy, M., Uma, S., Backiyarani, S. and Saraswathi, M.S. (2015). Genome-wide screening for novel, drought stress-responsive long non-coding RNAs in drought-stressed leaf transcriptome of drought-tolerant and -susceptible banana (Musa spp) cultivars using Illumina high-throughput sequencing. Plant Biotechnology Reports, 9: 279-286. [DOI:10.1007/s11816-015-0363-6]
23. Nejat, N. and Mantri, N. (2018). Emerging roles of long non-coding RNAs in plant response to biotic and abiotic stresses. Critical Reviews in Biotechnology, 38: 93-105. [DOI:10.1080/07388551.2017.1312270] [PMID]
24. Patra, G.K., Gupta, D., Rout, G.R. and Panda, S.K. (2023). Role of long non coding RNA in plants under abiotic and biotic stresses. Plant Physiology and Biochemistry, 194: 96-110. [DOI:10.1016/j.plaphy.2022.10.030] [PMID]
25. Qi, X., Xie, S., Liu, Y., Yi, F. and Yu, J. (2013). Genome-wide annotation of genes and noncoding RNAs of foxtail millet in response to simulated drought stress by deep sequencing. Plant Molecular Biology, 83: 459-473. [DOI:10.1007/s11103-013-0104-6] [PMID]
26. Qin, T., Zhao, H., Cui, P., Albesher, N. and Xionga, L. (2017). A nucleus-localized long non-coding rna enhances drought and salt stress tolerance. Plant Physiology, 175: 1321-1336. [DOI:10.1104/pp.17.00574] [PMID] [PMCID]
27. Raeesi Sadati, S.Y., Jahanbakhsh Godehkahriz, S., Ebadi, A. and Sedghi, M. (2021). Study of expression pattern of some transcription factors in wheat under drought stress and zinc nanoparticles. Plant Genetic Researches, 7(2): 135-144 (In Persian). [DOI:10.52547/pgr.7.2.11]
28. Rafeie, M., Amerian, M.R., Sorkhi, B., Heidari, P. and Asghari, H.R. (2020). Effect of exogenous brassinosteroid application on grain yield, some physiological traits and expression of genes related to this hormone signaling pathway in wheat under drought stress. Plant Genetic Researches, 6(2): 157-172 (In Persian). [DOI:10.29252/pgr.6.2.157]
29. Revelle, W. and Revelle, M.W. (2015). Package 'psych'. The comprehensive R archive network, 27: 337-338.
30. Sabaghpour, S., Seyedi, F., Mahmoodi, A., Safikhani, M., Pezeshkpour, P., Rostemi, B., Kamel, M., Ferayedi, Y., Alahyari, N. and Poursiabidi, M. (2013). Cultivar release: kimiya, a new high yielding lentil cultivar for moderate cold and semi warm climate of Iran. Seed and Plant Improvement Journal, 29: 397-399.
31. Singh, U., Khemka, N., Rajkumar, M.S., Garg, R. and Jain, M. (2017). PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea. Nucleic Acids Research, 45(22): 183. [DOI:10.1093/nar/gkx866] [PMID] [PMCID]
32. Sohrabi, S.S., Ismaili, A., Nazarian-Firouzabadi, F., Fallahi, H. and Hosseini, S.Z. (2022). Identification of key genes and molecular mechanisms associated with temperature stress in lentil. Gene, 807: 145952. [DOI:10.1016/j.gene.2021.145952] [PMID]
33. Sultana, R., Choudhary, A.K., Pal, A.K., Saxena, K.B., Prasad, B.D. and Singh, R. (2014) Abiotic stresses in major pulses: Current status and strategies. In: Gaur, R.K. and Sharma, P., eds., Approaches to Plant Stress and their Management. pp. 173-190. Springer Science & Business Media, Berlin, DE. [DOI:10.1007/978-81-322-1620-9_9]
34. Sun, X., Zheng, H. and Sui, N. (2018). Regulation mechanism of long non-coding RNA in plant response to stress. Biochemical and Biophysical Research Communications, 503: 402-407. [DOI:10.1016/j.bbrc.2018.07.072] [PMID]
35. Tan, X., Li, S., Hu, L. and Zhang, C. (2020). Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering. BMC Plant Biology, 20: 81. [DOI:10.1186/s12870-020-2286-9] [PMID] [PMCID]
36. Trivedi, P.K. and Asif, M.H. (2020). Updates on plant long non-coding RNAs (lncRNAs): the regulatory components. Plant Cell, Tissue and Organ Culture (PCTOC), 140: 259-269. [DOI:10.1007/s11240-019-01726-z]
37. Urquiaga, M.C.O., Thiebaut, F., Hemerly, A.S. and Ferreira, P.C.G. (2020). From trash to luxury: the potential role of plant lncRNA in DNA methylation during abiotic stress. Frontiers in Plant Science, 11: 603246. [DOI:10.3389/fpls.2020.603246] [PMID] [PMCID]
38. Waseem, M., Liu, Y. and Xia, R. (2021). Long non-coding RNAs, the dark matter: an emerging regulatory component in plants. International Journal of Molecular Sciences, 22(1): 86. [DOI:10.3390/ijms22010086] [PMID] [PMCID]
39. Weidong, Q., Hongping, C., Zuozhen, Y., Biaolin, H., Xiangdong, L., Bing, A., Yuan, L., Yu, H., Jiankun, X. and Fantao, Z. (2020). Systematic characterization of long non-coding RNAs and their responses to drought stress in dongxiang wild rice. Rice Science, 27: 21-31. [DOI:10.1016/j.rsci.2019.12.003]
40. Weidong, Q., Hongping, C., Zuozhen, Y., Biaolin, H., Xiangdong, L., Bing, A., Yuan, L., Yu, H., Jiankun, X. and Fantao, Z. (2020). Systematic characterization of long non-coding rnas and their responses to drought stress in dongxiang wild rice. Rice Science, 27: 21-31. [DOI:10.1016/j.rsci.2019.12.003]
41. Xin, M., Wang, Y., Yao, Y., Song, N., Hu, Z., Qin, D., Xie, C., Peng, H., Ni, Z. and Sun, Q. (2011). Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing. BMC Plant Biology, 11: 1-13. [DOI:10.1186/1471-2229-11-61] [PMID] [PMCID]
42. Zhang, C., Tang, G., Peng, X., Sun, F., Liu, S. and Xi, Y. (2018). Long non-coding RNAs of switchgrass (Panicum virgatum L.) in multiple dehydration stresses. BMC Plant Biology, 18: 79. [DOI:10.1186/s12870-018-1288-3] [PMID] [PMCID]
43. Zou, C., Guo, Z., Zhao, S., Chen, J., Zhang, C. and Han, H. (2023). Genome-wide analysis of long non-coding RNAs in sugar beet (Beta vulgaris L.) under drought stress. Frontiers in Plant Science, 14. https://doi.org/10.3389/fpls.2023.1118011 [DOI:10.3389/fpls.2023.1118011.] [PMID] [PMCID]
Send email to the article author



XML   Persian Abstract   Print


Download citation:
BibTeX | RIS | EndNote | Medlars | ProCite | Reference Manager | RefWorks
Send citation to:

Khadivar R, Ismaili A, Sohrabi S S, Torabi Podeh H. Identification and Functional Prediction of Long Non-Coding RNAs Responsive to Drought Stress in Lens culinaris L.. pgr 2023; 9 (2) :55-70
URL: http://pgr.lu.ac.ir/article-1-281-en.html


Rights and permissions
Creative Commons License This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
Volume 9, Issue 2 (2023) Back to browse issues page
پژوهش های ژنتیک گیاهی Plant Genetic Researches
Persian site map - English site map - Created in 0.06 seconds with 38 queries by YEKTAWEB 4657