In silico Genome-Wide Computational Profiling of Non-Coding RNA in Oil Palm Elaeis guineensis and its Pathogen Ganoderma boninense
Keywords:
Elaeis guineensis Jacq., Ganoderma boninense, Non-coding RNAAbstract
Oil palm plantation was first established in Malaysia in 1917. Since then, the oil palm industry in Malaysia flourished especially following the shifting of Deli Dura palm to Tenera palm in the 1960s, which contributed to a 30% increase in yield. However, the outbreak of basal stem rot disease caused by Ganoderma boninense has caused substantial yield losses. With no known cure to date, extensive molecular studies were conducted to better understand the underlying mechanism of G. boninense infection and the role of protein-coding genes as regulators in oil palms against G. boninense. The studies have demonstrated the importance of non-coding RNAs (ncRNAs) in the interaction between oil palm and G. boninense. However, there is still limited genome-scale identification for ncRNAs in oil palm (Elaeis guineensis jacq.) and its pathogen, G. boninense. In this study, we focused on the identification of small and medium-sized non-coding RNA using a computational approach and managed to predict 2,233 ncRNAs and 369 ncRNAs in the E. guineensis and G. boninense genomes, respectively. The identified ncRNAs include transfer RNA (tRNA), ribosomal RNA (rRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), and microRNA (miRNA). Although the number may be far fewer than the real number, the predicted ncRNAs here represent an almost complete dataset of small and medium-sized ncRNA in both the E. guineensis and G. boninense genomes. The information obtained may be useful to tackle the issue of G. boninense attack on oil palm plantations.
Downloads
Metrics
References
Alioto, T. S. 2007. U12DB: A database of orthologous U12-type spliceosomal introns. Nucleic Acids Research, 35: D110-115. DOI: https://doi.org/10.1093/nar/gkl796
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D. 1990. Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403–410. DOI: https://doi.org/10.1016/S0022-2836(05)80360-2
Amaral, P.P. & Mattick, J.S. 2008. Noncoding RNA in development. Mammalian Genome, 19(7–8): 454–492. DOI: https://doi.org/10.1007/s00335-008-9136-7
Astorkia, M., Hernández, M., Bocs, S., Ponce, K., León, O., Morales, S., Ritter, E. 2020. Analysis of the allelic variation in the Shell gene homolog of E. oleifera and design of species specific Shell primers. Euphytica, 216(1): 5. DOI: https://doi.org/10.1007/s10681-019-2538-7
Bhogireddy, S., Mangrauthia, S. K., Kumar, R., Pandey, A. K., Singh, S., Jain, A., Budak, H., Varshney, R.K. & Kudapa, H. 2021. Regulatory non-coding RNAs: a new frontier in regulation of plant biology. Functional and Integrative Genomics, 21(3–4): 313–330. DOI: https://doi.org/10.1007/s10142-021-00787-8
Brosius, J. 2005. Waste not, want not - Transcript excess in multicellular eukaryotes. Trends in Genetics, 21(5): 287–288. DOI: https://doi.org/10.1016/j.tig.2005.02.014
Camejo, D., Guzmán-Cedeño, Á. & Moreno, A. 2016. Reactive oxygen species, essential molecules, during plant-pathogen interactions. Plant Physiology and Biochemistry, 103: 10–23. DOI: https://doi.org/10.1016/j.plaphy.2016.02.035
Campo, S., Peris-Peris, C., Siré, C., Moreno, A. B., Donaire, L., Zytnicki, M., Notredame, C., Llave, C. & San Segundo, B. 2013. Identification of a novel microRNA (miRNA) from rice that targets an alternatively spliced transcript of the Nramp6 (Natural resistance-associated macrophage protein 6) gene involved in pathogen resistance. New Phytologist, 199(1): 212–227. DOI: https://doi.org/10.1111/nph.12292
Caruana, J. C., Dhar, N. & Raina, R. 2020. Overexpression of Arabidopsis microRNA167 induces salicylic acid-dependent defense against Pseudomonas syringae through the regulation of its targets ARF6 and ARF8. Plant Direct, 4(9): e00270. DOI: https://doi.org/10.1002/pld3.270
Chan, P.P., Lin, B.Y., Mak, A.J. & Lowe, T.M. 2021. TRNAscan-SE 2.0: Improved detection and functional classification of transfer RNA genes. Nucleic Acids Research, 49(16): 9077–9096. DOI: https://doi.org/10.1093/nar/gkab688
Chan, P.P. & Lowe, T.M. 2019. tRNAscan-SE: Searching for tRNA genes in genomic sequences. Methods in Molecular Biology, 1962: 1–14. DOI: https://doi.org/10.1007/978-1-4939-9173-0_1
Chaouch, S., Queval, G., Vanderauwera, S., Mhamdi, A., Vandorpe, M., Langlois-Meurinne, M., Van Breusegem, F., Saindrenan, P. & Noctor, G. 2010. Peroxisomal hydrogen peroxide is coupled to biotic defense responses by ISOCHORISMATE SYNTHASE1 in a daylength-related manner. Plant Physiology, 153(4): 1692–1705. DOI: https://doi.org/10.1104/pp.110.153957
Ciechanover, A. 1994. The ubiquitin-proteasome proteolytic pathway. Cell, 79(1): 13–21. https://doi.org/10.1016/0092-8674(94)90396-4 DOI: https://doi.org/10.1016/0092-8674(94)90396-4
Cochard, B., Amblard, P. & Durand-Gasselin, T. 2005. Oil palm genetic improvement and sustainable development. OCL - Oleagineux Corps Gras Lipides, 12(2): 141–147. DOI: https://doi.org/10.1051/ocl.2005.0141
Corley, R.H.V. & Tinker, P.B. 2015. The Oil Palm. 5th Ed.Wiley Balack-well. 674 pp. DOI: https://doi.org/10.1002/9781118953297
Crick, F.H. 1966. Codon—anticodon pairing: The wobble hypothesis. Journal of Molecular Biology, 19(2): 548–555. DOI: https://doi.org/10.1016/S0022-2836(66)80022-0
Dhillon, B., Hamelin, R.C. & Rollins, J.A. 2021. Transcriptional profile of oil palm pathogen, Ganoderma boninense, reveals activation of lignin degradation machinery and possible evasion of host immune response. BMC Genomics, 22(1). DOI: https://doi.org/10.1186/s12864-021-07644-9
Flood, J., Hasan, Y., Turner, P.D. & O’Grady, E.B. 2000. The spread of Ganoderma from infective sources in the field and its implications for management of the disease in oil palm. In: Ganoderma Diseases of Perennial Crops. CABI Wallingford UK. pp. 101-112. DOI: https://doi.org/10.1079/9780851993881.0101
Gebert, L.F.R. & MacRae, I.J. 2019. Regulation of microRNA function in animals. Nature Reviews Molecular Cell Biology, 20(1): 21–37. DOI: https://doi.org/10.1038/s41580-018-0045-7
Griffiths-Jones, S. 2006. Mirbase: Microrna sequences, targets and gene nomenclature. Nucleic Acids Research, 34(90001). DOI: https://doi.org/10.1093/nar/gkj112
Hari, R. & Parthasarathy, S. 2018. Prediction of coding and non-coding RNA. Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics: 230–240. DOI: https://doi.org/10.1016/B978-0-12-809633-8.20099-X
Hydbring, P. & Badalian-Very, G. 2013. Clinical applications of microRNAs. F1000Research, 2: 136. DOI: https://doi.org/10.12688/f1000research.2-136.v1
Jiang, N., Cui, J., Shi, Y., Yang, G., Zhou, X., Hou, X., Meng, J. & Luan, Y. 2019. Tomato lncRNA23468 functions as a competing endogenous RNA to modulate NBS-LRR genes by decoying miR482b in the tomato-Phytophthora infestans interaction. Horticulture Research, 6(1): 28. DOI: https://doi.org/10.1038/s41438-018-0096-0
Jiang, X., Qiao, F., Long, Y., Cong, H. & Sun, H. 2017. MicroRNA-like RNAs in plant pathogenic fungus Fusarium oxysporum f. sp. niveum are involved in toxin gene expression fine tuning. 3 Biotech, 7(5): 354. DOI: https://doi.org/10.1007/s13205-017-0951-y
Kalvari, I., Nawrocki, E. P., Argasinska, J., Quinones-Olvera, N., Finn, R.D., Bateman, A. & Petrov, A.I. 2018. Non-coding RNA analysis using The rfam database. Current Protocols in Bioinformatics, 62(1). DOI: https://doi.org/10.1002/cpbi.51
Ketting, R.F. 2011. MicroRNA biogenesis and function: An overview. Advances in Experimental Medicine and Biology, 700: 1–14. DOI: https://doi.org/10.1007/978-1-4419-7823-3_1
Li, C., Feng, Y., Coukos, G. & Zhang, L. 2009. Therapeutic microRNA strategies in human cancer. The AAPS Journal, 11(4): 747–757. DOI: https://doi.org/10.1208/s12248-009-9145-9
Li, X.P., Ma, X.C., Wang, H., Zhu, Y., Liu, X.X., Li, T.T., Zheng, Y.-P., Zhao, J.-Q., Zhang, J.-W., Huang, Y.-Y., Pu, M., Feng, H., Fan, J., Li, Y. & Wang, W.M. 2020. Osa-miR162a fine-tunes rice resistance to Magnaporthe oryzae and Yield. Rice, 13(1): 38. DOI: https://doi.org/10.1186/s12284-020-00396-2
Li, Y., Zhao, S.L., Li, J.L., Hu, X.H., Wang, H., Cao, X.L., Xu, Y.-J., Zhao, Z.-X., Xiao, Z.-Y., Yang, N., Fan, J., Huang, F. & Wang, W.M. 2017. Osa-miR169 negatively regulates rice immunity against the blast fungus Magnaporthe oryzae. Frontiers in Plant Science, 8: 2. DOI: https://doi.org/10.3389/fpls.2017.00002
Liang, J., Wen, J., Huang, Z., Chen, X.P., Zhang, B.X. & Chu, L. 2019. Small nucleolar RNAs: Insight into their function in cancer. Frontiers in Oncology, 9: 587. DOI: https://doi.org/10.3389/fonc.2019.00587
Malaysian Palm Oil Council. (n.d.). About Palm Oil. [WWW Document]. URL https://mpoc.org.my/about-palm-oil/ (accessed 10.9.22)
Mattick, J. & Amaral, P. 2022. RNA, the epicenter of genetic information. In: RNA, the Epicenter of Genetic Information. CRC Press: Boca Raton. 422 pp. DOI: https://doi.org/10.1201/9781003109242
Natarajan, B., Kalsi, H.S., Godbole, P., Malankar, N., Thiagarayaselvam, A., Siddappa, S., Thulasiram, H.V., Chakrabarti, S.K. & Banerjee, A.K. 2018. MiRNA160 is associated with local defense and systemic acquired resistance against Phytophthora infestans infection in potato. Journal of Experimental Botany, 69(8): 2023–2036. DOI: https://doi.org/10.1093/jxb/ery025
Navarro, L., Dunoyer, P., Jay, F., Arnold, B., Dharmasiri, N., Estelle, M., Voinnett, O. & Jones, J.D.G. 2006. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science, 312(5772): 436–439. DOI: https://doi.org/10.1126/science.1126088
Nawrocki, E.P., Burge, S.W., Bateman, A., Daub, J., Eberhardt, R.Y., Eddy, S.R., Floden, E.W., Gardner, P.P., Jones, T.A., Tate, J. & Finn, R.D. 2015. Rfam 12.0: Updates to the RNA families database. Nucleic Acids Research, 43(D1), D130–D137. DOI: https://doi.org/10.1093/nar/gku1063
Nawrocki, E.P. & Eddy, S.R. 2013. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics, 29(22): 2933–2935. DOI: https://doi.org/10.1093/bioinformatics/btt509
Nicolas, F.E. 2011. Experimental validation of microRNA targets using a luciferase reporter system. Methods in Molecular Biology, 732: 139–152. DOI: https://doi.org/10.1007/978-1-61779-083-6_11
Nuovo, G.J. 2010. In situ detection of microRNAs in paraffin embedded, formalin fixed tissues and the co-localization of their putative targets. Methods, 52(4): 307–315. DOI: https://doi.org/10.1016/j.ymeth.2010.08.009
O’Brien, J., Hayder, H., Zayed, Y. & Peng, C. 2018. Overview of microRNA biogenesis, mechanisms of actions, and circulation. Frontiers in Endocrinology, 9: 402. DOI: https://doi.org/10.3389/fendo.2018.00402
OpenStax. 2022. Microbiology. LibreTexts. 5177 pp. https://bio.libretexts.org/Bookshelves/Microbiology/Microbiology_(OpenStax)/10%3A_Biochemistry_of_the_Genome/10.03%3A_Structure_and_Function_of_RNA
Palazzo, A.F. & Lee, E.S. 2015. Non-coding RNA: What is functional and what is junk? Frontiers in Genetics, 6: 2. DOI: https://doi.org/10.3389/fgene.2015.00002
Pandey, B., Gupta, O.P., Pandey, D.M., Sharma, I. & Sharma, P. 2013. Identification of new stress-induced microRNA and their targets in wheat using computational approach. Plant Signaling and Behavior, 8(5): e23932. DOI: https://doi.org/10.4161/psb.23932
Pauli, A., Rinn, J.L. & Schier, A.F. 2011. Non-coding RNAs as regulators of embryogenesis. Nature Reviews Genetics, 12: 136–149. DOI: https://doi.org/10.1038/nrg2904
Qu, J., Zhao, M., Hsiang, T., Feng, X., Zhang, J. & Huang, C. 2016. Identification and characterization of small noncoding RNAs in genome sequences of the edible fungus Pleurotus ostreatus. BioMed Research International, 2016: 2503023. DOI: https://doi.org/10.1155/2016/2503023
Rahul, C.U. & Rajesh, M.K. 2016. Conserved miRNA detection in the ESTs of Ganoderma lucidum. Research Journal of Biotechnology, 11(5): 34–42.
Riolo, G., Cantara, S., Marzocchi, C. & Ricci, C. 2021. miRNA targets: From prediction tools to experimental validation. Methods and Protocols, 4(1): 1–20. DOI: https://doi.org/10.3390/mps4010001
Rooij, E., & Kauppinen, S. 2014. Development of micro RNA therapeutics is coming of age . EMBO Molecular Medicine, 6(7): 851–864. DOI: https://doi.org/10.15252/emmm.201100899
Roozbeh, H., Nor Azah, Y. & Dutse, S.W. 2013. Detection and control of Ganoderma boninense: Strategies and perspectives. SpringerPlus, 2: 555. DOI: https://doi.org/10.1186/2193-1801-2-555
Salamon, S., Żok, J., Gromadzka, K. & Błaszczyk, L. 2021. Expression patterns of mir398, mir167, and mir159 in the interaction between bread wheat (Triticum aestivum L.) and pathogenic Fusarium culmorum and beneficial Trichoderma fungi. Pathogens, 10(11): 1461. DOI: https://doi.org/10.3390/pathogens10111461
Sansom, S.E., Nuovo, G.J., Martin, M.M., Kotha, S.R., Parinandi, N. L. & Elton, T.S. 2010. miR-802 regulates human angiotensin II type 1 receptor expression in intestinal epithelial C2BBe1 cells. American Journal of Physiology - Gastrointestinal and Liver Physiology, 299(3): G632–G642. DOI: https://doi.org/10.1152/ajpgi.00120.2010
Siddiqui, Y., Surendran, A., Paterson, R.R.M., Ali, A. & Ahmad, K. 2021. Current strategies and perspectives in detection and control of basal stem rot of oil palm. Saudi Journal of Biological Sciences, 28(5): 2840–2849. DOI: https://doi.org/10.1016/j.sjbs.2021.02.016
Singh, R., Ong-Abdullah, M., Low, E.T.L., Manaf, M.A.A., Rosli, R., Nookiah, R., Ooi, L.C.-L., Ooi, S.-E., Chan, K.-L., Halim, M.A., Azizi, N., Nagappan, J., Bacher, B., Lakey, N., Smith, S.W., He, D., Hogan, M., Budiman, M.A., Lee, E.K., DeSalle, R., Kudrna, D., Goicoechea, J.L., Wing, R.A., Wilson, R.K., Fulton, R.S., Ordway, J.M., Martienssen, R.A. & Sambanthamurthi, R. 2013. Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds. Nature, 500(7462): 335–339. DOI: https://doi.org/10.1038/nature12309
Song, L., Fang, Y., Chen, L., Wang, J. & Chen, X. 2021. Role of non-coding RNAs in plant immunity. Plant Communications, 2(3): 100180. DOI: https://doi.org/10.1016/j.xplc.2021.100180
Soto-Suárez, M., Baldrich, P., Weigel, D., Rubio-Somoza, I. & San Segundo, B. 2017. The Arabidopsis miR396 mediates pathogen-associated molecular pattern-triggered immune responses against fungal pathogens. Scientific Reports, 7: 44898. DOI: https://doi.org/10.1038/srep44898
Sulaiman, S., Yusoff, N.S., Sheong, T.J. & Ping, L. Y. 2018. Deciphering the pan-genome of Ganoderma sp. To depict potential genomic components that contribute to Ganoderma boninense pathogenicity. Malaysian Applied Biology, 47(5): 71–80.
Sunkar, R. & Zhu, J.K. 2004. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. The Plant Cell, 16(8): 2001–2019. DOI: https://doi.org/10.1105/tpc.104.022830
Thomas, M., Lieberman, J. & Lal, A. 2010. Desperately seeking microRNA targets. Nature Structural and Molecular Biology, 17(10): 1169–1174. DOI: https://doi.org/10.1038/nsmb.1921
Trang, P., Weidhaas, J.B. & Slack, F.J. 2008. MicroRNAs as potential cancer therapeutics. Oncogene, 27 Suppl 2: S52–S57. DOI: https://doi.org/10.1038/onc.2009.353
Utomo, C., Tanjung, Z.A., Aditama, R., Buana, R.F.N., Pratomo, A.D M., Tryono, R. & Liwang, T. 2018. Draft genome sequence of the phytopathogenic fungus Ganoderma boninense, the causal agent of basal stem rot disease on oil palm. Genome Announcements, 6(17): e00122-18. DOI: https://doi.org/10.1128/genomeA.00122-18
Val-Torregrosa, B., Bundó, M., Martín-Cardoso, H., Bach-Pages, M., Chiou, T.J., Flors, V. & Segundo, B. S. 2022. Phosphate-induced resistance to pathogen infection in Arabidopsis. The Plant Journal : For Cell and Molecular Biology. 110(2): 452-469. DOI: https://doi.org/10.1111/tpj.15680
Wei, T., Tang, Y., Jia, P., Zeng, Y., Wang, B., Wu, P., Quan, Y., Chen, A., Li, Y. & Wu, J. 2021. A Cotton Lignin Biosynthesis Gene, GhLAC4, Fine-tuned by ghr-miR397 modulates plant resistance against Verticillium dahliae. Frontiers in Plant Science, 12. 743795. DOI: https://doi.org/10.3389/fpls.2021.743795
Published
How to Cite
Issue
Section
Any reproduction of figures, tables and illustrations must obtain written permission from the Chief Editor (wicki@ukm.edu.my). No part of the journal may be reproduced without the editor’s permission
