Akhter, Z., Bi, Z., Ali, K., Sun, C., Fiaz, S., Haider, F.U., and Bai, J. (2021). In response to abiotic stress, DNA methylation confers epigenetic changes in plants. Plants 10(6): 1096. doi: 10.3390/plants10061096.
Ali, A., Han, K., and Liang, P. (2021). Role of transposable elements in gene regulation in the human genome. Life 11(2): 118. doi: 10.3390/life11020118.
Almojil, D., Bourgeois, Y., Falis, M., Hariyani, I., Wilcox, J., and Boissinot, S. (2021). The structural, functional and evolutionary impact of transposable elements in eukaryotes. Genes 12(6): 918. doi: 10.3390/genes12060918.
Ariel, F.D., and Manavella, P.A. (2021). When junk DNA turns functional: transposon-derived non-coding RNAs in plants. J. Exp. Bot. 72(11): 4132-4143. doi: 10.1093/jxb/erab073.
Baduel, P., and Colot, V. (2021). The epiallelic potential of transposable elements and its evolutionary significance in plants. Philos. Trans. R. Soc. B. 376(1826): 20200123. doi: 10.1098/rstb.2020.0123.
Baduel, P., Leduque, B., Ignace, A., Gy, I., Gil Jr, J., Loudet, O., Colot, V., and Quadrana, L. (2021). Genetic and environmental modulation of transposition shapes the evolutionary potential of Arabidopsis thaliana. Genome Biol. 22(1): 138. doi: 10.1186/s13059-021-02348-5.
Baduel, P., and Quadrana, L. (2021). Jumpstarting evolution: How transposition can facilitate adaptation to rapid environmental changes. Curr. Opin. Plant Biol. 61: 102043. doi: 10.1016/j.pbi.2021.102043.
Barah, P., Jayavelu, N.D., Mundy, J., and Bones, A.M. (2013). Genome scale transcriptional response diversity among ten ecotypes of Arabidopsis thaliana during heat stress. Front. Plant Sci. 4: 532. doi: 10.3389/fpls.2013.00532.
Batista, R.A., and Köhler, C. (2020). Genomic imprinting in plants—revisiting existing models. Genes develop. 34(1-2): 24-36. doi: 10.1101/gad.332924.119.
Bej, S., and Basak, J. (2017). "Abiotic stress induced epigenetic modifications in plants: How much do we know?," in Plant Epigenetics. RNA Technologies, ed. N. Rajewsky, Jurga, S., Barciszewski, J. . Springer, Cham), 493-512.
Bennetzen, J.L., and Wang, H. (2014). The contributions of transposable elements to the structure, function, and evolution of plant genomes. Annu. Rev. Plant Biol. 65: 505-530. doi: 10.1146/annurev-arplant-050213-035811.
Benoit, M., Drost, H.-G., Catoni, M., Gouil, Q., Lopez-Gomollon, S., Baulcombe, D., and Paszkowski, J. (2019). Environmental and epigenetic regulation of Rider retrotransposons in tomato. PLoS Genet. 15(9): e1008370. doi: 10.1371/journal.pgen.1008370.
Bhat, A., Ghatage, T., Bhan, S., Lahane, G.P., Dhar, A., Kumar, R., Pandita, R.K., Bhat, K.M., Ramos, K.S., and Pandita, T.K. (2022). Role of transposable elements in genome stability: implications for health and disease. Inter. J Molec. Sci. 23(14): 7802. doi: 10.3390/ijms23147802.
Bourguet, P., Picard, C.L., Yelagandula, R., Pélissier, T., Lorković, Z.J., Feng, S., Pouch-Pélissier, M.-N., Schmücker, A., Jacobsen, S.E., and Berger, F. (2021). The histone variant H2A. W and linker histone H1 co-regulate heterochromatin accessibility and DNA methylation. Nat. Commun. 12(1): 2683. doi: 10.1038/s41467-021-22993-5.
Bousios, A., and Gaut, B.S. (2016). Mechanistic and evolutionary questions about epigenetic conflicts between transposable elements and their plant hosts. Curr. Opin. Plant Biol. 30: 123-133. doi: 10.1016/j.pbi.2016.02.009.
Bousios, A., Nützmann, H.-W., Buck, D., and Michieletto, D. (2020). Integrating transposable elements in the 3D genome. Mob. DNA 11: 1-10. doi: 10.1186/s13100-020-0202-3.
Casacuberta, E., and González, J. (2013). The impact of transposable elements in environmental adaptation. Mol. Ecol. 22(6): 1503-1517. doi: 10.1111/mec.12170.
Cavrak, V.V., Lettner, N., Jamge, S., Kosarewicz, A., Bayer, L.M., and Mittelsten Scheid, O. (2014). How a retrotransposon exploits the plant's heat stress response for its activation. PLoS Genet. 10(1): e1004115. doi: 10.1371/journal.pgen.1004115.
Chang, Y.N., Zhu, C., Jiang, J., Zhang, H., Zhu, J.K., and Duan, C.G. (2020). Epigenetic regulation in plant abiotic stress responses. J. Integr. Plant Biol. 62(5): 563-580. doi: 10.1111/jipb.12901.
Chen, C., Wang, M., Zhu, J., Tang, Y., Zhang, H., Zhao, Q., Jing, M., Chen, Y., Xu, X., and Jiang, J. (2022). Long-term effect of epigenetic modification in plant–microbe interactions: modification of DNA methylation induced by plant growth-promoting bacteria mediates promotion process. Microbiome 10(1): 36. doi: 10.1186/s40168-022-01236-9.
Choi, J.Y., and Lee, Y.C.G. (2020). Double-edged sword: the evolutionary consequences of the epigenetic silencing of transposable elements. PLoS Genet. 16(7): e1008872. doi: 10.1371/journal.pgen.1008872.
Chu, C., Tan, C., Yu, G., Zhong, S., Xu, S., and Yan, L. (2011). A novel retrotransposon inserted in the dominant Vrn-B1 allele confers spring growth habit in tetraploid wheat (Triticum turgidum L.). G3 (Bethesda) 1(7): 637-645. doi: 10.1534%2Fg3.111.001131.
Chuong, E.B., Elde, N.C., and Feschotte, C. (2017). Regulatory activities of transposable elements: from conflicts to benefits. Nat. Rev. Genet. 18(2): 71-86. doi: 10.1038/nrg.2016.139.
Colonna Romano, N., and Fanti, L. (2022). Transposable elements: major players in shaping genomic and evolutionary patterns. Cells 11(6): 1048. doi: 10.3390/cells11061048.
Cui, X., and Cao, X. (2014). Epigenetic regulation and functional exaptation of transposable elements in higher plants. Curr. Opin. Plant Biol. 21: 83-88. doi: 10.1016/j.pbi.2014.07.001.
Deneweth, J., Van de Peer, Y., and Vermeirssen, V. (2022). Nearby transposable elements impact plant stress gene regulatory networks: a meta-analysis in A. thaliana and S. lycopersicum. BMC Genomics 23(1): 1-19. doi: 10.1186/s12864-021-08215-8.
Deniz, Ö., Frost, J.M., and Branco, M.R. (2019). Regulation of transposable elements by DNA modifications. Nat. Rev. Genet. 20(7): 417-431. doi: 10.1038/s41576-019-0106-6.
Di, C., Yuan, J., Wu, Y., Li, J., Lin, H., Hu, L., Zhang, T., Qi, Y., Gerstein, M.B., and Guo, Y. (2014). Characterization of stress‐responsive lnc RNA s in Arabidopsis thaliana by integrating expression, epigenetic and structural features. Plant J. 80(5): 848-861. doi: 10.1111/tpj.12679.
Diehl, A.G., Ouyang, N., and Boyle, A.P. (2020). Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes. Nat. Commun. 11(1): 1796. doi: 10.1038/s41467-020-15520-5.
Domb, K., Katz, A., Harris, K.D., Yaari, R., Kaisler, E., Nguyen, V.H., Hong, U.V., Griess, O., Heskiau, K.G., and Ohad, N. (2020). DNA methylation mutants in Physcomitrella patens elucidate individual roles of CG and non-CG methylation in genome regulation. Proc. Natl. Acad. Sci. U.S.A. 117(52): 33700-33710. doi: 10.1073/pnas.2011361117.
Drongitis, D., Aniello, F., Fucci, L., and Donizetti, A. (2019). Roles of transposable elements in the different layers of gene expression regulation. Int. J. Mol. Sci. 20(22): 5755. doi: 10.3390/ijms20225755.
Dubin, M.J., Scheid, O.M., and Becker, C. (2018). Transposons: a blessing curse. Curr. Opin. Plant Biol. 42: 23-29. doi: 10.1016/j.pbi.2018.01.003.
Erdmann, R.M., and Picard, C.L. (2020). RNA-directed DNA methylation. PLoS Genet. 16(10): e1009034. doi: 10.1371/journal.pgen.1009034.
Fambrini, M., Usai, G., Vangelisti, A., Mascagni, F., and Pugliesi, C. (2020). The plastic genome: The impact of transposable elements on gene functionality and genomic structural variations. Genesis 58(12): e23399. doi: 10.1002/dvg.23399.
Finatto, T., de Oliveira, A.C., Chaparro, C., Da Maia, L.C., Farias, D.R., Woyann, L.G., Mistura, C.C., Soares-Bresolin, A.P., Llauro, C., and Panaud, O. (2015). Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice. Rice 8: 1-18. doi: 10.1186/s12284-015-0045-6.
Galindo-González, L., Sarmiento, F., and Quimbaya, M.A. (2018). Shaping plant adaptability, genome structure and gene expression through transposable element epigenetic control: focus on methylation. Agronomy 8(9): 180. doi: 10.3390/agronomy8090180
Gallusci, P., Agius, D.R., Moschou, P.N., Dobránszki, J., Kaiserli, E., and Martinelli, F. (2023). Deep inside the epigenetic memories of stressed plants. Trends Plant Sci. 28(2): 142-153. doi: 10.1016/j.tplants.2022.09.004.
Gao, Z., Liu, H.-L., Daxinger, L., Pontes, O., He, X., Qian, W., Lin, H., Xie, M., Lorkovic, Z.J., and Zhang, S. (2010). An RNA polymerase II-and AGO4-associated protein acts in RNA-directed DNA methylation. Nature. 465(7294): 106-109. doi: 10.1038/nature09025.
Gebrie, A. (2023). Transposable elements as essential elements in the control of gene expression. Mob. DNA 14(1): 9. doi: 10.1186/s13100-023-00297-3.
Ghasemi-Soloklui, A.A., Kordrostami, M., and Gharaghani, A. (2023). Environmental and geographical conditions influence color, physical properties, and physiochemical composition of pomegranate fruits. Sci. Rep. 13(1): 15447. doi: 10.1038/s41598-023-42749-z.
Gill, R.A., Scossa, F., King, G.J., Golicz, A.A., Tong, C., Snowdon, R.J., Fernie, A.R., and Liu, S. (2021). On the role of transposable elements in the regulation of gene expression and subgenomic interactions in crop genomes. Crit. Rev. Plant Sci. 40(2): 157-189. doi: 10.1080/07352689.2021.1920731.
Giménez-Orenga, K., and Oltra, E. (2023). "Transposable elements shaping the epigenome," in Handbook of Epigenetics, ed. T.O. Tollefsbol. Elsevier), 323-355.
Gogolev, Y.V., Ahmar, S., Akpinar, B.A., Budak, H., Kiryushkin, A.S., Gorshkov, V.Y., Hensel, G., Demchenko, K.N., Kovalchuk, I., and Mora-Poblete, F. (2021). Omics, epigenetics, and genome editing techniques for food and nutritional security. Plants 10(7): 1423. doi: 10.3390/plants10071423
Hannan Parker, A., Wilkinson, S.W., and Ton, J. (2022). Epigenetics: a catalyst of plant immunity against pathogens. New Phytol. 233(1): 66-83. doi: 10.1186/s12870-024-04829-8.
Hirayama, T., and Shinozaki, K. (2010). Research on plant abiotic stress responses in the post‐genome era: past, present and future. Plant J. 61(6): 1041-1052. doi: 10.1111/j.1365-313x.2010.04124.x.
Hirsch, C.D., and Springer, N.M. (2017). Transposable element influences on gene expression in plants. Biochim. Biophys. Acta - Gene Regul. Mech. 1860(1): 157-165. doi: 10.1016/j.bbagrm.2016.05.010.
Hoque, T.S., Sohag, A.A.M., Kordrostami, M., Hossain, M.A., Islam, M.S., Burritt, D.J., and Hossain, M.A. (2020). "The effect of exposure to a combination of stressors on rice productivity and grain yields," in Rice research for quality improvement: genomics and genetic engineering: volume 1: breeding techniques and abiotic stress tolerance, ed. A. Roychoudhury. Springer, Singapore), 675-727.
Horváth, V., Merenciano, M., and González, J. (2017). Revisiting the relationship between transposable elements and the eukaryotic stress response. Trends Genet. 33(11): 832-841. doi: 10.1016/j.tig.2017.08.007.
Hoseini, M., and Arzani, A. (2023). Epigenetic adaptation to drought and salinity in crop plants. J. Plant Mol. Breed. 11(2): 1-16. doi: 10.22058/JPMB.2024.2021261.1292.
Hoseini, M., Arzani, A., Saeidi, G., and Araniti, F. (2024). Agro-physiological and DNA methylation responses to salinity stress in wheat (Triticum aestivum L.), Aegilops cylindrica Host, and their introgressed lines. Plants 13(19): 2673. doi: 10.3390/plants13192673.
Howell, E.L., Wirz, C.D., Brossard, D., Jamieson, K.H., Scheufele, D.A., Winneg, K.M., and Xenos, M.A. (2018). National Academies of Sciences, Engineering, and Medicine report on genetically engineered crops influences public discourse. Politics Life Sci. 37(2): 250-261.
Ito, H., Gaubert, H., Bucher, E., Mirouze, M., Vaillant, I., and Paszkowski, J. (2011). An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature. 472(7341): 115-119. doi: 10.1038/nature09861.
Ito, H., Kim, J.-M., Matsunaga, W., Saze, H., Matsui, A., Endo, T.A., Harukawa, Y., Takagi, H., Yaegashi, H., and Masuta, Y. (2016). A stress-activated transposon in Arabidopsis induces transgenerational abscisic acid insensitivity. Sci. Rep. 6(1): 23181. doi: 10.1038/srep23181.
Jogam, P., Sandhya, D., Alok, A., Peddaboina, V., Allini, V.R., and Zhang, B. (2022). A review on CRISPR/Cas-based epigenetic regulation in plants. Int. J. Biol. Macromol. 219: 1261-1271. doi: 10.1016/j.ijbiomac.2022.08.182.
Jouffroy, O., Saha, S., Mueller, L., Quesneville, H., and Maumus, F. (2016). Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening. BMC Genomics 17(1): 1-15. doi: 10.1186/s12864-016-2980-z.
Kakoulidou, I., Avramidou, E.V., Baránek, M., Brunel-Muguet, S., Farrona, S., Johannes, F., Kaiserli, E., Lieberman-Lazarovich, M., Martinelli, F., and Mladenov, V. (2021). Epigenetics for crop improvement in times of global change. Biology 10(8): 766. doi: 10.3390/biology10080766.
Kanazawa, A., Liu, B., Kong, F., Arase, S., and Abe, J. (2009). Adaptive evolution involving gene duplication and insertion of a novel Ty1/copia-like retrotransposon in soybean. J. Mol. Evol. 69: 164-175. doi: 10.1007/s00239-009-9262-1.
Kent, T.V. (2023). Evolutionary consequences of plant genome structure. University of Toronto (Canada)-PhD thesis.
Kirov, I. (2023). Toward transgene-free transposon-mediated biological mutagenesis for plant breeding. Int. J. Mol. Sci. 24(23): 17054. doi: 10.3390/ijms242317054.
Klein, S.P., and Anderson, S.N. (2022). The evolution and function of transposons in epigenetic regulation in response to the environment. Curr. Opin. Plant Biol. 69: 102277. doi: 10.1016/j.pbi.2022.102277.
Kojima, K.K. (2019). Structural and sequence diversity of eukaryotic transposable elements. Genes Genet. Syst. 94(6): 233-252. doi: 10.1266/ggs.18-00024.
Korotko, U., Chwiałkowska, K., Sańko-Sawczenko, I., and Kwasniewski, M. (2021). DNA demethylation in response to heat stress in Arabidopsis thaliana. Int. J. Mol. Sci. 22(4): 1555. doi: 10.3390/ijms22041555.
Kremer, S.C., Linquist, S., Saylor, B., Elliott, T.A., Gregory, T.R., and Cottenie, K. (2020). Transposable element persistence via potential genome-level ecosystem engineering. BMC Genomics 21(1): 1-15. doi: 10.1186/s12864-020-6763-1.
Kulski, J.K. (2016). "Next-generation sequencing—an overview of the history, tools, and “Omic” applications," in Next generation sequencing-advances, applications and challenges, ed. J.K. Kulski. Intech Open), 61964.
Kumar, A., and Bennetzen, J.L. (1999). Plant retrotransposons. Annu. Rev. Genet. 33(1): 479-532. doi: 10.1146/annurev.genet.33.1.479.
Kumar, M., and Rani, K. (2023). Epigenomics in stress tolerance of plants under the climate change. Mol. Biol. Rep. 50(7): 6201-6216. doi: 10.1007/s11033-023-08539-6.
Kumar, S., Kumari, R., Sharma, V., and Sharma, V. (2013). Roles, and establishment, maintenance and erasing of the epigenetic cytosine methylation marks in plants. J. Genet. 92: 629-666. doi: 10.1007/s12041-013-0273-8.
Le, T.-N., Schumann, U., Smith, N.A., Tiwari, S., Au, P.C.K., Zhu, Q.-H., Taylor, J.M., Kazan, K., Llewellyn, D.J., Zhang, R., Dennis, E.S., and Wang, M.-B. (2014). DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis. Genome Biol. 15(9): 458. doi: 10.1186/s13059-014-0458-3.
Lerat, E., Casacuberta, J., Chaparro, C., and Vieira, C. (2019). On the importance to acknowledge transposable elements in epigenomic analyses. Genes 10(4): 258. doi: 10.3390/genes10040258.
Lin, R., Ding, L., Casola, C., Ripoll, D.R., Feschotte, C., and Wang, H. (2007). Transposase-derived transcription factors regulate light signaling in Arabidopsis. Science 318(5854): 1302-1305. doi: 10.1126/science.1146281.
Lippman, Z., May, B., Yordan, C., Singer, T., and Martienssen, R. (2003). Distinct mechanisms determine transposon inheritance and methylation via small interfering RNA and histone modification. PLoS Biol. 1(3): e67. doi: 10.1371/journal.pbio.0000067.
Lisch, D. (2013). How important are transposons for plant evolution? Nat. Rev. Genet. 14(1): 49-61. doi: 10.1038/nrg3374.
Liu, B., Kanazawa, A., Matsumura, H., Takahashi, R., Harada, K., and Abe, J. (2008). Genetic redundancy in soybean photoresponses associated with duplication of the phytochrome A gene. Genetics 180(2): 995-1007. doi: 10.1534/genetics.108.092742.
Liu, P., Cuerda-Gil, D., Shahid, S., and Slotkin, R.K. (2022). The epigenetic control of the transposable element life cycle in plant genomes and beyond. Annu. Rev. Genet. 56: 63-87. doi: 10.1146/annurev-genet-072920-015534.
Lv, Y., Hu, F., Zhou, Y., Wu, F., and Gaut, B.S. (2019). Maize transposable elements contribute to long non-coding RNAs that are regulatory hubs for abiotic stress response. BMC Genomics 20(1): 864. doi: 10.1186/s12864-019-6245-5.
Majid, A., Parray, G., Wani, S.H., Kordostami, M., Sofi, N., Waza, S.A., Shikari, A., and Gulzar, S. (2017). Genome editing and its necessity in agriculture. Int. J. Curr. Microbiol. Appl. Sci 6: 5435-5443. doi: 10.20546/ijcmas.2017.611.520.
Makarevitch, I., Waters, A.J., West, P.T., Stitzer, M., Hirsch, C.N., Ross-Ibarra, J., and Springer, N.M. (2015). Transposable elements contribute to activation of maize genes in response to abiotic stress. PLoS Genet. 11(1): e1004915. doi: 10.1371/journal.pgen.1004915.
Mao, H., Wang, H., Liu, S., Li, Z., Yang, X., Yan, J., Li, J., Tran, L.-S.P., and Qin, F. (2015). A transposable element in a NAC gene is associated with drought tolerance in maize seedlings. Nat. Commun. 6(1): 8326. doi: 10.1038/ncomms9326.
Marin, P., Genitoni, J., Barloy, D., Maury, S., Gibert, P., Ghalambor, C.K., and Vieira, C. (2020). Biological invasion: The influence of the hidden side of the (epi) genome. Func. Ecol. 34(2): 385-400. doi: 10.1111/1365-2435.13317.
Matsunaga, W., Ohama, N., Tanabe, N., Masuta, Y., Masuda, S., Mitani, N., Yamaguchi-Shinozaki, K., Ma, J.F., Kato, A., and Ito, H. (2015). A small RNA mediated regulation of a stress-activated retrotransposon and the tissue specific transposition during the reproductive period in Arabidopsis. Front. Plant Sci. 6: 48. doi: 10.3389/fpls.2015.00048.
Maupetit-Mehouas, S., and Vaury, C. (2020). Transposon reactivation in the germline may be useful for both transposons and their host genomes. Cells 9(5): 1172. doi: 10.3390/cells9051172.
McClintock, B. (1950). The origin and behavior of mutable loci in maize. Proc. Natl. Acad. Sci. U.S.A. 36(6): 344-355. doi: 10.1073/pnas.36.6.344.
McCue, A.D., Nuthikattu, S., Reeder, S.H., and Slotkin, R.K. (2012). Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA. PLoS Genet. 8(2): e1002474. doi: 10.1371/journal.pgen.1002474.
Merkulov, P., Gvaramiya, S., Dudnikov, M., Komakhin, R., Omarov, M., Kocheshkova, A., Konstantinov, Z., Soloviev, A., Karlov, G., and Divashuk, M. (2023). Cas9‐targeted Nanopore sequencing rapidly elucidates the transposition preferences and DNA methylation profiles of mobile elements in plants. J. Integr. Plant Biol. 65(10): 2242-2261. doi: 10.1111/jipb.13555.
Mhiri, C., Borges, F., and Grandbastien, M.-A. (2022). Specificities and dynamics of transposable elements in land plants. Biology 11(4): 488. doi: 10.3390/biology11040488.
Mirouze, M., Reinders, J., Bucher, E., Nishimura, T., Schneeberger, K., Ossowski, S., Cao, J., Weigel, D., Paszkowski, J., and Mathieu, O. (2009). Selective epigenetic control of retrotransposition in Arabidopsis. Nature. 461(7262): 427-430. doi: 10.1038/nature08328.
Mirouze, M., and Vitte, C. (2014). Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes. J. Exp. Bot. 65(10): 2801-2812. doi: 10.1093/jxb/eru120.
Mohan, C., Satish, L., Muthubharathi, B.C., Selvarajan, D., Easterling, M., and Yau, Y.-Y. (2022). "CRISPR-Cas technology: A genome-editing powerhouse for molecular plant breeding," in Biotechnological innovations for environmental bioremediation, ed. S. Arora, Kumar, A., Ogita, S., Yau, Y.Y.: Springer, Singapore), 803-879.
Mozgova, I., Mikulski, P., Pecinka, A., and Farrona, S. (2019). "Epigenetic mechanisms of abiotic stress response and memory in plants," in Epigenetics in plants of agronomic importance: Fundamentals and applications: Transcriptional regulation and chromatin remodelling in plants, ed. R. Alvarez-Venegas, De-la-Peña, C., Casas-Mollano, J. . Springer, Cham. ), 1-64.
Mustafin, R., and Khusnutdinova, E. (2019). The role of transposable elements in the ecological morphogenesis under the influence of stress. Vavilovskij ž. Genet. Sel. 23(4): 380-389. doi: 10.18699/VJ19.506.
Naito, K., Zhang, F., Tsukiyama, T., Saito, H., Hancock, C.N., Richardson, A.O., Okumoto, Y., Tanisaka, T., and Wessler, S.R. (2009). Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature. 461(7267): 1130-1134. doi: 10.1038/nature08479.
Negi, P., Rai, A.N., and Suprasanna, P. (2016). Moving through the stressed genome: emerging regulatory roles for transposons in plant stress response. Front. Plant Sci. 7: 1448. doi: 10.3389/fpls.2016.01448.
Nishihara, H. (2019). Transposable elements as genetic accelerators of evolution: contribution to genome size, gene regulatory network rewiring and morphological innovation. Genes Genet. Sys. 94(6): 269-281. doi: 10.1266/ggs.19-00029.
Nozawa, K., Masuda, S., Saze, H., Ikeda, Y., Suzuki, T., Takagi, H., Tanaka, K., Ohama, N., Niu, X., and Kato, A. (2022). Epigenetic regulation of ecotype-specific expression of the heat-activated transposon ONSEN. Front. Plant Sci. 13: 899105. doi: 10.3389/fpls.2022.899105.
Oliver, K.R., McComb, J.A., and Greene, W.K. (2013). Transposable elements: powerful contributors to angiosperm evolution and diversity. Genome Biol. Evol. 5(10): 1886-1901. doi: 10.1093%2Fgbe%2Fevt141.
Omony, J., Nussbaumer, T., and Gutzat, R. (2020). DNA methylation analysis in plants: review of computational tools and future perspectives. Brief. Bioinform. 21(3): 906-918. doi: 10.1093/bib/bbz039.
Pachamuthu, K., and Borges, F. (2023). Epigenetic control of transposons during plant reproduction: From meiosis to hybrid seeds. Curr. Opin. Plant Biol. 75: 102419. doi: 10.1016/j.pbi.2023.102419.
Palazzo, A., and Marsano, R.M. (2021). Transposable elements: A jump toward the future of expression vectors. Crit. Rev. Biotechnol. 41(5): 792-808. doi: 10.1080/07388551.2021.1888067.
Pandita, D., and Pandita, A. (2023). Plant Transposable Elements: Biology and Biotechnology. CRC Press.
Pegler, J.L., Oultram, J.M., Mann, C.W., Carroll, B.J., Grof, C.P., and Eamens, A.L. (2023). Miniature inverted-repeat transposable elements: small DNA transposons that have contributed to plant micro RNA gene evolution. Plants 12(5): 1101. doi: 10.3390/plants12051101
Pietzenuk, B., Markus, C., Gaubert, H., Bagwan, N., Merotto, A., Bucher, E., and Pecinka, A. (2016). Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements. Genome Biol. 17(1): 209. doi: 10.1186/s13059-016-1072-3.
Pisoschi, A.M., Pop, A., Iordache, F., Stanca, L., Predoi, G., and Serban, A.I. (2021). Oxidative stress mitigation by antioxidants - An overview on their chemistry and influences on health status. Eur. J. Medic. Chem. 209: 112891. doi: 10.1016/j.ejmech.2020.112891.
Platt, R.N., Blanco-Berdugo, L., and Ray, D.A. (2016). Accurate transposable element annotation is vital when analyzing new genome assemblies. Genome Biol. Evol. 8(2): 403-410. doi: 10.1093/gbe/evw009.
Pulido, M., and Casacuberta, J.M. (2023). Transposable element evolution in plant genome ecosystems. Curr. Opin. Plant Biol. 75: 102418. doi: 10.1016/j.pbi.2023.102418.
Qin, T., Zhao, H., Cui, P., Albesher, N., and Xiong, L. (2017). A nucleus-localized long non-coding RNA enhances drought and salt stress tolerance. Plant Physiol. 175(3): 1321-1336. doi: 10.1104/pp.17.00574.
Quesneville, H. (2020). Twenty years of transposable element analysis in the Arabidopsis thaliana genome. Mob. DNA 11(1): 1-13. doi: 10.1186/s13100-020-00223-x.
Ramakrishnan, M., Satish, L., Kalendar, R., Narayanan, M., Kandasamy, S., Sharma, A., Emamverdian, A., Wei, Q., and Zhou, M. (2021). The dynamism of transposon methylation for plant development and stress adaptation. Int. J. Mol. Sci. 22(21): 11387. doi: 10.3390/ijms222111387.
Ramakrishnan, M., Satish, L., Sharma, A., Kurungara Vinod, K., Emamverdian, A., Zhou, M., and Wei, Q. (2022). Transposable elements in plants: Recent advancements, tools and prospects. Plant Mol. Biol. Rep. 40(4): 628-645. doi: 10.1007/s11105-022-01342-w.
Rebollo, R., Horard, B., Hubert, B., and Vieira, C. (2010). Jumping genes and epigenetics: towards new species. Gene 454(1-2): 1-7. doi: 10.1016/j.gene.2010.01.003.
Rey, O., Danchin, E., Mirouze, M., Loot, C., and Blanchet, S. (2016). Adaptation to global change: a transposable element–epigenetics perspective. Trends Ecol. Evol. 31(7): 514-526. doi: 10.1016/j.tree.2016.03.013.
Rodríguez-Leal, D., Lemmon, Z.H., Man, J., Bartlett, M.E., and Lippman, Z.B. (2017). Engineering quantitative trait variation for crop improvement by genome editing. Cell 171(2): 470-480. e478. doi: 10.1016/j.cell.2017.08.030.
Roquis, D., Robertson, M., Yu, L., Thieme, M., Julkowska, M., and Bucher, E. (2021). Genomic impact of stress-induced transposable element mobility in Arabidopsis. Nucleic Acids Res. 49(18): 10431-10447. doi: 10.1093/nar/gkab828.
Rymen, B., Ferrafiat, L., and Blevins, T. (2020). Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants. Transcription 11(3-4): 172-191. doi: 10.1080/21541264.2020.1825906.
Sahebi, M., Hanafi, M.M., van Wijnen, A.J., Rice, D., Rafii, M., Azizi, P., Osman, M., Taheri, S., Bakar, M.F.A., and Isa, M.N.M. (2018). Contribution of transposable elements in the plant's genome. Gene 665: 155-166. doi: 10.1016/j.gene.2018.04.050.
Saika, H., Mori, A., Endo, M., and Toki, S. (2019). Targeted deletion of rice retrotransposon Tos17 via CRISPR/Cas9. Plant Cell Rep. 38: 455-458. doi: 10.1007/s00299-018-2357-7.
Schrader, L., and Schmitz, J. (2019). The impact of transposable elements in adaptive evolution. Mol. Ecol. 28(6): 1537-1549. doi: 10.1111/mec.14794.
Secco, D., Wang, C., Shou, H., Schultz, M.D., Chiarenza, S., Nussaume, L., Ecker, J.R., Whelan, J., and Lister, R. (2015). Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements. eLife 4: e09343. doi: 10.7554/eLife.09343.
Selma, S., and Orzáez, D. (2021). Perspectives for epigenetic editing in crops. Transgenic Res. 30(4): 381-400. doi: 10.1007/s11248-021-00252-z.
Shahid, S., and Slotkin, R.K. (2020). The current revolution in transposable element biology enabled by long reads. Curr. Opin. Plant Biol. 54: 49-56. doi: 10.1016/j.pbi.2019.12.012.
Shanker, A.K., Bhanu, D., and Maheswari, M. (2020). Epigenetics and transgenerational memory in plants under heat stress. Plant Physiol. Rep. 25(4): 583-593. doi: 10.3389/fpls.2022.1075279.
Shin, H., Choi, W.L., Lim, J.Y., and Huh, J.H. (2022). Epigenome editing: targeted manipulation of epigenetic modifications in plants. Genes Genom. 44: 307–315. doi: 10.1007/s13258-021-01199-5.
Shinozaki, K., Yamaguchi-Shinozaki, K., and Seki, M. (2003). Regulatory network of gene expression in the drought and cold stress responses. Curr. Opin. Plant Biol. 6(5): 410-417. doi: 10.1016/s1369-5266(03)00092-x.
Slotkin, R.K., and Martienssen, R. (2007). Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 8(4): 272-285. doi: 10.1038/nrg2072.
Steimer, A., Amedeo, P., Afsar, K., Fransz, P., Scheid, O.M., and Paszkowski, J. (2000). Endogenous targets of transcriptional gene silencing in Arabidopsis. Plant Cell 12(7): 1165-1178. doi: 10.1105/tpc.12.7.1165.
Stitzer, M.C., Anderson, S.N., Springer, N.M., and Ross-Ibarra, J. (2021). The genomic ecosystem of transposable elements in maize. PLoS Genetics 17(10): e1009768. doi: 10.1371/journal.pgen.1009768.
Stuart, T. (2018). Genomic impacts of transposable elements in Arabidopsis. Ph.D., The University of Western Australia.
Sun, C., Ali, K., Yan, K., Fiaz, S., Dormatey, R., Bi, Z., and Bai, J. (2021). Exploration of epigenetics for improvement of drought and other stress resistance in crops: A review. Plants 10(6): 1226. doi: 10.3390/plants10061226
Sun, L., Jing, Y., Liu, X., Li, Q., Xue, Z., Cheng, Z., Wang, D., He, H., and Qian, W. (2020). Heat stress-induced transposon activation correlates with 3D chromatin organization rearrangement in Arabidopsis. Nat. Commun. 11(1): 1886. doi: 10.1038/s41467-020-15809-5.
Tsukahara, S., Kobayashi, A., Kawabe, A., Mathieu, O., Miura, A., and Kakutani, T. (2009). Bursts of retrotransposition reproduced in Arabidopsis. Nature 461(7262): 423-426. doi: 10.1038/nature08351.
Underwood, C.J., and Choi, K. (2019). Heterogeneous transposable elements as silencers, enhancers and targets of meiotic recombination. Chromosoma 128(3): 279-296. doi: 10.1007/s00412-019-00718-4.
Urich, M.A., Nery, J.R., Lister, R., Schmitz, R.J., and Ecker, J.R. (2015). MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat. Prot. 10(3): 475-483. doi: 10.1038/nprot.2014.114.
Usha, T., Panda, P., Goyal, A.K., Kukanur, A.A., Kamala, A., Prasannakumar, M., Sidhalinghamurthy, K., and Middha, S.K. (2022). "Whole-genome sequencing of plants: past, present, and future," in Plant Genomics for Sustainable Agriculture, ed. R.L. Singh, Mondal, S., Parihar, A., Singh, P.K. . Springer, Singapore), 191-239.
Vigneau, J., and Borg, M. (2021). The epigenetic origin of life history transitions in plants and algae. Plant Reprod. 34(4): 267-285. doi: 10.1007/s00497-021-00422-3.
Viviani, A., Ventimiglia, M., Fambrini, M., Vangelisti, A., Mascagni, F., Pugliesi, C., and Usai, G. (2021). Impact of transposable elements on the evolution of complex living systems and their epigenetic control. Biosystems 210: 104566. doi: 10.1016/j.biosystems.2021.104566.
Wang, D., Qu, Z., Yang, L., Zhang, Q., Liu, Z.H., Do, T., Adelson, D.L., Wang, Z.Y., Searle, I., and Zhu, J.K. (2017). Transposable elements (TE s) contribute to stress‐related long intergenic noncoding RNA s in plants. Plant J. 90(1): 133-146. doi: 10.1111/tpj.13481.
Wang, X., Ai, G., Zhang, C., Cui, L., Wang, J., Li, H., Zhang, J., and Ye, Z. (2016). Expression and diversification analysis reveals transposable elements play important roles in the origin of L ycopersicon‐specific lnc RNA s in tomato. New Phytol. 209(4): 1442-1455. doi: 10.1111/nph.13718.
Wang, X., Morton, J.A., Pellicer, J., Leitch, I.J., and Leitch, A.R. (2021). Genome downsizing after polyploidy: mechanisms, rates and selection pressures. Plant J. 107(4): 1003-1015. doi: 10.1111/tpj.15363.
Wells, J.N., and Feschotte, C. (2020). A field guide to eukaryotic transposable elements. Annu. Rev. Genet. 54: 539-561. doi: 10.1146/annurev-genet-040620-022145.
Wicker, T. (2018). Impact of transposable elements on genome structure and evolution in wheat. Genome Biol. 19: 103. doi: 10.1186/s13059-018-1479-0.
Wierzbicki, A.T., Haag, J.R., and Pikaard, C.S. (2008). Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 135(4): 635-648. doi: 10.1016/j.cell.2008.09.035.
Wright, D.A., and Voytas, D.F. (1998). Potential retroviruses in plants: Tat1 is related to a group of Arabidopsis thaliana Ty3/gypsy retrotransposons that encode envelope-like proteins. Genet. 149(2): 703-715. doi: 10.1093/genetics/149.2.703.
Xu, K., Xu, X., Fukao, T., Canlas, P., Maghirang-Rodriguez, R., Heuer, S., Ismail, A.M., Bailey-Serres, J., Ronald, P.C., and Mackill, D.J. (2006). Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature. 442(7103): 705-708. doi: 10.1038/nature04920.
Yan, L., Fu, D., Li, C., Blechl, A., Tranquilli, G., Bonafede, M., Sanchez, A., Valarik, M., Yasuda, S., and Dubcovsky, J. (2006). The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proc. Natl. Acad. Sci. USA 103(51): 19581-19586. doi: 10.1073/pnas.0607142103.
Yasuda, K., Ito, M., Sugita, T., Tsukiyama, T., Saito, H., Naito, K., Teraishi, M., Tanisaka, T., and Okumoto, Y. (2013). Utilization of transposable element mPing as a novel genetic tool for modification of the stress response in rice. Mol. Breed. 32: 505-516. doi: 10.1007/s11032-013-9885-1.
Zhang, H., He, Q., Xing, L., Wang, R., Wang, Y., Liu, Y., Zhou, Q., Li, X., Jia, Z., and Liu, Z. (2023). The haplotype-resolved genome assembly of autotetraploid rhubarb Rheum officinale provides insights into its genome evolution and massive accumulation of anthraquinones. Plant Commun. 5(1): 100677. doi: 10.1016/j.xplc.2023.100677.
Zhang, Y., He, F., Zhang, Y., Dai, Q., Li, Q., Nan, J., Miao, R., and Cheng, B. (2022). Exploration of the regulatory relationship between KRAB-Zfp clusters and their target transposable elements via a gene editing strategy at the cluster specific linker-associated sequences by CRISPR-Cas9. Mob. DNA 13(1): 25. doi: 10.1186/s13100-022-00279-x.
Zhao, X., Li, J., Lian, B., Gu, H., Li, Y., and Qi, Y. (2018). Global identification of Arabidopsis lncRNAs reveals the regulation of MAF4 by a natural antisense RNA. Nat. Comm. 9(1): 5056. doi: 10.1038/s41467-018-07500-7.
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