Due to the important role of miRNA in regulation of plant gene expression, researchers have focused on the prediction, identification, functional and evolutionary analysis of miRNA. As genome sequencing has been completed in many species, the integration of genomic sequences with evolutionary data of miRNA provides more and more evidence and hypotheses for the origin and evolution of miRNA. However, the evolution of miRNA in plants has not been extensively reviewed. In this article, we reviewed several aspects of the evolution of miRNA in plants, including the origin hypothesis of miRNA, the birth and death of miRNA, and the functional evolution of miRNA, which provides a reference for future research.
[1] Bartel DP. MicroRNAs: target recognition and regulatory functions. Cell, 2009, 136(2): 215-233.
[2] Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell, 1993, 75(5): 843-854.
[3] Cuperus JT, Fahlgren N, Carrington JC. Evolution and functional diversification of MIRNA genes. Plant Cell, 2011, 23(2): 431-442.
[4] 成永强, 李正平, 王愈聪, 范永山. MicroRNA分析方法进展. 化学进展, 2010, 22(8): 1509-1517.
[5] Axtell MJ, Bartel DP. Antiquity of microRNAs and their targets in land plants. Plant Cell, 2005, 17(6): 1658-1673.
[6] Zhang BH, Pan XP, Cannon CH, Cobb GP, Anderson TA. Conservation and divergence of plant microRNA genes. Plant J, 2006, 46(2): 243-259.
[7] Allen E, Xie ZX, Gustafson AM, Sung GH, Spatafora JW, Carrington JC. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet, 2004, 36(12): 1282-1290.
[8] Voinnet O. Origin, biogenesis, and activity of plant microRNAs. Cell, 2009, 136(4): 669-687.
[9] Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC. High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One, 2007, 2(2): e219.
[10] Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev, 2006, 20(24): 3407-3425.
[11] Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP. MicroRNAs in plants. Genes Dev, 2002, 16(13): 1616-1626.
[12] Arteaga-Vázquez M, Caballero-Pérez J, Vielle-Calzada JP. A family of micrornas present in plants and animals. Plant Cell, 2006, 18(12): 3355-3369.
[13] Ibáñez-Ventoso C, Vora M, Driscoll M. Sequence relationships among C. elegans, D. melanogaster and human microRNAs highlight the extensive conservation of microRNAs in biology. PLoS One, 2008, 3(7): e2818.
[14] Sunkar R, Jagadeeswaran G. In silico identification of conserved microRNAs in large number of diverse plant species. BMC Plant Biol, 2008, 8(1): 37.
[15] Tang GL. Plant microRNAs: an insight into their gene structures and evolution. Semin Cell Dev Biol, 2010, 21(8): 782-789.
[16] Ma ZR, Coruh C, Axtell MJ. Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus. Plant Cell, 2010, 22(4): 1090-1103.
[17] Ason B, Darnell DK, Wittbrodt B, Berezikov E, Kloosterman WP, Wittbrodt J, Antin PB, Plasterk RHA. Differences in vertebrate microRNA expression. Proc Natl Acad Sci USA, 2006, 103(39): 14385-14389.
[18] Shabalina SA, Koonin EV. Origins and evolution of eukaryotic RNA interference. Trends Ecol Evol, 2008, 23(10): 578-587.
[19] Zhang Y, Jiang WK, Gao LZ. Evolution of microRNA genes in Oryza sativa and Arabidopsis thaliana: an update of the inverted duplication model. PLoS One, 2011, 6(12): e28073.
[20] Maher C, Stein L, Ware D. Evolution of Arabidopsis microRNA families through duplication events. Genome Res, 2006, 16(4): 510-519.
[21] Wang S, Zhu QH, Guo XY, Gui YJ, Bao JD, Helliwell C, Fan LJ. Molecular evolution and selection of a gene encoding two tandem microRNAs in rice. FEBS Lett, 2007, 581(24): 4789-4793.
[22] Guddeti S, Zhang DC, Li AL, Leseberg CH, Kang H, Li XG, Zhai WX, Johns MA, Mao L. Molecular evolution of the rice miR395 gene family. Cell Res, 2005, 15(8): 631-638.
[23] de Felippes FF, Schneeberger K, Dezulian T, Huson DH, Weigel D. Evolution of Arabidopsis thaliana microRNAs from random sequences. RNA, 2008, 14(12): 2455-2459.
[24] Svoboda P, Di Cara A. Hairpin RNA: a secondary structure of primary importance. Cell Mol Life Sci
