Conservation and Evolution of miRNAs and Other Small RNAs in Terrestrial Plants

ZHANG Jun-hong; ZHANG Shou-gong; TONG Zai-kang; LI Wan-feng; HAN Su-ying; QI Li-wang

Volume 26 Issue S1

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Conservation and Evolution of miRNAs and Other Small RNAs in Terrestrial Plants

1.
Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
2.
The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural and Forestry University, Lin'an 311300, Zhejiang, China
3.
Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
4.
1. Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China

Received Date: 2013-08-21

Abstract

Non-coding small RNAs (ncsRNAs) are endogenous RNA molecule, 20—26 nucleotides in length, which have been found in diverse plants and function as transcriptional and post-transcriptional regulators of gene expression. The microRNAs (miRNAs) and other ncsRNAs play essential roles in development and physiologic process of plants. The miRNAs and other ncsRNAs are conserved among terrestrial plants, and the innovation of miRNAs and other ncsRNAs appears to be associated with the advent of evolution lineages of terrestrial plants, indicating that ncsRNAs have huge impacts on plant phylogeny. This review summarizes the conservation of miRNAs and other ncsRNAs, and their functions in plants. The vital roles of ncsRNAs during the in the evolution of terrestrial plants are also discussed.
- non-coding small RNA,
- miRNA,
- conservation,
- evolution

References

[1]	Bartel D P. MicroRNAs: genomics, biogenesis, mechanism, and function[J]. Cell, 2004, 116(2):281-297
[2]	Jones-Rhoades M W, Bartel D P, Bartel B. MicroRNAs and Their Regulatory Roles in Plants[J]. Annu Rev Plant Biol, 2006, 57:19-53
[3]	Ghildiyal M, Zamore P D. Small silencing RNAs: an expanding universe[J]. Nat Rev Genet, 2009, 10(2):94-108
[4]	Hammond S M. Dicing and slicing: the core machinery of the RNA interference pathway[J]. Febs Lett, 2005, 579(26):5822-5829
[5]	Xie Z, Johansen L K, Gustafson A M, et al. Genetic and functional diversification of small RNA pathways in plants[J]. PLoS Biol, 2004, 2(5):642-652
[6]	Schauer S E, Jacobsen S E, Meinke D W, et al. DICER-LIKE1: blind men and elephants in Arabidopsis development[J]. Trends Plant Sci, 2002, 7(11):487-491
[7]	Allen E, Xie Z X, Gustafson A M, et al. microRNA-directed phasing during trans-acting siRNA biogenesis in plants[J]. Cell, 2005, 121(2):207-221
[8]	Felippes F F, Weigel D. Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173[J]. Embo Rep, 2009, 10(3):264-270
[9]	Cuperus J T, Carbonell A, Fahlgren N, et al. Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis[J]. Nat Struct Mol Biol, 2010, 17(8):997-1003
[10]	Katiyar-Agarwal S, Morgan R, Dahlbeck D, et al. A pathogen-inducible endogenous siRNA in plant immunity[J]. Proc Natl Acad Sci U S A, 2006, 103(47):18002-18007
[11]	Borsani O, Zhu J, Verslues P E, et al. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis[J]. Cell, 2005, 123(7):1279-1291
[12]	Deleris A, Gallego-Bartolome J, Bao J, et al. Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense[J]. Science, 2006, 313(5783):68-71
[13]	Dunoyer P, Himber C, Ruiz-Ferrer V, et al. Intra and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways[J]. Nat Genet, 2007, 39(7):848-856
[14]	Chapman E J, Carrington J C. Specialization and evolution of endogenous small RNA pathways[J]. Nat Rev Genet, 2007, 8(11):884-896
[15]	Matzke M, Kanno T, Daxinger L, et al. RNA-mediated chromatin-based silencing in plants[J]. Curr Opin Cell Biol, 2009, 21(3):367-376
[16]	Chellappan P, Xia J, Zhou X, et al. siRNAs from miRNA sites mediate DNA methylation of target genes[J]. Nucleic Acids Res, 2010, 38(20):6883-6894
[17]	Lu C, Tej S S, Luo S, et al. Elucidation of the small RNA component of the transcriptome[J]. Science, 2005, 309(5740):1567-1569
[18]	Morin R D, Aksay G, Dolgosheina E, et al. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa[J]. Genome Res, 2008, 18(4):571-584
[19]	Dolgosheina E V, Morin R D, Aksay G, et al. Conifers have a unique small RNA silencing signature[J]. RNA, 2008, 14(8):1508-1515
[20]	Yakovlev I A, Fossdal C G, Johnsen O. MicroRNAs, the epigenetic memory and climatic adaptation in Norway spruce[J]. New Phytol, 2010, 187(4):1154-1169
[21]	Axtell M J, Snyder J A, Bartel D P. Common functions for diverse small RNAs of land plants[J]. Plant Cell, 2007, 19(6):1750-1769
[22]	Ahuja M R, Neale D B. Evolution of Genome Size in Conifers[J]. Silvae Genetica, 2005, 54(3):126-137
[23]	Vazquez F, Blevins T, Ailhas J, et al. Evolution of Arabidopsis MIR genes generates novel microRNA classes[J]. Nucleic Acids Res, 2008, 36(20):6429-6438
[24]	Tedder P, Zubko E, Westhead D R, et al. Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA[J]. RNA, 2009, 15(6):1012-1020
[25]	Pang M, Woodward A W, Agarwal V, et al. Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.)[J]. Genome Biol, 2009, 10(11):R122
[26]	Wan L C, Wang F, Guo X, et al. Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing[J]. BMC Plant Biol, 2012, 12:146
[27]	Zhang J, Wu T, Li L, et al. Dynamic expression of small RNA populations in larch (Larix leptolepis)[J]. Planta, 2013, 237(1):89-101
[28]	Zhang J, Zhang S, Han S, et al. Genome-wide identification of microRNAs in larch and stage-specific modulation of 11 conserved microRNAs and their targets during somatic embryogenesis[J]. Planta, 2012, 236(2):647-657
[29]	Juarez M T, Kui J S, Thomas J, et al. microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity[J]. Nature, 2004, 428(6978):84-88
[30]	Parry G, Calderon-Villalobos L I, Prigge M, et al. Complex regulation of the TIR1/AFB family of auxin receptors[J]. Proc Natl Acad Sci USA, 2009, 106(52):22540-22545
[31]	Liu H H, Tian X, Li Y J, et al. Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana[J]. RNA, 2008, 14(5):836-843
[32]	Molnar A, Schwach F, Studholme D J, et al. miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii[J]. Nature, 2007, 447(7148):1126-1129
[33]	Lu S, Sun Y H, Amerson H, et al. MicroRNAs in loblolly pine (Pinus taeda L.) and their association with fusiform rust gall development[J]. Plant J, 2007, 51:1077-1098
[34]	Wan L C, Zhang H, Lu S, et al. Transcriptome-wide identification and characterization of miRNAs from Pinus densata[J]. BMC Genomics, 2012, 13:132
[35]	Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data[J]. Nucleic Acids Res, 2011, 39(1):152-157
[36]	Bowe L M, Gwe'naële C,dePamphilis C W. Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers[J]. Proc Natl Acad Sci USA, 2000, 97:4092-4097
[37]	Yang H, Matsubayashi Y, Nakamura K, et al. Oryza sativa PSK gene encodes a precursor of phytosulfokine-alpha, a sulfated peptide growth factor found in plants[J]. Proc Natl Acad Sci USA, 1999, 96(23):13560-13565
[38]	Lindsey K, Casson S, Chilley P. peptides:new signaling molecules in plants[J]. Trends Plant Sci, 2002, 7(2):78-83
[39]	Howell M D, Fahlgren N, Chapman E J, et al. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA and tasiRNA-directed targeting[J]. Plant Cell, 2007, 19(3):926-942
[40]	Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, et al. Widespread translational inhibition by plant miRNAs and siRNAs[J]. Science, 2008, 320(5880):1185-1190
[41]	Bao N, Lye K W, Barton M K. MicroRNA binding sites in Arabidopsis class Ⅲ HD-ZIP mRNAs are required for methylation of the template chromosome[J]. Dev Cell, 2004, 7(5):653-662
[42]	Khraiwesh B, Arif M A, Seumel G I, et al. Transcriptional control of gene expression by microRNAs[J]. Cell, 2010, 140(1):111-122
[43]	Peragine A, Yoshikawa M, Wu G, et al. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis[J]. Genes Dev, 2004, 18(19):2368-2379
[44]	Vazquez F, Vaucheret H, Rajagopalan R, et al. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs[J]. Mol Cell, 2004, 16(1):69-79
[45]	Wassenegger M, Krczal G. Nomenclature and functions of RNA-directed RNA polymerases[J]. Trends Plant Sci, 2006, 11(3):142-151
[46]	Matzke M, Kanno T, Huettel B, et al. Targets of RNA-directed DNA methylation[J]. Curr Opin Plant Biol, 2007, 10(5):512-519
[47]	Jia Y, Lisch D R, Ohtsu K, et al. Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24 nt small RNAs[J]. PLoS Genet, 2009, 5(11):e1000737
[48]	Wu L, Zhou H, Zhang Q, et al. DNA Methylation Mediated by a MicroRNA Pathway[J]. Mol Cell, 2010, 38(3):465-475
[49]	Allen E, Xie Z X, Gustafson A M, et al. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana[J]. Nature Genetics, 2004, 36(12):1282-1290
[50]	Nystedt B, Street N R, Wetterbom A, et al. The Norway spruce genome sequence and conifer genome evolution[J]. Nature, 2013, 497(7451):579-584
[51]	Ibarra-Laclette E, Lyons E, Hernandez-Guzman G, et al. Architecture and evolution of a minute plant genome[J]. Nature, 2013, 498(7452):94-98
[52]	Filonova L H, Bozhkov P V, von Arnold S. Developmental pathway of somatic embryogenesis in Picea abies as revealed by time-lapse tracking[J]. J Exp Bot, 2000, 51(343):249-264
[53]	Cairney J, Pullman G S. The cellular and molecular biology of conifer embryogenesis[J]. New Phytol, 2007, 176(3):511-536
[54]	Kirst M, Johnson A F, Baucom C, et al. Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana[J]. Proc Natl Acad Sci USA, 2003, 100(12):7383-7388
[55]	Lorenz W W, Sun F, Liang C, et al. Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analyses of expressed sequence tag libraries[J]. Tree Physiol, 2006, 26(1):1-16
[56]	Cairney J, Zheng L, Cowels A, et al. Expressed sequence tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis[J]. Plant Mol Biol, 2006, 62(4-5):485-501
[57]	Vernoux T, Benfey P N. Signals that regulate stem cell activity during plant development[J]. Curr Opin Genet Dev, 2005, 15(4):388-394
[58]	Williams L, Grigg S P, Xie M, et al. Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166g and its AtHD-ZIP target genes[J]. Development, 2005, 132(16):3657-3668
[59]	Rhoades M W, Reinhart B J, Lim L P, et al. Prediction of plant microRNA targets[J]. Cell, 2002, 110(4):513-520
[60]	Luo Y C, Zhou H, Li Y, et al. Rice embryogenic calli express a unique set of microRNAs, suggesting regulatory roles of microRNAs in plant post-embryogenic development[J]. Febs Lett, 2006, 580(21):5111-5116
[61]	Wu X M, Liu M Y, Ge X X, et al. Stage and tissue-specific modulation of ten conserved miRNAs and their targets during somatic embryogenesis of Valencia sweet orange[J]. Planta, 2011, 233(3):495-505
[62]	Nodine M D, Bartel D P. MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis[J]. Genes Dev, 2010, 24(23):2678-2692
[63]	Willmann M R, Mehalick A J, Packer R L, et al. MicroRNAs regulate the timing of embryo maturation in Arabidopsis[J]. Plant Physiol, 2011, 155(4):1871-1884
[64]	Oh T J, Wartell R M, Cairney J, et al. Evidence for stage-specific modulation of specific microRNAs (miRNAs) and miRNA proces sing components in zygotic embryo and female gametophyte of loblolly pine (Pinus taeda)[J]. New Phytol, 2008, 179(1):67-80
[65]	Braybrook S A, Stone S L, Park S, et al. Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis[J]. Proc Natl Acad Sci USA, 2006, 103(9):3468-3473
[66]	Holdsworth M J, Bentsink L, Soppe W J. Molecular networks regulating Arabidopsis seed maturation, after-ripening, dormancy and germination[J]. New Phytol, 2008, 179(1):33-54

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Conservation and Evolution of miRNAs and Other Small RNAs in Terrestrial Plants

1. Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China

2. The Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural and Forestry University, Lin'an 311300, Zhejiang, China

3. Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China

4. 1. Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China

Received Date: 2013-08-21

Abstract: Non-coding small RNAs (ncsRNAs) are endogenous RNA molecule, 20—26 nucleotides in length, which have been found in diverse plants and function as transcriptional and post-transcriptional regulators of gene expression. The microRNAs (miRNAs) and other ncsRNAs play essential roles in development and physiologic process of plants. The miRNAs and other ncsRNAs are conserved among terrestrial plants, and the innovation of miRNAs and other ncsRNAs appears to be associated with the advent of evolution lineages of terrestrial plants, indicating that ncsRNAs have huge impacts on plant phylogeny. This review summarizes the conservation of miRNAs and other ncsRNAs, and their functions in plants. The vital roles of ncsRNAs during the in the evolution of terrestrial plants are also discussed.

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Reference (66)

[1]	Bartel D P. MicroRNAs: genomics, biogenesis, mechanism, and function[J]. Cell, 2004, 116(2):281-297
[2]	Jones-Rhoades M W, Bartel D P, Bartel B. MicroRNAs and Their Regulatory Roles in Plants[J]. Annu Rev Plant Biol, 2006, 57:19-53
[3]	Ghildiyal M, Zamore P D. Small silencing RNAs: an expanding universe[J]. Nat Rev Genet, 2009, 10(2):94-108
[4]	Hammond S M. Dicing and slicing: the core machinery of the RNA interference pathway[J]. Febs Lett, 2005, 579(26):5822-5829
[5]	Xie Z, Johansen L K, Gustafson A M, et al. Genetic and functional diversification of small RNA pathways in plants[J]. PLoS Biol, 2004, 2(5):642-652
[6]	Schauer S E, Jacobsen S E, Meinke D W, et al. DICER-LIKE1: blind men and elephants in Arabidopsis development[J]. Trends Plant Sci, 2002, 7(11):487-491
[7]	Allen E, Xie Z X, Gustafson A M, et al. microRNA-directed phasing during trans-acting siRNA biogenesis in plants[J]. Cell, 2005, 121(2):207-221
[8]	Felippes F F, Weigel D. Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173[J]. Embo Rep, 2009, 10(3):264-270
[9]	Cuperus J T, Carbonell A, Fahlgren N, et al. Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis[J]. Nat Struct Mol Biol, 2010, 17(8):997-1003
[10]	Katiyar-Agarwal S, Morgan R, Dahlbeck D, et al. A pathogen-inducible endogenous siRNA in plant immunity[J]. Proc Natl Acad Sci U S A, 2006, 103(47):18002-18007
[11]	Borsani O, Zhu J, Verslues P E, et al. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis[J]. Cell, 2005, 123(7):1279-1291
[12]	Deleris A, Gallego-Bartolome J, Bao J, et al. Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense[J]. Science, 2006, 313(5783):68-71
[13]	Dunoyer P, Himber C, Ruiz-Ferrer V, et al. Intra and intercellular RNA interference in Arabidopsis thaliana requires components of the microRNA and heterochromatic silencing pathways[J]. Nat Genet, 2007, 39(7):848-856
[14]	Chapman E J, Carrington J C. Specialization and evolution of endogenous small RNA pathways[J]. Nat Rev Genet, 2007, 8(11):884-896
[15]	Matzke M, Kanno T, Daxinger L, et al. RNA-mediated chromatin-based silencing in plants[J]. Curr Opin Cell Biol, 2009, 21(3):367-376
[16]	Chellappan P, Xia J, Zhou X, et al. siRNAs from miRNA sites mediate DNA methylation of target genes[J]. Nucleic Acids Res, 2010, 38(20):6883-6894
[17]	Lu C, Tej S S, Luo S, et al. Elucidation of the small RNA component of the transcriptome[J]. Science, 2005, 309(5740):1567-1569
[18]	Morin R D, Aksay G, Dolgosheina E, et al. Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa[J]. Genome Res, 2008, 18(4):571-584
[19]	Dolgosheina E V, Morin R D, Aksay G, et al. Conifers have a unique small RNA silencing signature[J]. RNA, 2008, 14(8):1508-1515
[20]	Yakovlev I A, Fossdal C G, Johnsen O. MicroRNAs, the epigenetic memory and climatic adaptation in Norway spruce[J]. New Phytol, 2010, 187(4):1154-1169
[21]	Axtell M J, Snyder J A, Bartel D P. Common functions for diverse small RNAs of land plants[J]. Plant Cell, 2007, 19(6):1750-1769
[22]	Ahuja M R, Neale D B. Evolution of Genome Size in Conifers[J]. Silvae Genetica, 2005, 54(3):126-137
[23]	Vazquez F, Blevins T, Ailhas J, et al. Evolution of Arabidopsis MIR genes generates novel microRNA classes[J]. Nucleic Acids Res, 2008, 36(20):6429-6438
[24]	Tedder P, Zubko E, Westhead D R, et al. Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA[J]. RNA, 2009, 15(6):1012-1020
[25]	Pang M, Woodward A W, Agarwal V, et al. Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.)[J]. Genome Biol, 2009, 10(11):R122
[26]	Wan L C, Wang F, Guo X, et al. Identification and characterization of small non-coding RNAs from Chinese fir by high throughput sequencing[J]. BMC Plant Biol, 2012, 12:146
[27]	Zhang J, Wu T, Li L, et al. Dynamic expression of small RNA populations in larch (Larix leptolepis)[J]. Planta, 2013, 237(1):89-101
[28]	Zhang J, Zhang S, Han S, et al. Genome-wide identification of microRNAs in larch and stage-specific modulation of 11 conserved microRNAs and their targets during somatic embryogenesis[J]. Planta, 2012, 236(2):647-657
[29]	Juarez M T, Kui J S, Thomas J, et al. microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity[J]. Nature, 2004, 428(6978):84-88
[30]	Parry G, Calderon-Villalobos L I, Prigge M, et al. Complex regulation of the TIR1/AFB family of auxin receptors[J]. Proc Natl Acad Sci USA, 2009, 106(52):22540-22545
[31]	Liu H H, Tian X, Li Y J, et al. Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana[J]. RNA, 2008, 14(5):836-843
[32]	Molnar A, Schwach F, Studholme D J, et al. miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii[J]. Nature, 2007, 447(7148):1126-1129
[33]	Lu S, Sun Y H, Amerson H, et al. MicroRNAs in loblolly pine (Pinus taeda L.) and their association with fusiform rust gall development[J]. Plant J, 2007, 51:1077-1098
[34]	Wan L C, Zhang H, Lu S, et al. Transcriptome-wide identification and characterization of miRNAs from Pinus densata[J]. BMC Genomics, 2012, 13:132
[35]	Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data[J]. Nucleic Acids Res, 2011, 39(1):152-157
[36]	Bowe L M, Gwe'naële C,dePamphilis C W. Phylogeny of seed plants based on all three genomic compartments: Extant gymnosperms are monophyletic and Gnetales' closest relatives are conifers[J]. Proc Natl Acad Sci USA, 2000, 97:4092-4097
[37]	Yang H, Matsubayashi Y, Nakamura K, et al. Oryza sativa PSK gene encodes a precursor of phytosulfokine-alpha, a sulfated peptide growth factor found in plants[J]. Proc Natl Acad Sci USA, 1999, 96(23):13560-13565
[38]	Lindsey K, Casson S, Chilley P. peptides:new signaling molecules in plants[J]. Trends Plant Sci, 2002, 7(2):78-83
[39]	Howell M D, Fahlgren N, Chapman E J, et al. Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA and tasiRNA-directed targeting[J]. Plant Cell, 2007, 19(3):926-942
[40]	Brodersen P, Sakvarelidze-Achard L, Bruun-Rasmussen M, et al. Widespread translational inhibition by plant miRNAs and siRNAs[J]. Science, 2008, 320(5880):1185-1190
[41]	Bao N, Lye K W, Barton M K. MicroRNA binding sites in Arabidopsis class Ⅲ HD-ZIP mRNAs are required for methylation of the template chromosome[J]. Dev Cell, 2004, 7(5):653-662
[42]	Khraiwesh B, Arif M A, Seumel G I, et al. Transcriptional control of gene expression by microRNAs[J]. Cell, 2010, 140(1):111-122
[43]	Peragine A, Yoshikawa M, Wu G, et al. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis[J]. Genes Dev, 2004, 18(19):2368-2379
[44]	Vazquez F, Vaucheret H, Rajagopalan R, et al. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs[J]. Mol Cell, 2004, 16(1):69-79
[45]	Wassenegger M, Krczal G. Nomenclature and functions of RNA-directed RNA polymerases[J]. Trends Plant Sci, 2006, 11(3):142-151
[46]	Matzke M, Kanno T, Huettel B, et al. Targets of RNA-directed DNA methylation[J]. Curr Opin Plant Biol, 2007, 10(5):512-519
[47]	Jia Y, Lisch D R, Ohtsu K, et al. Loss of RNA-dependent RNA polymerase 2 (RDR2) function causes widespread and unexpected changes in the expression of transposons, genes, and 24 nt small RNAs[J]. PLoS Genet, 2009, 5(11):e1000737
[48]	Wu L, Zhou H, Zhang Q, et al. DNA Methylation Mediated by a MicroRNA Pathway[J]. Mol Cell, 2010, 38(3):465-475
[49]	Allen E, Xie Z X, Gustafson A M, et al. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana[J]. Nature Genetics, 2004, 36(12):1282-1290
[50]	Nystedt B, Street N R, Wetterbom A, et al. The Norway spruce genome sequence and conifer genome evolution[J]. Nature, 2013, 497(7451):579-584
[51]	Ibarra-Laclette E, Lyons E, Hernandez-Guzman G, et al. Architecture and evolution of a minute plant genome[J]. Nature, 2013, 498(7452):94-98
[52]	Filonova L H, Bozhkov P V, von Arnold S. Developmental pathway of somatic embryogenesis in Picea abies as revealed by time-lapse tracking[J]. J Exp Bot, 2000, 51(343):249-264
[53]	Cairney J, Pullman G S. The cellular and molecular biology of conifer embryogenesis[J]. New Phytol, 2007, 176(3):511-536
[54]	Kirst M, Johnson A F, Baucom C, et al. Apparent homology of expressed genes from wood-forming tissues of loblolly pine (Pinus taeda L.) with Arabidopsis thaliana[J]. Proc Natl Acad Sci USA, 2003, 100(12):7383-7388
[55]	Lorenz W W, Sun F, Liang C, et al. Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analyses of expressed sequence tag libraries[J]. Tree Physiol, 2006, 26(1):1-16
[56]	Cairney J, Zheng L, Cowels A, et al. Expressed sequence tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis[J]. Plant Mol Biol, 2006, 62(4-5):485-501
[57]	Vernoux T, Benfey P N. Signals that regulate stem cell activity during plant development[J]. Curr Opin Genet Dev, 2005, 15(4):388-394
[58]	Williams L, Grigg S P, Xie M, et al. Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166g and its AtHD-ZIP target genes[J]. Development, 2005, 132(16):3657-3668
[59]	Rhoades M W, Reinhart B J, Lim L P, et al. Prediction of plant microRNA targets[J]. Cell, 2002, 110(4):513-520
[60]	Luo Y C, Zhou H, Li Y, et al. Rice embryogenic calli express a unique set of microRNAs, suggesting regulatory roles of microRNAs in plant post-embryogenic development[J]. Febs Lett, 2006, 580(21):5111-5116
[61]	Wu X M, Liu M Y, Ge X X, et al. Stage and tissue-specific modulation of ten conserved miRNAs and their targets during somatic embryogenesis of Valencia sweet orange[J]. Planta, 2011, 233(3):495-505
[62]	Nodine M D, Bartel D P. MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis[J]. Genes Dev, 2010, 24(23):2678-2692
[63]	Willmann M R, Mehalick A J, Packer R L, et al. MicroRNAs regulate the timing of embryo maturation in Arabidopsis[J]. Plant Physiol, 2011, 155(4):1871-1884
[64]	Oh T J, Wartell R M, Cairney J, et al. Evidence for stage-specific modulation of specific microRNAs (miRNAs) and miRNA proces sing components in zygotic embryo and female gametophyte of loblolly pine (Pinus taeda)[J]. New Phytol, 2008, 179(1):67-80
[65]	Braybrook S A, Stone S L, Park S, et al. Genes directly regulated by LEAFY COTYLEDON2 provide insight into the control of embryo maturation and somatic embryogenesis[J]. Proc Natl Acad Sci USA, 2006, 103(9):3468-3473
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Conservation and Evolution of miRNAs and Other Small RNAs in Terrestrial Plants

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通讯作者: 陈斌, bchen63@163.com

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Conservation and Evolution of miRNAs and Other Small RNAs in Terrestrial Plants

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