Skip to main content
SpringerLink
Log in

An Evolutionary View of the Biogenesis and Function of Rice Small RNAs

  • Chapter
  • First Online:
Plant Epigenetics

Part of the book series: RNA Technologies ((RNATECHN))

  • 2630 Accesses

Abstract

Small RNAs are key players in transcriptional and posttranscriptional gene silencing. The rice genus Oryza comprises two domesticated species and 22 wild species. Using deep-sequencing technology, a variety of small RNAs, such as microRNAs (miRNAs) and small interfering RNAs (siRNAs), have been characterized in Asian-cultivated rice (Oryza sativa) and its wild relatives. These RNA species are processed by different types of DICER-LIKE proteins (DCL) and/or RNA-dependent RNA polymerases (RDRs) and are loaded into distinct types of ARGONAUTE (AGO) family members. Compared with Arabidopsis, rice has an expanded number of core genes in RNA-silencing pathways, resulting from multiple gene duplication events, and functional diversification of these genes remains largely unexplored. Rice also has an evolutionarily dynamic small RNA repertoire, with several special classes of small RNAs unique to rice or to monocots. While miRNAs can serve as a driving force for rice domestication, knowledge about evolutionary trajectories and specialized functions of rice small RNAs is still lacking to a large extent. In this chapter, we summarize our current understanding of the evolution of biogenesis and functional diversity of rice small RNAs.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 299.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abe M, Yoshikawa T, Nosaka M et al (2010) WAVY LEAF1, an ortholog of Arabidopsis HEN1, regulates shoot development by maintaining microRNA and trans-acting small interfering RNA accumulation in rice. Plant Physiol 154:1335–1346

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Allen E, Xie Z, Gustafson AM et al (2005) microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121:207–221

    Article  CAS  PubMed  Google Scholar 

  • Arikit S, Xia R, Kakrana A et al (2014) An atlas of soybean small RNAs identifies phased siRNAs from hundreds of coding genes. Plant Cell 26:4584–4601

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Assis R, Bachtrog D (2013) Neofunctionalization of young duplicate genes in drosophila. Proc Natl Acad Sci USA 110:17409–17414

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Axtell MJ (2013) Classification and comparison of small RNAs from plants. Annu Rev Plant Biol 64:137–159

    Article  CAS  PubMed  Google Scholar 

  • Axtell MJ, Bowman JL (2008) Evolution of plant microRNAs and their targets. Trends Plant Sci 13:343–349

    Article  CAS  PubMed  Google Scholar 

  • Axtell MJ, Jan C, Rajagopalan R et al (2006) A two-hit trigger for siRNA biogenesis in plants. Cell 127:565–577

    Article  CAS  PubMed  Google Scholar 

  • Axtell MJ, Westholm JO, Lai EC (2011) Vive la difference: biogenesis and evolution of microRNAs in plants and animals. Genome Biol 12:221

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Baldrich P, Hsing YI, San Segundo B (2016) Genome-wide analysis of polycistronic microRNAs in cultivated and wild rice. Genome Biol Evol 8:1104–1114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Belhaj K, Chaparro-Garcia A, Kamoun S et al (2013) Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system. Plant Methods 9:39

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Berezikov E (2011) Evolution of microRNA diversity and regulation in animals. Nat Rev Genet 12:846–860

    Article  CAS  PubMed  Google Scholar 

  • Bologna NG, Voinnet O (2014) The diversity, biogenesis, and activities of endogenous silencing small RNAs in Arabidopsis. Annu Rev Plant Biol 65:473–503

    Article  CAS  PubMed  Google Scholar 

  • Burroughs AM, Ando Y, Aravind L (2014) New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing. Wiley Interdiscip Rev RNA 5:141–181

    Article  CAS  PubMed  Google Scholar 

  • Campo S, Peris-Peris C, Sire C et al (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 Phytol 199:212–227

    Article  CAS  PubMed  Google Scholar 

  • Carrington JC, Ambros V (2003) Role of microRNAs in plant and animal development. Science 301:336–338

    Article  CAS  PubMed  Google Scholar 

  • Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136:642–655

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen X (2009) Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol 25:21–44

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chen JF, Huang QF, Gao DY et al (2013a) Whole-genome sequencing of Oryza Brachyantha reveals mechanisms underlying Oryza genome evolution. Nat Commun 4:1595

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chen Z, Li F, Yang S et al (2013b) Identification and functional analysis of flowering related microRNAs in common wild rice (Oryza rufipogon Griff.) PLoS One 8:e82844

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chitwood DH, Sinha NR (2014) Plant development: small RNAs and the metamorphosis of leaves. Curr Biol 24:R1087–R1089

    Article  CAS  PubMed  Google Scholar 

  • Chuck G, O’Connor D (2010) Small RNAs going the distance during plant development. Curr Opin Plant Biol 13:40–45

    Article  CAS  PubMed  Google Scholar 

  • Cuperus JT, Fahlgren N, Carrington JC (2011) Evolution and functional diversification of MIRNA genes. Plant Cell 23:431–442

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Diaz-Pendon JA, Li F, Li WX et al (2007) Suppression of antiviral silencing by cucumber mosaic virus 2b protein in Arabidopsis is associated with drastically reduced accumulation of three classes of viral small interfering RNAs. Plant Cell 19:2053–2063

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Donaire L, Barajas D, Martinez-Garcia B et al (2008) Structural and genetic requirements for the biogenesis of tobacco rattle virus-derived small interfering RNAs. J Virol 82:5167–5177

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fahlgren N, Howell MD, Kasschau KD et al (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One 2:e219

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fang X, Qi Y (2016) RNAi in plants: an Argonaute-centered view. Plant Cell 28:272–285

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fay JC, Wu CI (2000) Hitchhiking under positive Darwinian selection. Genetics 155:1405–1413

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fei Q, Xia R, Meyers BC (2013) Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks. Plant Cell 25:2400–2415

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fei Q, Li P, Teng C et al (2015) Secondary siRNAs from medicago NB-LRRs modulated via miRNA-target interactions and their abundances. Plant J 83:451–465

    Article  CAS  PubMed  Google Scholar 

  • Fei Q, Yang L, Liang W et al (2016) Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways. J Exp Bot 67:6037–6049

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fu YX, Li WH (1993) Statistical tests of neutrality of mutations. Genetics 133:693–709

    CAS  PubMed  PubMed Central  Google Scholar 

  • Garcia-Ruiz H, Takeda A, Chapman EJ et al (2010) Arabidopsis RNA-dependent RNA polymerases and Dicer-like proteins in antiviral defense and small interfering RNA biogenesis during turnip mosaic virus infection. Plant Cell 22:481–496

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Goff SA, Ricke D, Lan TH et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100

    Article  CAS  PubMed  Google Scholar 

  • Guo X, Gui Y, Wang Y et al (2008) Selection and mutation on microRNA target sequences during rice evolution. BMC Genomics 9:454

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Harushima Y, Nakagahra M, Yano M et al (2002) Diverse variation of reproductive barriers in three intraspecific rice crosses. Genetics 160:313–322

    PubMed  PubMed Central  Google Scholar 

  • Havecker ER, Wallbridge LM, Hardcastle TJ et al (2010) The Arabidopsis RNA-directed DNA methylation Argonautes functionally diverge based on their expression and interaction with target loci. Plant Cell 22:321–334

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • He L, Xie M, Huang J et al (2016) Efficient and specific inhibition of plant microRNA function by anti-microRNA oligonucleotides (AMOs) in vitro and in vivo. Plant Cell Rep 35:933–945

    Article  CAS  PubMed  Google Scholar 

  • He Z, Zhai W, Wen H et al (2011) Two evolutionary histories in the genome of rice: the roles of domestication genes. PLoS Genet 7:e1002100

    Google Scholar 

  • Huang X, Kurata N, Wei X et al (2012) A map of rice genome variation reveals the origin of cultivated rice. Nature 490:497–501

    Article  CAS  PubMed  Google Scholar 

  • International Brachypodium I (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–768

    Article  CAS  Google Scholar 

  • Itoh JI, Kitano H, Matsuoka M et al (2000) Shoot organization genes regulate shoot apical meristem organization and the pattern of leaf primordium initiation in rice. Plant Cell 12:2161–2174

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jacquemin J, Bhatia D, Singh K et al (2013) The international Oryza map alignment project: development of a genus-wide comparative genomics platform to help solve the 9 billion-people question. Curr Opin Plant Biol 16:147–156

    Article  CAS  PubMed  Google Scholar 

  • Jeong DH, Park S, Zhai J et al (2011) Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage. Plant Cell 23:4185–4207

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jiao Y, Wang Y, Xue D et al (2010) Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice. Nat Genet 42:541–544

    Article  CAS  PubMed  Google Scholar 

  • Johnson C, Kasprzewska A, Tennessen K et al (2009) Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res 19:1429–1440

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jones-Rhoades MW, Bartel DP, Bartel B (2004) MicroRNAsand their regulatory roles in plants. Annu Rev Plant Biol 57:19–53

    Article  CAS  Google Scholar 

  • Kapoor M, Arora R, Lama T et al (2008) Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families and their expression analysis during reproductive development and stress in rice. BMC Genomics 9:451

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Khush GS (1997) Origin, dispersal, cultivation and variation of rice. Plant Mol Biol 35:25–34

    Article  CAS  PubMed  Google Scholar 

  • Kolaczkowski B, Hupalo DN, Kern AD (2011) Recurrent adaptation in RNA interference genes across the drosophila phylogeny. Mol Biol Evol 28:1033–1042

    Article  CAS  PubMed  Google Scholar 

  • Komiya R, Ohyanagi H, Niihama M et al (2014) Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs. Plant J 78:385–397

    Article  CAS  PubMed  Google Scholar 

  • Kong X, Zhang M, Xu X et al (2014) System analysis of microRNAs in the development and aluminium stress responses of the maize root system. Plant Biotechnol J 12:1108–1121

    Article  CAS  PubMed  Google Scholar 

  • Lelandais-Briere C, Sorin C, Declerck M et al (2010) Small RNA diversity in plants and its impact in development. Curr Genomics 11:14–23

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Li F, Pignatta D, Bendix C et al (2012) MicroRNA regulation of plant innate immune receptors. Proc Natl Acad Sci USA 109:1790–1795

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu H, Nonomura KI (2016) A wide reprogramming of histone H3 modifications during male meiosis I in rice is dependent on the Argonaute protein MEL1. J Cell Sci 129:3553–3561

    Article  CAS  PubMed  Google Scholar 

  • Liu B, Li P, Li X et al (2005) Loss of function of OsDCL1 affects microRNA accumulation and causes developmental defects in rice. Plant Physiol 139:296–305

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu B, Chen Z, Song X et al (2007) Oryza sativa Dicer-like4 reveals a key role for small interfering RNA silencing in plant development. Plant Cell 19:2705–2718

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Q, Wang H, Zhu L et al (2013a) Genome-wide identification and analysis of miRNA-related single nucleotide polymorphisms (SNPs) in rice. Rice (NY) 6:10

    Article  Google Scholar 

  • Liu Y, Wang Y, Zhu QH et al (2013b) Identification of phasiRNAs in wild rice (Oryza rufipogon). Plant Signal Behav 8:e25079

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Liu Q, Wang H, Hu H et al (2015) Genome-wide identification and evolutionary analysis of positively selected miRNA genes in domesticated rice. Mol Genet Genomics 290:593–602

    Article  CAS  PubMed  Google Scholar 

  • Lu C, Chen J, Zhang Y et al (2012) Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa. Mol Biol Evol 29:1005–1017

    Article  CAS  PubMed  Google Scholar 

  • Ma JB, Ye K, Patel DJ (2004) Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain. Nature 429:318–322

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Margis R, Fusaro AF, Smith NA et al (2006) The evolution and diversification of Dicers in plants. FEBS Lett 580:2442–2450

    Article  CAS  PubMed  Google Scholar 

  • Matzke MA, Mosher RA (2014) RNA-directed DNA methylation: an epigenetic pathway of increasing complexity. Nat Rev Genet 15:394–408

    Article  CAS  PubMed  Google Scholar 

  • Meyer RS, Choi JY, Sanches M et al (2016) Domestication history and geographical adaptation inferred from a SNP map of African rice. Nat Genet 48:1083–1088

    Article  CAS  PubMed  Google Scholar 

  • Mi S, Cai T, Hu Y et al (2008) Sorting of small RNAs into Arabidopsis Argonaute complexes is directed by the 5′ terminal nucleotide. Cell 133:116–127

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miura K, Ikeda M, Matsubara A et al (2010) OsSPL14 promotes panicle branching and higher grain productivity in rice. Nat Genet 42:545–549

    Article  CAS  PubMed  Google Scholar 

  • Mukherjee K, Campos H, Kolaczkowski B (2013) Evolution of animal and plant Dicers: early parallel duplications and recurrent adaptation of antiviral RNA binding in plants. Mol Biol Evol 30:627–641

    Article  CAS  PubMed  Google Scholar 

  • Nagasaki H, Itoh J, Hayashi K et al (2007) The small interfering RNA production pathway is required for shoot meristem initiation in rice. Proc Natl Acad Sci USA 104:14867–14871

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nishimura A, Ito M, Kamiya N et al (2002) OsPNH1 regulates leaf development and maintenance of the shoot apical meristem in rice. Plant J 30:189–201

    Article  CAS  PubMed  Google Scholar 

  • Nonomura K, Morohoshi A, Nakano M et al (2007) A germ cell specific gene of the Argonaute family is essential for the progression of premeiotic mitosis and meiosis during sporogenesis in rice. Plant Cell 19:2583–2594

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nosaka M, Itoh J, Nagato Y et al (2012) Role of transposon-derived small RNAs in the interplay between genomes and parasitic DNA in rice. PLoS Genet 8:e1002953

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nozawa M, Miura S, Nei M (2012) Origins and evolution of microRNA genes in plant species. Genome Biol Evol 4:230–239

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Obbard DJ, Jiggins FM, Bradshaw NJ et al (2011) Recent and recurrent selective sweeps of the antiviral RNAi gene Argonaute-2 in three species of drosophila. Mol Biol Evol 28:1043–1056

    Article  CAS  PubMed  Google Scholar 

  • Oka H-I (1988) Origin of cultivated rice. Elsevier/JSSP, Tokyo

    Google Scholar 

  • Ou-Yang F, Luo QJ, Zhang Y et al (2013) Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice. Funct Integr Genomics 13:207–216

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parker GS, Maity TS, Bass BL (2008) dsRNA binding properties of RDE-4 and TRBP reflect their distinct roles in RNAi. J Mol Biol 384:967–979

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Piriyapongsa J, Jordan IK (2008) Dual coding of siRNAs and miRNAs by plant transposable elements. RNA 14:814–821

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pontier D, Picart C, Roudier F et al (2012) NERD, a plant-specific GW protein, defines an additional RNAi-dependent chromatin-based pathway in Arabidopsis. Mol Cell 48:121–132

    Article  CAS  PubMed  Google Scholar 

  • Project I R G S (2005) The map-based sequence of the rice genome. Nature 436:793–800

    Article  CAS  Google Scholar 

  • Qian Y, Cheng Y, Cheng X et al (2011) Identification and characterization of Dicer-like, Argonaute and RNA-dependent RNA polymerase gene families in maize. Plant Cell Rep 30:1347–1363

    Article  CAS  PubMed  Google Scholar 

  • Rivas FV, Tolia NH, Song JJ et al (2005) Purified Argonaute2 and an siRNA form recombinant human RISC. Nat Struct Mol Biol 12:340–349

    Article  CAS  PubMed  Google Scholar 

  • Ruiz-Ferrer V, Voinnet O (2009) Roles of plant small RNAs in biotic stress responses. Annu Rev Plant Biol 60:485–510

    Article  CAS  PubMed  Google Scholar 

  • Shan Q, Wang Y, Li J et al (2014) Genome editing in rice and wheat using the CRISPR/Cas system. Nat Protoc 9:2395–2410

    Article  CAS  PubMed  Google Scholar 

  • Shivaprasad PV, Chen HM, Patel K et al (2012) A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. Plant Cell 24:859–874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Simon SA, Meyers BC (2011) Small RNA-mediated epigenetic modifications in plants. Curr Opin Plant Biol 14:148–155

    Article  CAS  PubMed  Google Scholar 

  • Slotkin RK, Martienssen R (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8:272–285

    Article  CAS  PubMed  Google Scholar 

  • Song X, Li P, Zhai J et al (2012a) Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. Plant J 69:462–474

    Article  CAS  PubMed  Google Scholar 

  • Song X, Wang D, Ma L et al (2012b) Rice RNA-dependent RNA polymerase 6 acts in small RNA biogenesis and spikelet development. Plant J 71:378–389

    CAS  PubMed  Google Scholar 

  • Stroud H, Greenberg MV, Feng S et al (2013) Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome. Cell 152:352–364

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sunkar R, Chinnusamy V, Zhu J et al (2007) Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci 12:301–309

    Article  CAS  PubMed  Google Scholar 

  • Ta KN, Sabot F, Adam H et al (2016) miR2118-triggered phased siRNAs are differentially expressed during the panicle development of wild and domesticated African rice species. Rice (NY) 9:10

    Article  CAS  Google Scholar 

  • Tajima F (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123:585–595

    CAS  PubMed  PubMed Central  Google Scholar 

  • Takanashi H, Ohnishi T, Mogi M et al (2011) DCL2 is highly expressed in the egg cell in both rice and Arabidopsis. Plant Signal Behav 6:604–606

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tang T, Lu J, Huang J et al (2006) Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication. PLoS Genet 2:e199

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Toriba T, Suzaki T, Yamaguchi T et al (2010) Distinct regulation of adaxial-abaxial polarity in anther patterning in rice. Plant Cell 22:1452–1462

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Urayama S, Moriyama H, Aoki N et al (2010) Knock-down of OsDCL2 in rice negatively affects maintenance of the endogenous dsRNA virus, Oryza sativa endornavirus. Plant Cell Physiol 51:58–67

    Article  CAS  PubMed  Google Scholar 

  • Vaucheret H (2008) Plant Argonautes. Trends Plant Sci 13:350–358

    Article  CAS  PubMed  Google Scholar 

  • Vazquez F, Blevins T, Ailhas J et al (2008) Evolution of Arabidopsis MIR genes generates novel microRNA classes. Nucleic Acids Res 36:6429–6438

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Voinnet O (2009) Origin, biogenesis, and activity of plant microRNAs. Cell 136:669–687

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Shen D, Bo S et al (2010a) Sequence variation and selection of small RNAs in domesticated rice. BMC Evol Biol 10:119

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wang XB, Wu Q, Ito T et al (2010b) RNAi-mediated viral immunity requires amplification of virus-derived siRNAs in Arabidopsis thaliana. Proc Natl Acad Sci USA 107:484–489

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Bai XF, Yan CH et al (2012) Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication. New Phytol 196:914–925

    Article  CAS  PubMed  Google Scholar 

  • Wang MH, Yu Y, Haberer G et al (2014) The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat Genet 46:982–988

    Article  CAS  PubMed  Google Scholar 

  • Wang H, Jiao X, Kong X et al (2016) A signaling cascade from miR444 to RDR1 in rice antiviral RNA silencing pathway. Plant Physiol 170:2365–2377

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wei L, Gu L, Song X et al (2014) Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice. Proc Natl Acad Sci USA 111:3877–3882

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wen M, Xie M, He L et al (2016) Expression variations of miRNAs and mRNAs in rice (Oryza sativa). Genome Biol Evol 8(11):3529–3544. doi:10.1093/gbe/evw252

    Article  PubMed  PubMed Central  Google Scholar 

  • Willmann MR, Endres MW, Cook RT et al (2011) The functions of RNA-dependent RNA polymerases in Arabidopsis. Arabidopsis Book 9:e0146

    Article  PubMed  PubMed Central  Google Scholar 

  • Wing RA, Ammiraju JS, Luo M et al (2005) The Oryza Map Alignment Project: the golden path to unlocking the genetic potential of wild rice species. Plant Mol Biol 59:53–62

    Google Scholar 

  • Wu L, Zhang Q, Zhou H et al (2009) Rice microRNA effector complexes and targets. Plant Cell 21:3421–3435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wu L, Zhou H, Zhang Q et al (2010) DNA methylation mediated by a microRNA pathway. Mol Cell 38:465–475

    Article  CAS  PubMed  Google Scholar 

  • Wu J, Yang Z, Wang Y et al (2015) Viral-inducible Argonaute18 confers broad-spectrum virus resistance in rice by sequestering a host microRNA. Elife 4. doi: 10.7554/eLife.05733

  • Xia R, Xu J, Arikit S et al (2015) Extensive families of miRNAs and PHAS loci in Norway spruce demonstrate the origins of complex phasiRNA networks in seed plants. Mol Biol Evol 32:2905–2918

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xie J, Yang X, Song Y et al (2016) Adaptive evolution and functional innovation of Populus-specific recently evolved microRNAs. New Phytol 213:206–219

    Article  PubMed  CAS  Google Scholar 

  • Yang Y, Zhong J, Ouyang YD et al (2013) The integrative expression and co-expression analysis of the AGO gene family in rice. Gene 528:221–235

    Article  CAS  PubMed  Google Scholar 

  • Yu J, Hu S, Wang J et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92

    Article  CAS  PubMed  Google Scholar 

  • Yu J, Wang J, Lin W et al (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3:e38

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yu YC, Tang T, Qian Q et al (2009) Independent losses of function in a polyphenol oxidase in rice: differentiation in grain discoloration between subspecies and the role of positive selection under domestication (vol 20, pp 2946, 2008). Plant Cell 21:1020–1020

    Article  CAS  Google Scholar 

  • Zhai J, Jeong DH, De Paoli E et al (2011) MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes Dev 25:2540–2553

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhai L, Sun W, Zhang K et al (2014) Identification and characterization of Argonaute gene family and meiosis-enriched Argonaute during sporogenesis in maize. J Integr Plant Biol 56:1042–1052

    Article  CAS  PubMed  Google Scholar 

  • Zhai J, Zhang H, Arikit S et al (2015) Spatiotemporally dynamic, cell-type-dependent premeiotic and meiotic phasiRNAs in maize anthers. Proc Natl Acad Sci USA 112:3146–3151

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Y, Jiang WK, Gao LZ (2011) Evolution of microRNA genes in Oryza sativa and Arabidopsis thaliana: an update of the inverted duplication model. PLoS One 6:e28073

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang YC, Yu Y, Wang CY et al (2013) Overexpression of microRNA OsmiR397 improves rice yield by increasing grain size and promoting panicle branching. Nat Biotech 31: 848–852

    Google Scholar 

  • Zhang QJ, Zhu T, Xia EH et al (2014) Rapid diversification of five Oryza AA genomes associated with rice adaptation. Proc Natl Acad Sci USA 111:E4954–E4962

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang H, Xia R, Meyers BC et al (2015) Evolution, functions, and mysteries of plant Argonaute proteins. Curr Opin Plant Biol 27:84–90

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Xia R, Kuang H et al (2016a) The diversification of plant NBS-LRR defense genes directs the evolution of microRNAs that target them. Mol Biol Evol 33:2692–2705

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang H, Tao Z, Hong H et al (2016b) Transposon-derived small RNA is responsible for modified function of WRKY45 locus. Nat Plants 2:16016

    Article  CAS  PubMed  Google Scholar 

  • Zhu Q, Ge S (2005) Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. New Phytol 167:249–265

    Article  CAS  PubMed  Google Scholar 

  • Zong J, Yao X, Yin J et al (2009) Evolution of the RNA-dependent RNA polymerase (RdRP) genes: duplications and possible losses before and after the divergence of major eukaryotic groups. Gene 447:29–39

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by National Science Foundation of China (31170308 and 91231117 to T.T.), the Science Foundation for Outstanding Young Teachers in Higher Education of Guangdong (Yq2013005) and the Fundamental Research Funds for the Central Universities (16lgjc75) to T. T., and the General Financial Grant from the China Postdoctoral Science Foundation (2013M531981) to M.W.

Author information

Authors and Affiliations

  1. State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, Sun Yat-sen University, Xingangxi Road No. 135, Guangzhou, 510275, Guangdong, China

    Tian Tang, Pei Lin & Yushuai Wang

  2. Program in Emerging Infectious Diseases, Duke–National University of Singapore Graduate Medical School, Singapore, 169857, Singapore

    Ming Wen

Authors
  1. Tian Tang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ming Wen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Pei Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yushuai Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Tian Tang .

Editor information

Editors and Affiliations

  1. Max Delbrück Center for Molecular Medicine, Berlin Institute for Medical Systems Biology, Berlin, Germany

    Nikolaus Rajewsky

  2. Nanobiomedical Center, Adam Mickiewicz University, Poznań, Poland

    Stefan Jurga

  3. Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

    Jan Barciszewski

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Cite this chapter

Tang, T., Wen, M., Lin, P., Wang, Y. (2017). An Evolutionary View of the Biogenesis and Function of Rice Small RNAs. In: Rajewsky, N., Jurga, S., Barciszewski, J. (eds) Plant Epigenetics. RNA Technologies. Springer, Cham. https://doi.org/10.1007/978-3-319-55520-1_4

Download citation

Publish with us

Policies and ethics

Search

Navigation