果树miRNAs研究进展
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摘要
模式植物的研究表明,miRNA作为一种转录后调控因子,在植物的生长发育、逆境胁迫应答等生物学过程中发挥着重要的调节作用。截至目前,虽然已经从多种果树中鉴定了大量的miRNAs,但大多数miRNAs的靶基因和功能特性还不清楚。笔者总结了目前果树中miRNAs的研究进展,特别是miRNAs在葡萄(Vitis vinifera)、桃(Prunus per-sica)、梨(Pyrus spp.)、苹果(Malus domestica)和柑橘(Citrus spp.)等具有重要经济价值的果树等方面的作用,比如调控果树生长发育与果实品质、激素信号转导和环境胁迫应答。探讨了果树miRNAs的前景和研究方向。
The functional studies, mostly from model species, have revealed that miRNAs are majorpost-transcriptional regulators of gene expression in plants and are implicated in fundamental biologicalprocesses, such as plant development and abiotic/biotic stress responses. miRNAs have been detected indifferent parts of fruit trees, including leaves, inflorescence, roots and fruits, and there are significantdifferences in expression levels among different parts or in different developmental processes. With therapid development of sequencing technology, a substantial number of miRNAs have been identified in aseries of fruit crops sofar, while the target mRNAs and functions remain largely uncharacterized. Thepresent review summarizes the progress in miRNA research in fruit crops, especially the role of miR-NAs on the economically important species, such as grapes, peaches, pears, apples, oranges, and so on.Some studies show grapes have the ability of anti-abiotic/biotic stress attributed to the significant ex-pression of miRNAs and the miRNAs also respond to exogenous hormones. The above-mentioned abi-otic/biotic stress responses to miRNAs are also observed in apples, oranges, pears and peaches. In ap-ples, miRNAs regulates the metabolic pathways of IAA, ABA, GA, and thus regulates the process offlower bud differentiation and juvenile period. Moreover, the activation of miRNAs influences the fruitsize of apples as well. Boron and magnesium are implicated in citrus tree development and fruit quality,and some studies have found that miRNAs are widely involved in the response of citrus to boron andmagnesium by regulating auxin synthesis, leaf morphogenesis, antioxidant system and boron transport.In citrus, miRNAs are also active in apomixis, somatic embryogenesis and cytoplasmic male sterile hy-brids. Color is a part of fruit quality. The miRNAs are involved in carotenoid metabolism and then influ-ence the citrus fruit color. Some research have showed orange juice sacs are related to the expression ofmiRNAs, while the quantity of juice sacs affects the taste of citrus. This function of fruit quality regula-tion is also found in pears. The target gene of miRNAs in pears encodes some enzymes, which is relatedto the formation of lignin and stone cells. The role of miRNAs in bud dormancy and dormancy releaseof pears was also detected. Except for the above-mentioned fruit trees, twith some additional fruit trees,the miRNAs and its targe genes have been researched, such as papayas, bananas, strawberries, litchi,etc. We also discuss the future miRNA research prospects in fruit trees:( Ⅰ) To use RLM-RACE, 3'PPMRACE, degradome sequencing and genetic transformation technology to enhance the ability of pre-dicting and validating miRNAs target genes,( Ⅱ) to enhance the research on miRANs and its targetgenes in fruit trees by the creation of efficient transformation germplasm resources of fruit trees, tran-sient transformation, virus vector-mediated transformation or natural variation materials of fruit tree va-rieties for some fruit trees with low efficiency of genetic transformation,,( Ⅲ) to construct molecularregulation of important biological processes mediated by target miRNAs-target genes by means of vari-ous genomics and other bioinformatics methods, to combine the results of functional genomics,and tosystematically analyse the regulation mechanism of plant development or stress response, in which thattarget miRNAs and its Target genes are involved,(Ⅳ) to discover many conservative, non-conservativeand fruit-specific miRNAs and(Ⅴ) to declare how miRNAs regulates some specific traits of fruit trees,such as flower bud formation, bud dormancy, juvenile transformation, fruit coloring and cell engineer-ing breeding, etc.
The functional studies, mostly from model species, have revealed that miRNAs are majorpost-transcriptional regulators of gene expression in plants and are implicated in fundamental biologicalprocesses, such as plant development and abiotic/biotic stress responses. miRNAs have been detected indifferent parts of fruit trees, including leaves, inflorescence, roots and fruits, and there are significantdifferences in expression levels among different parts or in different developmental processes. With therapid development of sequencing technology, a substantial number of miRNAs have been identified in aseries of fruit crops sofar, while the target mRNAs and functions remain largely uncharacterized. Thepresent review summarizes the progress in miRNA research in fruit crops, especially the role of miR-NAs on the economically important species, such as grapes, peaches, pears, apples, oranges, and so on.Some studies show grapes have the ability of anti-abiotic/biotic stress attributed to the significant ex-pression of miRNAs and the miRNAs also respond to exogenous hormones. The above-mentioned abi-otic/biotic stress responses to miRNAs are also observed in apples, oranges, pears and peaches. In ap-ples, miRNAs regulates the metabolic pathways of IAA, ABA, GA, and thus regulates the process offlower bud differentiation and juvenile period. Moreover, the activation of miRNAs influences the fruitsize of apples as well. Boron and magnesium are implicated in citrus tree development and fruit quality,and some studies have found that miRNAs are widely involved in the response of citrus to boron andmagnesium by regulating auxin synthesis, leaf morphogenesis, antioxidant system and boron transport.In citrus, miRNAs are also active in apomixis, somatic embryogenesis and cytoplasmic male sterile hy-brids. Color is a part of fruit quality. The miRNAs are involved in carotenoid metabolism and then influ-ence the citrus fruit color. Some research have showed orange juice sacs are related to the expression ofmiRNAs, while the quantity of juice sacs affects the taste of citrus. This function of fruit quality regula-tion is also found in pears. The target gene of miRNAs in pears encodes some enzymes, which is relatedto the formation of lignin and stone cells. The role of miRNAs in bud dormancy and dormancy releaseof pears was also detected. Except for the above-mentioned fruit trees, twith some additional fruit trees,the miRNAs and its targe genes have been researched, such as papayas, bananas, strawberries, litchi,etc. We also discuss the future miRNA research prospects in fruit trees:( Ⅰ) To use RLM-RACE, 3'PPMRACE, degradome sequencing and genetic transformation technology to enhance the ability of pre-dicting and validating miRNAs target genes,( Ⅱ) to enhance the research on miRANs and its targetgenes in fruit trees by the creation of efficient transformation germplasm resources of fruit trees, tran-sient transformation, virus vector-mediated transformation or natural variation materials of fruit tree va-rieties for some fruit trees with low efficiency of genetic transformation,,( Ⅲ) to construct molecularregulation of important biological processes mediated by target miRNAs-target genes by means of vari-ous genomics and other bioinformatics methods, to combine the results of functional genomics,and tosystematically analyse the regulation mechanism of plant development or stress response, in which thattarget miRNAs and its Target genes are involved,(Ⅳ) to discover many conservative, non-conservativeand fruit-specific miRNAs and(Ⅴ) to declare how miRNAs regulates some specific traits of fruit trees,such as flower bud formation, bud dormancy, juvenile transformation, fruit coloring and cell engineer-ing breeding, etc.
引文
[1] LEE R C,FEINBAUM R L,AMBROS V. The C. elegans heter-ochronic gene lin-4 encodes small RNAs with antisense comple-mentarity to lin-14[J]. Cell,1993,75(5):843-854.
[2] REINHART B J,WEINSTEIN E G,RHOADES M W,BAR-TEL B,BARTEL D P. MicroRNAs in plants[J]. Genes Develop-ment,2002,16(13):1616-1626.
[3] ROGERS K,CHEN X. Biogenesis,Turnover,and mode of ac-tion of plant microRNAs[J]. The Plant Cell,2013,25(7):2383-2399.
[4] JONES-RHOADES M W,BARTEL D P,BARTEL B. MicroR-NAs and their regulatory roles in plants[J]. Annual Review ofPlant Biology,2006,57(1):19-53.
[5] LEE Y,KIM M,HAN J,YEOM K H,LEE S,BAEK S H,KIMV N. MicroRNA genes are transcribed by RNA polymerase II[J]. Embo Journal,2004,23(20):4051-60.
[6] KURIHARA Y,WATANABE Y. Arabidopsis micro-RNA bio-genesis through Dicer-like 1 protein functions[J]. Proceedingsof the National Academy of Sciences of the United States ofAmerica,2004,101(34):12753-12758.
[7] JIE L J,YONG Y Z,BIN Y,JUN L,MEI C X. Methylation pro-tects miRNAs and siRNAs from a 3’-end uridylation activity inArabidopsis[J]. Current Biology,2005,16(15):1501-1507.
[8] PARK M Y,WU G,GONZALEZ-SULSER A,VAUCHERETH,POETHIG R S. Nuclear processing and export of microR-NAs in Arabidopsis[J]. Proceedings of the National Academyof Sciences of the United States of America,2005,102(10):3691-3696.
[9] VOINNET O. Origin,biogenesis,and activity of plant microR-NAs[J]. Cell,2009,136(4):669-687.
[10] LIU Y X,WANG M,WANG X J. Endogenous small RNA clus-ters in plants[J]. Genomics, Proteomics&Bioinformatics,2014,12(2):64.
[11] SOLOFOHARIVELO M C,AP V D W,STEPHAN D,BURG-ER J T,MURRAY S L. MicroRNAs in fruit trees:discovery,di-versity and future research directions[J]. Plant Biology,2014,16(5):856-865.
[12] MICA E,PICCOLO V,DELLEDONNE M,FERRARINI A,PE-ZZOTTI M,CASATI C,FABBRO C D,VALLE G,POLICRITIA,MORGANTE M. High throughput approaches reveal splic-ing of primary microRNA transcripts and tissue specific expres-sion of mature microRNAs in Vitis vinifera[J]. BMC Genomics,2010,11(1):109.
[13] PANTALEO V,SZITTYA G,MOXON S,MIOZZI L,MOULT-ON V,DALMAY T,BURGYAN J. Identification of grapevinemicroRNAs and their targets using high-throughput sequencingand degradome analysis[J]. The Plant Journal,2010,62(6):960-976.
[14] WANG C,HAN J,LIU C,KIBET K N,KAYESH E,SHANG-GUAN L,LI X,FANG J. Identification of microRNAs fromAmur grape(Vitis amurensis Rupr.)by deep sequencing andanalysis of microRNA variations with bioinformatics[J]. BMCGenomics,2012,13(1):122.
[15] SONG C,JIA Q,FANG J,LI F,WANG C,ZHANG Z. Compu-tational identification of citrus microRNAs and target analysis incitrus expressed sequence tags[J]. Plant Biology,2010,12(6):927-934.
[16] XU Q,LIU Y,ZHU A,WU X,YE J,YU K,GUO W,DENG X.Discovery and comparative profiling of microRNAs in a sweetorange red-flesh mutant and its wild type[J]. BMC Genomics,2010,11(1):246.
[17] ZHANG J,AI X,GUO W,PENG S,DENG X,HU C. Identifica-tion of miRNAs and their target genes using deep sequencingand degradome analysis in Trifoliate Orange[Poncirus trifoliate(L.)Raf][J]. Molecular Biotechnology,2012,51(1):44-57.
[18] XIA R,ZHU H,AN Y Q,BEERS E P,LIU Z R. Apple miRNAsand tasiRNAs with novel regulatory networks[J]. Genome Biol-ogy,2012,13(6):R47.
[19] BARAKAT A,SRIRAM A,PARK J,ZHEBENTYAYEVA T,MAIN D,ABBOTT A. Genome wide identification of chillingresponsive microRNAs in Prunus persica[J]. BMC Genomics,2012,13(1):481.
[20] ELDEM V,?ELIKKOL AK AY U,OZHUNER E,BAK?R Y,URANBEY S,UNVER T. Genome-wide identification of miR-NAs responsive to drought in peach(Prunus persica)by high-throughput deep sequencing[J]. PLoS One,2012,7(12):e50298.
[21] ARYAL R,YANG X,YU Q,SUNKAR R,LI L,MING R.Asymmetric purine-pyrimidine distribution in cellular smallRNA population of papaya[J]. BMC Genomics,2012,13(1):682.
[22] LIANG G,LI Y,HE H,WANG F,YU D. Identification of miR-NAs and miRNA-mediated regulatory pathways in Carica papa-ya[J]. Planta,2013,238(4):739-752.
[23] DSOUZA M,LARSEN N,OVERBEEK R. Searching for pat-terns in genomic data[J]. Trends in Genetics,1997,13(12):497-498.
[24] XIE F L,HUANG S Q,GUO K,XIANG A L,ZHU Y Y,NIE L,YANG Z M. Computational identification of novel microRNAsand targets in Brassica napus[J]. FEBS Letters,2007,581(7):1464-1474.
[25] ZHANG Y. miRU:an automated plant miRNA target predictionserver[J]. Nucleic Acids Research,2005,33(Suppl. 2):W701-W704.
[26] DAI X,ZHAO P X. psRNATarget:a plant small RNA targetanalysis server[J]. Nucleic Acids Research,2011,39:155-159.
[27] ANDRéS-LEóN E,Nú?EZ-TORRES R,ROJAS A M. miAR-ma-Seq:a comprehensive tool for miRNA,mRNA and circRNAanalysis[J]. Scientific Reports,2016,6:25749.
[28] STEPHEN D,SSU-WEI H,SHAWN C,B. G R,J. H J,MAT-TEO P. A na?ve Bayesian classifier for identifying plant microR-NAs[J]. The Plant Journal,2016,86(6):481-492.
[29] BONNET E,WUYTS J,ROUZ P,VAN DE PEER Y. Detectionof 91 potential conserved plant microRNAs in Arabidopsis thali-ana and Oryza sativa identifies important target genes[J]. Proceedings of the National Academy of Sciences of the United Statesof America,2004,101(31):11511-11516.
[30] JONES-RHOADES M W,BARTEL D P. Computational identifi-cation of plant microRNAs and their targets,including a stress-induced miRNA[J]. Molecular Cell,2004,14(6):787-799.
[31] DEZULIAN T,REMMERT M,PALATNIK J F,WEIGEL D,HUSON D H. Identification of plant microRNA homologs[J].Bioinformatics,2006,22(3):359-360.
[32] JAILLON O, AURY J M, NOEL B,……, WINCKER P Thegrapevine genome sequence suggests ancestral hexaploidizationin major angiosperm phyla[J]. Nature,2007,449(7161):463.
[33] KULLAN J B,PINTO D L P,BERTOLINI E,FASOLI M,ZE-NONI S,TORNIELLI G B,PEZZOTTI M,MEYERS B C,FA-RINA L,PèM E,MICA E. miRVine:a microRNA expressionatlas of grapevine based on small RNA sequencing[J]. BMC Ge-nomics,2015,16(1):393.
[34] ALABI O J,ZHENG Y,JAGADEESWARAN G,SUNKAR R,NAIDU R A. High-throughput sequence analysis of small RNAsin grapevine(Vitis vinifera L.)affected by grapevine leafrolldisease[J]. Molecular Plant Pathology,2012,13(9):1060-1076.
[35] PAGLIARANI C,VITALI M,FERRERO M,VITULO N,IN-CARBONE M,LOVISOLO C,VALLE G,SCHUBERT A. Ac-cumulation of microRNAs differentially modulated by droughtis affected by grafting in grapevine[J]. Plant Physiology,2017,173(4):2180-2195.
[36] PAIM D L, BRANCADORO L, DAL SANTO S, DELORENZIS G,PEZZOTTI M,MEYERS B C,P M E,MICAE. The influence of genotype and environment on small RNAprofiles in grapevine berry[J]. Frontiers Plant Science,2016,7:1459.
[37] ZHAO F,WANG C,HAN J,ZHU X,LI X,WANG X,FANG J.Characterization of miRNAs responsive to exogenous ethylenein grapevine berries at whole genome level[J]. Functional&In-tegrative Genomics,2017,17(2):213-235.
[38] WANG M,SUN X,WANG C,CUI L,CHEN L,ZHANG C,SHANGGUAN L,FANG J. Characterization of miR061 and itstarget genes in grapevine responding to exogenous gibberellicacid[J]. Functional&Integrative Genomics,2017,17(5):537-549.
[39] YE K,CHEN Y,HU X,GUO J. Computational identification ofmicroRNAs and their targets in apple[J]. Genes&Genomics,2013,35(3):377-385.
[40] GLEAVE A P,AMPOMAH-DWAMENA C,BERTHOLD S,DEJNOPRAT S,KARUNAIRETNAM S,NAIN B,WANG YY,CROWHURST R N,MACDIARMID R M. Identificationand characterisation of primary microRNAs from apple(Malusdomestica cv. Royal Gala)expressed sequence tags[J]. Tree Ge-netics&Genomes,2008,4(2):343-358.
[41] VARKONYI-GASIC E,GOULD N,SANDANAYAKA M,SUTHERLAND P,MACDIARMID R M. Characterisation ofmicroRNAs from apple(Malus domestica‘Royal Gala’)vascu-lar tissue and phloem sap[J]. BMC Plant Biology,2010,10(1):159.
[42] XING L,ZHANG D,LI Y,ZHAO C,ZHANG S,SHEN Y,ANN,HAN M. Genome-wide identification of vegetative phasetransition-associated microRNAs and target predictions using de-gradome sequencing in Malus hupehensis[J]. BMC Genomics,2014,15(1):1125.
[43] GUO X,MA Z,ZHANG Z,CHENG L,ZHANG X,LI T. SmallRNA-sequencing links physiological changes and RdDM pro-cess to vegetative-to-floral transition in apple[J]. Frontiers PlantScience,2017,8:873.
[44] XING L,ZHANG D,ZHAO C,LI Y,MA J,AN N,HAN M.Shoot bending promotes flower bud formation by miRNA-medi-ated regulation in apple(Malus domestica Borkh.)[J]. PlantBiotechnology Journal,2016,14(2):749-770.
[45] SONG C,ZHANG D,ZHENG L,ZHANG J,ZHANG B,LUOW,LI Y,LI G,MA J,HAN M. miRNA and degradome sequenc-ing reveal miRNA and their target genes that may mediate shootgrowth in spur type mutant‘Yanfu 6’[J]. Frontiers Plant Sci-ence,2017,8:441.
[46] AN N,FAN S,YANG Y,CHEN X L,DONG F,WANG Y B,XING L B,ZHAO C P,HAN M Y,Identification and character-ization of miRNAs in self-rooted and grafted Malus reveals criti-cal networks associated with flowering[J]. International Journalof Molecular Sciences,2018,19(8):2384.
[47] YU X,DU B,GAO Z,ZHANG S,TU X,CHEN X,ZHANG Z,QU S. Apple ring rot-responsive putative microRNAs revealedby high-throughput sequencing in Malus×domestica Borkh.[J]. Molecular Biology Reports,2014,41(8):5273-5286.
[48] MA C,LU Y,BAI S,ZHANG W,DUAN X,MENG D,WANGZ,WANG A,ZHOU Z,LI T. Cloning and Characterization ofmiRNAs and their targets,including a novel miRNA-targetedNBS-LRR protein class gene in apple(Golden Delicious)[J].Molecular Plant,2014,7(1):218-230.
[49] KAJA E,SZCZE?NIAK M W,JENSEN P J,AXTELL M J,MCNELLIS T,MAKA?OWSKA I. Identification of apple miR-NAs and their potential role in fire blight resistance[J]. Tree Ge-netics&Genomes,2015,11(1):812.
[50] YAO J, XU J, CORNILLE A,……, GLEAVE A P. A microRNAallele that emerged prior to apple domestication may underliefruit size evolution[J]. The Plant Journal,2015,84(2):417-427.
[51] YU X Y,HOU Y J,CHEN W P,WANG S H,WANG P H,QUS C. Malus hupehensis miR168 targets to ARGONAUTE1 andcontributes to the resistance against Botryosphaeria dothidea in-fection by altering defense responses[J]. Plant Cell Physiol,2017,58(9):1541-1557.
[52] SUNKAR R,JAGADEESWARAN G. In silico identification ofconserved microRNAs in large number of diverse plant species[J]. BMC Plant Biology,2008,8(1):37.
[53] WU X,LIU M,XU Q,GUO W. Identification and characteriza-tion of microRNAs from citrus expressed sequence tags[J].Tree Genetics&Genomes,2011,7(1):117-133.
[54] ZHANG B,PAN X,WANG Q,COBB G P,ANDERSON T A.Identification and characterization of new plant microRNAs us-ing EST analysis[J]. Cell Research,2005,15(5):336-360.
[55] FANG Y N,QIU W M,WANG Y,WU X M,XU Q,GUO W W.Identification of differentially expressed microRNAs from amale sterile Ponkan mandarin(Citrus reticulata Blanco)and itsfertile wild type by small RNA and degradome sequencing[J].Tree Genetics&Genomes,2014,10(6):1567-1581.
[56] SONG C,CHEN W,ZHANG C,KORIR N K,YU H,MA Z,FANG J. Deep sequencing discovery of novel and conserved mi-croRNAs in trifoliate orange(Citrus trifoliata)[J]. BMC Ge-nomics,2010,11(1):431.
[57] ZHANG X,LI X,LIU J. Identification of conserved and novelcold-responsive microRNAs in Trifoliate Orange(Poncirus tri-foliata(L.)Raf.)using high-throughput sequencing[J]. PlantMolecular Biology Reporter,2014,32(2):328-341.
[58] LENG X P,SONG C N,HAN J,SHANGGUAN L F,FANG JG,WANG C. Determination of the precise sequences of compu-tationally predicted miRNAs in Citrus reticulata by miR-RACEand characterization of the related target genes using RLM-RACE[J]. Gene,2016,575(2):498-505.
[59] LU Y B,YANG L T,QI Y P,LI Y,LI Z,CHEN Y B,HUANGZ R,CHEN L S. Identification of boron-deficiency-responsivemicroRNAs in Citrus sinensis roots by Illumina sequencing[J].BMC Plant Biology,2014,14(1):123.
[60] LU Y B,QI Y P,YANG L T,GUO P,LI Y,CHEN L S. Boron-deficiency-responsive microRNAs and their targets in Citrus si-nensis leaves[J]. BMC Plant Biology,2015,15(1):271.
[61] HUANG J H,QI Y P,WEN S X,GUO P,CHEN X M,CHEN LS. Illumina microRNA profiles reveal the involvement ofmiR397a in Citrus adaptation to long-term boron toxicity viamodulating secondary cell-wall biosynthesis[J]. Scientific Re-ports,2016,6:22900.
[62] JIN L F,LIU Y Z,YIN X X,PENG S A. Transcript analysis ofcitrus miRNA397 and its target LAC7 reveals a possible role inresponse to boron toxicity[J]. Acta Physiologiae Plantarum,2016,38(1):18.
[63] RAWAT N,KIRAN S P,DU D,GMITTER F G,DENG Z. Com-prehensive meta-analysis,co-expression,and miRNA nested net-work analysis identifies gene candidates in citrus against Huan-glongbing disease[J]. BMC Plant Biology,2015,15(1):184.
[64] ZHAO H.W.,SUN R.B.,ALBRECHT U,PADMANABHAN C,WANG A,COFFEY M,GIRKE T,WANG,Z H,CLOSE T J,ROOSE,M,YOKOMI R K,FOLIMONOVA S,VIDALAKISG,ROUSE R,BOWMAN K D,JIN H L. Small RNA profilingreveals phosphorus deficiency as a contributing factor in symp-tom expression for Citrus Huanglongbing disease[J]. MolecularPlant,2013,6(2):301-310.
[65] XIE R,ZHANG J,MA Y,PAN X,DONG C,PANG S,HE S,DENG L,YI S,ZHENG Y,LV Q. Combined analysis of mRNAand miRNA identifies dehydration and salinity responsive keymolecular players in citrus roots[J]. Scientific Reports,2017,7:42094.
[66] WU X,KOU S,LIU Y,FANG Y,XU Q,GUO W. Genomewideanalysis of small RNAs in nonembryogenic and embryogenic tis-sues of citrus:microRNA-and siRNA-mediated transcript cleav-age involved in somatic embryogenesis[J]. Plant BiotechnologyJournal,2015,13(3):383-394.
[67] LONG J M,LIU Z,WU X M,FANG Y N,JIA H H,XIE Z Z,DENG X X,GUO W W. Genome-scale mRNA and small RNAtranscriptomic insights into initiation of citrus apomixis[J]. Jour-nal of Experimental Botany,2016,67(19):5743-5756.
[68] FANG Y N,ZHENG B B,WANG L,YANG W,WU X M,XUQ,GUO W W. High-throughput sequencing and degradomeanalysis reveal altered expression of miRNAs and their targetsin a male-sterile cybrid pummelo(Citrus grandis)[J]. BMC Ge-nomics,2016,17(1):591.
[69] ZHANG J,WANG M,CHENG F,DAI C,SUN Y,LU J,HUANG Y,LI M,HE Y,WANG F,FAN B. Identification of mi-croRNAs correlated with citrus granulation based on bioinfor-matics and molecular biology analysis[J]. Postharvest Biologyand Technology,2016,118:59-67.
[70] NIU Q F,QIAN M J,LIU G Q,YANG F X,TENG Y W. Ageome-wide identification and characterization of mircoRNAsand their targets in‘Suli’pear(Pyrus pyrifolia white peargroup)[J]. Planta,2013,238(6):1095-1112.
[71] WU J,WANG D,LIU Y,WANG L,QIAO X,ZHANG S. Identi-fication of miRNAs involved in pear fruit development and qual-ity[J]. BMC Genomics,2014,15(1):953.
[72] HENG W,JIA B,HUANG H N,YANG J Y,WANG Z T,LIUP,LIU L,YE Z F,ZHU L W. Identification of russet-associatedmicroRNAs in the exocarp of a Dangshansuli pear mutant(Py-rus bretschneideri Rehd.)by high-throughput sequencing[J].Tree Genetics&Genomes,2016,12(6):107.
[73] CHENG X,YAN C,ZHANG J,MA C,LI S,JIN Q,ZHANG N,CAO Y,LIN Y,CAI Y. The effect of different pollination on theexpression of Dangshan Su Pear microRNA[J]. BioMed Re-search International,2017,2:1-18.
[74] BAI S,SAITO T,ITO A,TUAN P A,XU Y,TENG Y,MORI-GUCHI T. Small RNA and PARE sequencing in flower bud re-veal the involvement of sRNAs in endodormancy release of Jap-anese pear(Pyrus pyrifolia‘Kosui’)[J]. BMC Genomics,2016,17(1):230.
[75] NIU Q F,LI J Z,CAI D Y,QIAN M J,JIA H M,BAI S L,HUS-SAIN S,LIU G Q,TENG Y W,ZHENG X Y. Dormancy-associ-ated MADS-box genes and microRNAs jointly control dorman-cy transition in pear(Pyrus pyrifolia white pear group)flowerbud[J]. Journal of Experimental Botany,2016,67(1):239-257.
[76] ZHANG Y,YU M,YU H,HAN J,SONG C,MA R,FANG J.Computational identification of microRNAs in peach expressedsequence tags and validation of their precise sequences by miR-RACE[J]. Molecular Biology Reports,2012,39(2):1975-1987.
[77] LUO X,GAO Z,SHI T,CHENG Z,ZHANG Z,NI Z. Identifica-tion of miRNAs and their target genes in peach(Prunus persicaL.)using high-throughput sequencing and degradome analysis[J]. PLoS One,2013,8(11):e79090.
[78] ZHANG Y,BAI Y,HAN J,CHEN M,KAYESH E,JIANG W,FANG J. Bioinformatics prediction of miRNAs in the Prunuspersica genome with validation of their precise sequences bymiR-RACE[J]. Journal of Plant Physiology,2013,170(1):80-92.
[79] ZHANG Y,HAN J,YU M,MA R,PERVAIZ T,FANG J. Char-acterization of target mRNAs for Prunus persica microRNAs us-ing an integrated strategy of PLM-RACE,PPM-RACE and qRT-PCR[J]. Scientia Horticulturae,2014,170:8-16.
[80] ZHANG C,ZHANG B,MA R,YU M,GUO S,GUO L,KORIRN K. Identification of known and novel microRNAs and theirtargets in peach(Prunus persica)fruit by high-throughput se-quencing[J]. PLoS One,2016,11(7):e0159253.
[81] PEKMEZCI A K,KARAKüLAH G,UNVER T. Discovery ofdrought-responsive transposable element-related peach miRNAs[J]. BioRxiv,2017,5:143115.
[82] ARYAL R,JAGADEESWARAN G,ZHENG Y,YU Q,SUNK-AR R,MING R. Sex specific expression and distribution ofsmall RNAs in papaya[J]. BMC Genomics,2014,15(1):20.
[83] BI F,MENG X,MA C,YI G. Identification of miRNAs in-volved in fruit ripening in Cavendish bananas by deep sequenc-ing[J]. BMC Genomics,2015,16(1):776.
[84] DAN M,HUANG M H,LIAO F,QIN R Y,LIANG X J,ZHANG E Z,HUANG M K,HUANG Z Y,HE Q G. Identifica-tion of ethylene responsive miRNAs and their targets from new-ly harvested banana fruits using high-throughput sequencing[J].Journal of Agricultural and Food Chemistry,2018,66(40):10628-10639.
[85] SAMPANGI-RAMAIAH M H,RAVISHANKAR K V,REKHAA,HUNASHIKATTI L R. A contig-based computational predic-tion of conserved miRNAs and their probable role in regulationof cuticular wax biosynthesis in banana[J]. Plant Molecular Bi-ology Reporter,2016,35(2):1-12.
[86] XIA R,YE S,LIU Z,MEYERS B C,LIU Z. Novel and recentlyevolved microRNA clusters regulate expansive F-BOX gene net-works through phased small interfering RNAs in wild diploidstrawberry[J]. Plant Physiology,2015,169(1):594-610.
[87]?URBANOVSKI N,BRILLI M,MOSER M,SI-AMMOUR A.A highly specific microRNA-mediated mechanism silencesLTR retrotransposons of strawberry[J]. The Plant Journal,2016,85(1):70-82.
[88] WANG Y,ZHANG J X.,CUI W X.,GUAN C Y,MAO W J,ZHANG Z H. Improvement in fruit quality by overexpressingmiR399a in woodland strawberry[J]. Journal of Agriculturaland Food Chemistry,2017,65(34):7361-7370.
[89] YAO F,ZHU H,YI C,QU H,JIANG Y. MicroRNAs and tar-gets in senescent litchi fruit during ambient storage and post-cold storage shelf life[J]. BMC Plant Biology,2015,15(1):181.
[90] LIU R,LAI B,HU B,QIN Y,HU G,ZHAO J. Identification ofmicroRNAs and their target genes related to the accumulation ofanthocyanins in Litchi chinensis by high-throughput sequencingand degradome analysis[J]. Frontiers Plant Science,2017,7:2059.
[91] JIA L,ZHANG D,QI X,MA B,XIANG Z,HE N. Identificationof the conserved and novel miRNAs in mulberry by high-throughput sequencing[J]. PLoS One,2014,9(8):e104409.
[92] BALOCH I A,BAROZAI M Y K,DIN M. Identification andcharacterization of 25 micrornas and their targeted proteins inapricot(Prunus armeniaca L.)[J]. Journal of Animal&PlantSciences,2015,25(5):1466-1476.
[93] AVSAR B,ESMAEILI ALIABADI D. Putative microRNA anal-ysis of the kiwifruit Actinidia chinensis through genomic data[J]. International Journal of Life Sciences Biotechnology andPharma Research,2015,4(2):96-99.
[94] SAMINATHAN T,BODUNRIN A,SINGH N V,DEVARAJANR,NIMMAKAYALA P,JEFF M,ARADHYA M,REDDY U K.Genome-wide identification of microRNAs in pomegranate(Pu-nica granatum L.)by high-throughput sequencing[J]. BMCPlant Biology,2016,16(1):122.
[95] YUE J,LU X,ZHANG H,GE J,GAO X,LIU Y. Identificationof conserved and novel microRNAs in blueberry[J]. FrontiersPlant Science,2017,8:1155.
[96] CHEN M,MENG Y,MAO C,CHEN D,WU P. Methodologicalframework for functional characterization of plant microRNAs[J]. Journal of Experimental Botany,2010,61(9):2271-2280.
[97] SCHWAB R,OSSOWSKI S,WARTHMANN N,WEIGEL D.Directed gene silencing with artificial microRNAs[J]. MethodsMol Biology,2010,592(592):71-88.
[98] TANG G,YAN J,GU Y,QIAO M,FAN R,MAO Y,TANG X.Construction of short tandem target mimic(STTM)to block thefunctions of plant and animal microRNAs[J]. Methods,2012,58(2):118-125.
[99] YAN J,GU Y,JIA X,KANG W,PAN S,TANG X,CHEN X,TANG G. Effective small RNA destruction by the expression ofa short tandem target mimic in Arabidopsis[J]. The Plant Cell,2012,24(2):415-427.
[100] ZHU H,XIA R,ZHAO B,AN Y,DARDICK C D,CALLAH-AN A M,LIU Z. Unique expression,processing regulation,andregulatory network of peach(Prunus persica)miRNAs[J].BMC Plant Biology,2012,12(1):149.
[101] SONG C,YU M,HAN J,WANG C,LIU H,ZHANG Y,FANGJ. Validation and characterization of Citrus sinensis microRNAsand their target genes[J]. BMC Research Notes,2012,5(1):235.
[2] REINHART B J,WEINSTEIN E G,RHOADES M W,BAR-TEL B,BARTEL D P. MicroRNAs in plants[J]. Genes Develop-ment,2002,16(13):1616-1626.
[3] ROGERS K,CHEN X. Biogenesis,Turnover,and mode of ac-tion of plant microRNAs[J]. The Plant Cell,2013,25(7):2383-2399.
[4] JONES-RHOADES M W,BARTEL D P,BARTEL B. MicroR-NAs and their regulatory roles in plants[J]. Annual Review ofPlant Biology,2006,57(1):19-53.
[5] LEE Y,KIM M,HAN J,YEOM K H,LEE S,BAEK S H,KIMV N. MicroRNA genes are transcribed by RNA polymerase II[J]. Embo Journal,2004,23(20):4051-60.
[6] KURIHARA Y,WATANABE Y. Arabidopsis micro-RNA bio-genesis through Dicer-like 1 protein functions[J]. Proceedingsof the National Academy of Sciences of the United States ofAmerica,2004,101(34):12753-12758.
[7] JIE L J,YONG Y Z,BIN Y,JUN L,MEI C X. Methylation pro-tects miRNAs and siRNAs from a 3’-end uridylation activity inArabidopsis[J]. Current Biology,2005,16(15):1501-1507.
[8] PARK M Y,WU G,GONZALEZ-SULSER A,VAUCHERETH,POETHIG R S. Nuclear processing and export of microR-NAs in Arabidopsis[J]. Proceedings of the National Academyof Sciences of the United States of America,2005,102(10):3691-3696.
[9] VOINNET O. Origin,biogenesis,and activity of plant microR-NAs[J]. Cell,2009,136(4):669-687.
[10] LIU Y X,WANG M,WANG X J. Endogenous small RNA clus-ters in plants[J]. Genomics, Proteomics&Bioinformatics,2014,12(2):64.
[11] SOLOFOHARIVELO M C,AP V D W,STEPHAN D,BURG-ER J T,MURRAY S L. MicroRNAs in fruit trees:discovery,di-versity and future research directions[J]. Plant Biology,2014,16(5):856-865.
[12] MICA E,PICCOLO V,DELLEDONNE M,FERRARINI A,PE-ZZOTTI M,CASATI C,FABBRO C D,VALLE G,POLICRITIA,MORGANTE M. High throughput approaches reveal splic-ing of primary microRNA transcripts and tissue specific expres-sion of mature microRNAs in Vitis vinifera[J]. BMC Genomics,2010,11(1):109.
[13] PANTALEO V,SZITTYA G,MOXON S,MIOZZI L,MOULT-ON V,DALMAY T,BURGYAN J. Identification of grapevinemicroRNAs and their targets using high-throughput sequencingand degradome analysis[J]. The Plant Journal,2010,62(6):960-976.
[14] WANG C,HAN J,LIU C,KIBET K N,KAYESH E,SHANG-GUAN L,LI X,FANG J. Identification of microRNAs fromAmur grape(Vitis amurensis Rupr.)by deep sequencing andanalysis of microRNA variations with bioinformatics[J]. BMCGenomics,2012,13(1):122.
[15] SONG C,JIA Q,FANG J,LI F,WANG C,ZHANG Z. Compu-tational identification of citrus microRNAs and target analysis incitrus expressed sequence tags[J]. Plant Biology,2010,12(6):927-934.
[16] XU Q,LIU Y,ZHU A,WU X,YE J,YU K,GUO W,DENG X.Discovery and comparative profiling of microRNAs in a sweetorange red-flesh mutant and its wild type[J]. BMC Genomics,2010,11(1):246.
[17] ZHANG J,AI X,GUO W,PENG S,DENG X,HU C. Identifica-tion of miRNAs and their target genes using deep sequencingand degradome analysis in Trifoliate Orange[Poncirus trifoliate(L.)Raf][J]. Molecular Biotechnology,2012,51(1):44-57.
[18] XIA R,ZHU H,AN Y Q,BEERS E P,LIU Z R. Apple miRNAsand tasiRNAs with novel regulatory networks[J]. Genome Biol-ogy,2012,13(6):R47.
[19] BARAKAT A,SRIRAM A,PARK J,ZHEBENTYAYEVA T,MAIN D,ABBOTT A. Genome wide identification of chillingresponsive microRNAs in Prunus persica[J]. BMC Genomics,2012,13(1):481.
[20] ELDEM V,?ELIKKOL AK AY U,OZHUNER E,BAK?R Y,URANBEY S,UNVER T. Genome-wide identification of miR-NAs responsive to drought in peach(Prunus persica)by high-throughput deep sequencing[J]. PLoS One,2012,7(12):e50298.
[21] ARYAL R,YANG X,YU Q,SUNKAR R,LI L,MING R.Asymmetric purine-pyrimidine distribution in cellular smallRNA population of papaya[J]. BMC Genomics,2012,13(1):682.
[22] LIANG G,LI Y,HE H,WANG F,YU D. Identification of miR-NAs and miRNA-mediated regulatory pathways in Carica papa-ya[J]. Planta,2013,238(4):739-752.
[23] DSOUZA M,LARSEN N,OVERBEEK R. Searching for pat-terns in genomic data[J]. Trends in Genetics,1997,13(12):497-498.
[24] XIE F L,HUANG S Q,GUO K,XIANG A L,ZHU Y Y,NIE L,YANG Z M. Computational identification of novel microRNAsand targets in Brassica napus[J]. FEBS Letters,2007,581(7):1464-1474.
[25] ZHANG Y. miRU:an automated plant miRNA target predictionserver[J]. Nucleic Acids Research,2005,33(Suppl. 2):W701-W704.
[26] DAI X,ZHAO P X. psRNATarget:a plant small RNA targetanalysis server[J]. Nucleic Acids Research,2011,39:155-159.
[27] ANDRéS-LEóN E,Nú?EZ-TORRES R,ROJAS A M. miAR-ma-Seq:a comprehensive tool for miRNA,mRNA and circRNAanalysis[J]. Scientific Reports,2016,6:25749.
[28] STEPHEN D,SSU-WEI H,SHAWN C,B. G R,J. H J,MAT-TEO P. A na?ve Bayesian classifier for identifying plant microR-NAs[J]. The Plant Journal,2016,86(6):481-492.
[29] BONNET E,WUYTS J,ROUZ P,VAN DE PEER Y. Detectionof 91 potential conserved plant microRNAs in Arabidopsis thali-ana and Oryza sativa identifies important target genes[J]. Proceedings of the National Academy of Sciences of the United Statesof America,2004,101(31):11511-11516.
[30] JONES-RHOADES M W,BARTEL D P. Computational identifi-cation of plant microRNAs and their targets,including a stress-induced miRNA[J]. Molecular Cell,2004,14(6):787-799.
[31] DEZULIAN T,REMMERT M,PALATNIK J F,WEIGEL D,HUSON D H. Identification of plant microRNA homologs[J].Bioinformatics,2006,22(3):359-360.
[32] JAILLON O, AURY J M, NOEL B,……, WINCKER P Thegrapevine genome sequence suggests ancestral hexaploidizationin major angiosperm phyla[J]. Nature,2007,449(7161):463.
[33] KULLAN J B,PINTO D L P,BERTOLINI E,FASOLI M,ZE-NONI S,TORNIELLI G B,PEZZOTTI M,MEYERS B C,FA-RINA L,PèM E,MICA E. miRVine:a microRNA expressionatlas of grapevine based on small RNA sequencing[J]. BMC Ge-nomics,2015,16(1):393.
[34] ALABI O J,ZHENG Y,JAGADEESWARAN G,SUNKAR R,NAIDU R A. High-throughput sequence analysis of small RNAsin grapevine(Vitis vinifera L.)affected by grapevine leafrolldisease[J]. Molecular Plant Pathology,2012,13(9):1060-1076.
[35] PAGLIARANI C,VITALI M,FERRERO M,VITULO N,IN-CARBONE M,LOVISOLO C,VALLE G,SCHUBERT A. Ac-cumulation of microRNAs differentially modulated by droughtis affected by grafting in grapevine[J]. Plant Physiology,2017,173(4):2180-2195.
[36] PAIM D L, BRANCADORO L, DAL SANTO S, DELORENZIS G,PEZZOTTI M,MEYERS B C,P M E,MICAE. The influence of genotype and environment on small RNAprofiles in grapevine berry[J]. Frontiers Plant Science,2016,7:1459.
[37] ZHAO F,WANG C,HAN J,ZHU X,LI X,WANG X,FANG J.Characterization of miRNAs responsive to exogenous ethylenein grapevine berries at whole genome level[J]. Functional&In-tegrative Genomics,2017,17(2):213-235.
[38] WANG M,SUN X,WANG C,CUI L,CHEN L,ZHANG C,SHANGGUAN L,FANG J. Characterization of miR061 and itstarget genes in grapevine responding to exogenous gibberellicacid[J]. Functional&Integrative Genomics,2017,17(5):537-549.
[39] YE K,CHEN Y,HU X,GUO J. Computational identification ofmicroRNAs and their targets in apple[J]. Genes&Genomics,2013,35(3):377-385.
[40] GLEAVE A P,AMPOMAH-DWAMENA C,BERTHOLD S,DEJNOPRAT S,KARUNAIRETNAM S,NAIN B,WANG YY,CROWHURST R N,MACDIARMID R M. Identificationand characterisation of primary microRNAs from apple(Malusdomestica cv. Royal Gala)expressed sequence tags[J]. Tree Ge-netics&Genomes,2008,4(2):343-358.
[41] VARKONYI-GASIC E,GOULD N,SANDANAYAKA M,SUTHERLAND P,MACDIARMID R M. Characterisation ofmicroRNAs from apple(Malus domestica‘Royal Gala’)vascu-lar tissue and phloem sap[J]. BMC Plant Biology,2010,10(1):159.
[42] XING L,ZHANG D,LI Y,ZHAO C,ZHANG S,SHEN Y,ANN,HAN M. Genome-wide identification of vegetative phasetransition-associated microRNAs and target predictions using de-gradome sequencing in Malus hupehensis[J]. BMC Genomics,2014,15(1):1125.
[43] GUO X,MA Z,ZHANG Z,CHENG L,ZHANG X,LI T. SmallRNA-sequencing links physiological changes and RdDM pro-cess to vegetative-to-floral transition in apple[J]. Frontiers PlantScience,2017,8:873.
[44] XING L,ZHANG D,ZHAO C,LI Y,MA J,AN N,HAN M.Shoot bending promotes flower bud formation by miRNA-medi-ated regulation in apple(Malus domestica Borkh.)[J]. PlantBiotechnology Journal,2016,14(2):749-770.
[45] SONG C,ZHANG D,ZHENG L,ZHANG J,ZHANG B,LUOW,LI Y,LI G,MA J,HAN M. miRNA and degradome sequenc-ing reveal miRNA and their target genes that may mediate shootgrowth in spur type mutant‘Yanfu 6’[J]. Frontiers Plant Sci-ence,2017,8:441.
[46] AN N,FAN S,YANG Y,CHEN X L,DONG F,WANG Y B,XING L B,ZHAO C P,HAN M Y,Identification and character-ization of miRNAs in self-rooted and grafted Malus reveals criti-cal networks associated with flowering[J]. International Journalof Molecular Sciences,2018,19(8):2384.
[47] YU X,DU B,GAO Z,ZHANG S,TU X,CHEN X,ZHANG Z,QU S. Apple ring rot-responsive putative microRNAs revealedby high-throughput sequencing in Malus×domestica Borkh.[J]. Molecular Biology Reports,2014,41(8):5273-5286.
[48] MA C,LU Y,BAI S,ZHANG W,DUAN X,MENG D,WANGZ,WANG A,ZHOU Z,LI T. Cloning and Characterization ofmiRNAs and their targets,including a novel miRNA-targetedNBS-LRR protein class gene in apple(Golden Delicious)[J].Molecular Plant,2014,7(1):218-230.
[49] KAJA E,SZCZE?NIAK M W,JENSEN P J,AXTELL M J,MCNELLIS T,MAKA?OWSKA I. Identification of apple miR-NAs and their potential role in fire blight resistance[J]. Tree Ge-netics&Genomes,2015,11(1):812.
[50] YAO J, XU J, CORNILLE A,……, GLEAVE A P. A microRNAallele that emerged prior to apple domestication may underliefruit size evolution[J]. The Plant Journal,2015,84(2):417-427.
[51] YU X Y,HOU Y J,CHEN W P,WANG S H,WANG P H,QUS C. Malus hupehensis miR168 targets to ARGONAUTE1 andcontributes to the resistance against Botryosphaeria dothidea in-fection by altering defense responses[J]. Plant Cell Physiol,2017,58(9):1541-1557.
[52] SUNKAR R,JAGADEESWARAN G. In silico identification ofconserved microRNAs in large number of diverse plant species[J]. BMC Plant Biology,2008,8(1):37.
[53] WU X,LIU M,XU Q,GUO W. Identification and characteriza-tion of microRNAs from citrus expressed sequence tags[J].Tree Genetics&Genomes,2011,7(1):117-133.
[54] ZHANG B,PAN X,WANG Q,COBB G P,ANDERSON T A.Identification and characterization of new plant microRNAs us-ing EST analysis[J]. Cell Research,2005,15(5):336-360.
[55] FANG Y N,QIU W M,WANG Y,WU X M,XU Q,GUO W W.Identification of differentially expressed microRNAs from amale sterile Ponkan mandarin(Citrus reticulata Blanco)and itsfertile wild type by small RNA and degradome sequencing[J].Tree Genetics&Genomes,2014,10(6):1567-1581.
[56] SONG C,CHEN W,ZHANG C,KORIR N K,YU H,MA Z,FANG J. Deep sequencing discovery of novel and conserved mi-croRNAs in trifoliate orange(Citrus trifoliata)[J]. BMC Ge-nomics,2010,11(1):431.
[57] ZHANG X,LI X,LIU J. Identification of conserved and novelcold-responsive microRNAs in Trifoliate Orange(Poncirus tri-foliata(L.)Raf.)using high-throughput sequencing[J]. PlantMolecular Biology Reporter,2014,32(2):328-341.
[58] LENG X P,SONG C N,HAN J,SHANGGUAN L F,FANG JG,WANG C. Determination of the precise sequences of compu-tationally predicted miRNAs in Citrus reticulata by miR-RACEand characterization of the related target genes using RLM-RACE[J]. Gene,2016,575(2):498-505.
[59] LU Y B,YANG L T,QI Y P,LI Y,LI Z,CHEN Y B,HUANGZ R,CHEN L S. Identification of boron-deficiency-responsivemicroRNAs in Citrus sinensis roots by Illumina sequencing[J].BMC Plant Biology,2014,14(1):123.
[60] LU Y B,QI Y P,YANG L T,GUO P,LI Y,CHEN L S. Boron-deficiency-responsive microRNAs and their targets in Citrus si-nensis leaves[J]. BMC Plant Biology,2015,15(1):271.
[61] HUANG J H,QI Y P,WEN S X,GUO P,CHEN X M,CHEN LS. Illumina microRNA profiles reveal the involvement ofmiR397a in Citrus adaptation to long-term boron toxicity viamodulating secondary cell-wall biosynthesis[J]. Scientific Re-ports,2016,6:22900.
[62] JIN L F,LIU Y Z,YIN X X,PENG S A. Transcript analysis ofcitrus miRNA397 and its target LAC7 reveals a possible role inresponse to boron toxicity[J]. Acta Physiologiae Plantarum,2016,38(1):18.
[63] RAWAT N,KIRAN S P,DU D,GMITTER F G,DENG Z. Com-prehensive meta-analysis,co-expression,and miRNA nested net-work analysis identifies gene candidates in citrus against Huan-glongbing disease[J]. BMC Plant Biology,2015,15(1):184.
[64] ZHAO H.W.,SUN R.B.,ALBRECHT U,PADMANABHAN C,WANG A,COFFEY M,GIRKE T,WANG,Z H,CLOSE T J,ROOSE,M,YOKOMI R K,FOLIMONOVA S,VIDALAKISG,ROUSE R,BOWMAN K D,JIN H L. Small RNA profilingreveals phosphorus deficiency as a contributing factor in symp-tom expression for Citrus Huanglongbing disease[J]. MolecularPlant,2013,6(2):301-310.
[65] XIE R,ZHANG J,MA Y,PAN X,DONG C,PANG S,HE S,DENG L,YI S,ZHENG Y,LV Q. Combined analysis of mRNAand miRNA identifies dehydration and salinity responsive keymolecular players in citrus roots[J]. Scientific Reports,2017,7:42094.
[66] WU X,KOU S,LIU Y,FANG Y,XU Q,GUO W. Genomewideanalysis of small RNAs in nonembryogenic and embryogenic tis-sues of citrus:microRNA-and siRNA-mediated transcript cleav-age involved in somatic embryogenesis[J]. Plant BiotechnologyJournal,2015,13(3):383-394.
[67] LONG J M,LIU Z,WU X M,FANG Y N,JIA H H,XIE Z Z,DENG X X,GUO W W. Genome-scale mRNA and small RNAtranscriptomic insights into initiation of citrus apomixis[J]. Jour-nal of Experimental Botany,2016,67(19):5743-5756.
[68] FANG Y N,ZHENG B B,WANG L,YANG W,WU X M,XUQ,GUO W W. High-throughput sequencing and degradomeanalysis reveal altered expression of miRNAs and their targetsin a male-sterile cybrid pummelo(Citrus grandis)[J]. BMC Ge-nomics,2016,17(1):591.
[69] ZHANG J,WANG M,CHENG F,DAI C,SUN Y,LU J,HUANG Y,LI M,HE Y,WANG F,FAN B. Identification of mi-croRNAs correlated with citrus granulation based on bioinfor-matics and molecular biology analysis[J]. Postharvest Biologyand Technology,2016,118:59-67.
[70] NIU Q F,QIAN M J,LIU G Q,YANG F X,TENG Y W. Ageome-wide identification and characterization of mircoRNAsand their targets in‘Suli’pear(Pyrus pyrifolia white peargroup)[J]. Planta,2013,238(6):1095-1112.
[71] WU J,WANG D,LIU Y,WANG L,QIAO X,ZHANG S. Identi-fication of miRNAs involved in pear fruit development and qual-ity[J]. BMC Genomics,2014,15(1):953.
[72] HENG W,JIA B,HUANG H N,YANG J Y,WANG Z T,LIUP,LIU L,YE Z F,ZHU L W. Identification of russet-associatedmicroRNAs in the exocarp of a Dangshansuli pear mutant(Py-rus bretschneideri Rehd.)by high-throughput sequencing[J].Tree Genetics&Genomes,2016,12(6):107.
[73] CHENG X,YAN C,ZHANG J,MA C,LI S,JIN Q,ZHANG N,CAO Y,LIN Y,CAI Y. The effect of different pollination on theexpression of Dangshan Su Pear microRNA[J]. BioMed Re-search International,2017,2:1-18.
[74] BAI S,SAITO T,ITO A,TUAN P A,XU Y,TENG Y,MORI-GUCHI T. Small RNA and PARE sequencing in flower bud re-veal the involvement of sRNAs in endodormancy release of Jap-anese pear(Pyrus pyrifolia‘Kosui’)[J]. BMC Genomics,2016,17(1):230.
[75] NIU Q F,LI J Z,CAI D Y,QIAN M J,JIA H M,BAI S L,HUS-SAIN S,LIU G Q,TENG Y W,ZHENG X Y. Dormancy-associ-ated MADS-box genes and microRNAs jointly control dorman-cy transition in pear(Pyrus pyrifolia white pear group)flowerbud[J]. Journal of Experimental Botany,2016,67(1):239-257.
[76] ZHANG Y,YU M,YU H,HAN J,SONG C,MA R,FANG J.Computational identification of microRNAs in peach expressedsequence tags and validation of their precise sequences by miR-RACE[J]. Molecular Biology Reports,2012,39(2):1975-1987.
[77] LUO X,GAO Z,SHI T,CHENG Z,ZHANG Z,NI Z. Identifica-tion of miRNAs and their target genes in peach(Prunus persicaL.)using high-throughput sequencing and degradome analysis[J]. PLoS One,2013,8(11):e79090.
[78] ZHANG Y,BAI Y,HAN J,CHEN M,KAYESH E,JIANG W,FANG J. Bioinformatics prediction of miRNAs in the Prunuspersica genome with validation of their precise sequences bymiR-RACE[J]. Journal of Plant Physiology,2013,170(1):80-92.
[79] ZHANG Y,HAN J,YU M,MA R,PERVAIZ T,FANG J. Char-acterization of target mRNAs for Prunus persica microRNAs us-ing an integrated strategy of PLM-RACE,PPM-RACE and qRT-PCR[J]. Scientia Horticulturae,2014,170:8-16.
[80] ZHANG C,ZHANG B,MA R,YU M,GUO S,GUO L,KORIRN K. Identification of known and novel microRNAs and theirtargets in peach(Prunus persica)fruit by high-throughput se-quencing[J]. PLoS One,2016,11(7):e0159253.
[81] PEKMEZCI A K,KARAKüLAH G,UNVER T. Discovery ofdrought-responsive transposable element-related peach miRNAs[J]. BioRxiv,2017,5:143115.
[82] ARYAL R,JAGADEESWARAN G,ZHENG Y,YU Q,SUNK-AR R,MING R. Sex specific expression and distribution ofsmall RNAs in papaya[J]. BMC Genomics,2014,15(1):20.
[83] BI F,MENG X,MA C,YI G. Identification of miRNAs in-volved in fruit ripening in Cavendish bananas by deep sequenc-ing[J]. BMC Genomics,2015,16(1):776.
[84] DAN M,HUANG M H,LIAO F,QIN R Y,LIANG X J,ZHANG E Z,HUANG M K,HUANG Z Y,HE Q G. Identifica-tion of ethylene responsive miRNAs and their targets from new-ly harvested banana fruits using high-throughput sequencing[J].Journal of Agricultural and Food Chemistry,2018,66(40):10628-10639.
[85] SAMPANGI-RAMAIAH M H,RAVISHANKAR K V,REKHAA,HUNASHIKATTI L R. A contig-based computational predic-tion of conserved miRNAs and their probable role in regulationof cuticular wax biosynthesis in banana[J]. Plant Molecular Bi-ology Reporter,2016,35(2):1-12.
[86] XIA R,YE S,LIU Z,MEYERS B C,LIU Z. Novel and recentlyevolved microRNA clusters regulate expansive F-BOX gene net-works through phased small interfering RNAs in wild diploidstrawberry[J]. Plant Physiology,2015,169(1):594-610.
[87]?URBANOVSKI N,BRILLI M,MOSER M,SI-AMMOUR A.A highly specific microRNA-mediated mechanism silencesLTR retrotransposons of strawberry[J]. The Plant Journal,2016,85(1):70-82.
[88] WANG Y,ZHANG J X.,CUI W X.,GUAN C Y,MAO W J,ZHANG Z H. Improvement in fruit quality by overexpressingmiR399a in woodland strawberry[J]. Journal of Agriculturaland Food Chemistry,2017,65(34):7361-7370.
[89] YAO F,ZHU H,YI C,QU H,JIANG Y. MicroRNAs and tar-gets in senescent litchi fruit during ambient storage and post-cold storage shelf life[J]. BMC Plant Biology,2015,15(1):181.
[90] LIU R,LAI B,HU B,QIN Y,HU G,ZHAO J. Identification ofmicroRNAs and their target genes related to the accumulation ofanthocyanins in Litchi chinensis by high-throughput sequencingand degradome analysis[J]. Frontiers Plant Science,2017,7:2059.
[91] JIA L,ZHANG D,QI X,MA B,XIANG Z,HE N. Identificationof the conserved and novel miRNAs in mulberry by high-throughput sequencing[J]. PLoS One,2014,9(8):e104409.
[92] BALOCH I A,BAROZAI M Y K,DIN M. Identification andcharacterization of 25 micrornas and their targeted proteins inapricot(Prunus armeniaca L.)[J]. Journal of Animal&PlantSciences,2015,25(5):1466-1476.
[93] AVSAR B,ESMAEILI ALIABADI D. Putative microRNA anal-ysis of the kiwifruit Actinidia chinensis through genomic data[J]. International Journal of Life Sciences Biotechnology andPharma Research,2015,4(2):96-99.
[94] SAMINATHAN T,BODUNRIN A,SINGH N V,DEVARAJANR,NIMMAKAYALA P,JEFF M,ARADHYA M,REDDY U K.Genome-wide identification of microRNAs in pomegranate(Pu-nica granatum L.)by high-throughput sequencing[J]. BMCPlant Biology,2016,16(1):122.
[95] YUE J,LU X,ZHANG H,GE J,GAO X,LIU Y. Identificationof conserved and novel microRNAs in blueberry[J]. FrontiersPlant Science,2017,8:1155.
[96] CHEN M,MENG Y,MAO C,CHEN D,WU P. Methodologicalframework for functional characterization of plant microRNAs[J]. Journal of Experimental Botany,2010,61(9):2271-2280.
[97] SCHWAB R,OSSOWSKI S,WARTHMANN N,WEIGEL D.Directed gene silencing with artificial microRNAs[J]. MethodsMol Biology,2010,592(592):71-88.
[98] TANG G,YAN J,GU Y,QIAO M,FAN R,MAO Y,TANG X.Construction of short tandem target mimic(STTM)to block thefunctions of plant and animal microRNAs[J]. Methods,2012,58(2):118-125.
[99] YAN J,GU Y,JIA X,KANG W,PAN S,TANG X,CHEN X,TANG G. Effective small RNA destruction by the expression ofa short tandem target mimic in Arabidopsis[J]. The Plant Cell,2012,24(2):415-427.
[100] ZHU H,XIA R,ZHAO B,AN Y,DARDICK C D,CALLAH-AN A M,LIU Z. Unique expression,processing regulation,andregulatory network of peach(Prunus persica)miRNAs[J].BMC Plant Biology,2012,12(1):149.
[101] SONG C,YU M,HAN J,WANG C,LIU H,ZHANG Y,FANGJ. Validation and characterization of Citrus sinensis microRNAsand their target genes[J]. BMC Research Notes,2012,5(1):235.