{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T17:56:25Z","timestamp":1784224585320,"version":"3.55.0"},"reference-count":57,"publisher":"Springer Science and Business Media LLC","issue":"S2","license":[{"start":{"date-parts":[[2018,5,1]],"date-time":"2018-05-01T00:00:00Z","timestamp":1525132800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Genomics"],"published-print":{"date-parts":[[2018,5]]},"DOI":"10.1186\/s12864-018-4457-8","type":"journal-article","created":{"date-parts":[[2018,5,9]],"date-time":"2018-05-09T08:07:28Z","timestamp":1525853248000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["Genome-wide identification and comprehensive analysis of microRNAs and phased small interfering RNAs in watermelon"],"prefix":"10.1186","volume":"19","author":[{"given":"Li","family":"Liu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuchao","family":"Ren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junqiang","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingyi","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaotuo","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peiran","family":"Liao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shipeng","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramanjulu","family":"Sunkar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun","family":"Zheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2018,5,9]]},"reference":[{"issue":"4","key":"4457_CR1","doi-asserted-by":"publisher","first-page":"669","DOI":"10.1016\/j.cell.2009.01.046","volume":"136","author":"O Voinnet","year":"2009","unstructured":"Voinnet O. Origin, biogenesis, and activity of plant MicroRNAs. Cell. 2009; 136(4):669\u201387.","journal-title":"Cell"},{"issue":"4","key":"4457_CR2","doi-asserted-by":"publisher","first-page":"361","DOI":"10.1016\/j.gde.2012.04.004","volume":"22","author":"X Chen","year":"2012","unstructured":"Chen X. Small RNAs in development\u2013insights from plants. Curr Opin Genet Dev. 2012; 22(4):361\u20137.","journal-title":"Curr Opin Genet Dev"},{"issue":"4","key":"4457_CR3","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1016\/j.tplants.2012.01.010","volume":"17","author":"R Sunkar","year":"2012","unstructured":"Sunkar R, Li Y-F, Jagadeeswaran G. Functions of microRNAs in plant stress responses. Trends Plant Sci. 2012; 17(4):196\u2013203.","journal-title":"Trends Plant Sci"},{"key":"4457_CR4","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1146\/annurev.cellbio.042308.113417","volume":"25","author":"X Chen","year":"2009","unstructured":"Chen X. Small RNAs and their roles in plant development. Annu Rev Cell Dev. 2009; 25:21\u201344.","journal-title":"Annu Rev Cell Dev"},{"issue":"17","key":"4457_CR5","doi-asserted-by":"publisher","first-page":"1484","DOI":"10.1016\/S0960-9822(02)01017-5","volume":"12","author":"W Park","year":"2002","unstructured":"Park W, Li J, Song R, Messing J, Chen X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol. 2002; 12(17):1484\u201395.","journal-title":"Curr Biol"},{"issue":"2","key":"4457_CR6","doi-asserted-by":"publisher","first-page":"281","DOI":"10.1016\/S0092-8674(04)00045-5","volume":"116","author":"DP Bartel","year":"2004","unstructured":"Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004; 116(2):281\u201397.","journal-title":"Cell"},{"key":"4457_CR7","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1146\/annurev.arplant.57.032905.105218","volume":"57","author":"MW Jones-Rhoades","year":"2006","unstructured":"Jones-Rhoades MW, Bartel DP, Bartel B. MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol. 2006; 57:19\u201353.","journal-title":"Annu Rev Plant Biol"},{"issue":"6","key":"4457_CR8","doi-asserted-by":"publisher","first-page":"817","DOI":"10.1111\/j.1744-7909.2007.00499.x","volume":"49","author":"R Sunkar","year":"2007","unstructured":"Sunkar R, Zhu J-K. MicroRNAs and short-interfering RNAs in plants. J Integr Plant Biol. 2007; 49(6):817\u201326.","journal-title":"J Integr Plant Biol"},{"issue":"4","key":"4457_CR9","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1038\/nrg3162","volume":"13","author":"AE Pasquinelli","year":"2012","unstructured":"Pasquinelli AE. MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nat Rev Genet. 2012; 13(4):271\u201382.","journal-title":"Nat Rev Genet"},{"key":"4457_CR10","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1146\/annurev-arplant-050312-120043","volume":"64","author":"MJ Axtell","year":"2013","unstructured":"Axtell MJ. Classification and comparison of small RNAs from plants. Annu Rev Plant Biol. 2013; 64:137\u201359.","journal-title":"Annu Rev Plant Biol"},{"issue":"5858","key":"4457_CR11","doi-asserted-by":"publisher","first-page":"1931","DOI":"10.1126\/science.1149460","volume":"318","author":"S Vasudevan","year":"2007","unstructured":"Vasudevan S, Tong Y, Steitz JA. Switching from repression to activation: microRNAs can up-regulate translation. Science. 2007; 318(5858):1931\u20134.","journal-title":"Science"},{"issue":"3","key":"4457_CR12","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1002\/wrna.121","volume":"3","author":"S Vasudevan","year":"2012","unstructured":"Vasudevan S. Posttranscriptional upregulation by microRNAs. Wiley Interdiscip Rev RNA. 2012; 3(3):311\u201330.","journal-title":"Wiley Interdiscip Rev RNA"},{"issue":"10","key":"4457_CR13","doi-asserted-by":"publisher","first-page":"1326","DOI":"10.1080\/15476286.2015.1112487","volume":"14","author":"M Xiao","year":"2017","unstructured":"Xiao M, Li J, Li W, Wang Y, Wu F, Xi Y, Zhang L, Ding C, Luo H, Li Y, et al. MicroRNAs activate gene transcription epigenetically as an enhancer trigger. RNA Biol. 2017; 14(10):1326\u201334.","journal-title":"RNA Biol"},{"issue":"7","key":"4457_CR14","doi-asserted-by":"publisher","first-page":"2400","DOI":"10.1105\/tpc.113.114652","volume":"25","author":"Q Fei","year":"2013","unstructured":"Fei Q, Xia R, Meyers BC. Phased, secondary, small interfering RNAs in posttranscriptional regulatory networks. Plant Cell. 2013; 25(7):2400\u201315.","journal-title":"Plant Cell"},{"issue":"2","key":"4457_CR15","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1016\/j.cell.2005.04.004","volume":"121","author":"E Allen","year":"2005","unstructured":"Allen E, Xie Z, Gustafson AM, Carrington JC. microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell. 2005; 121(2):207\u201321.","journal-title":"Cell"},{"issue":"36","key":"4457_CR16","doi-asserted-by":"publisher","first-page":"12984","DOI":"10.1073\/pnas.0506426102","volume":"102","author":"Z Xie","year":"2005","unstructured":"Xie Z, Allen E, Wilken A, Carrington JC. DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc Natl Acad Sci USA. 2005; 102(36):12984\u20139.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"3","key":"4457_CR17","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1105\/tpc.107.050062","volume":"19","author":"MD Howell","year":"2007","unstructured":"Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC. Genome-Wide Analysis of the RNA-DEPENDENT RNA POLYMERASE6\/DICER-LIKE4 Pathway in Arabidopsis Reveals Dependency on miRNA- and tasiRNA-Directed Targeting. Plant Cell. 2007; 19(3):926\u201342.","journal-title":"Plant Cell"},{"issue":"8","key":"4457_CR18","doi-asserted-by":"publisher","first-page":"1429","DOI":"10.1101\/gr.089854.108","volume":"19","author":"C Johnson","year":"2009","unstructured":"Johnson C, Kasprzewska A, Tennessen K, Fernandes J, Nan G-L, Walbot V, Sundaresan V, Vance V, Bowman LH. Clusters and superclusters of phased small RNAs in the developing inflorescence of rice. Genome Res. 2009; 19(8):1429\u201340.","journal-title":"Genome Res"},{"issue":"3","key":"4457_CR19","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1111\/j.1365-313X.2011.04805.x","volume":"69","author":"X Song","year":"2012","unstructured":"Song X, Li P, Zhai J, Zhou M, Ma L, Liu B, Jeong DH, Nakano M, Cao S, Liu C, et al. Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. Plant J. 2012; 69(3):462\u201374.","journal-title":"Plant J"},{"issue":"3","key":"4457_CR20","doi-asserted-by":"publisher","first-page":"565","DOI":"10.1016\/j.cell.2006.09.032","volume":"127","author":"MJ Axtell","year":"2006","unstructured":"Axtell MJ, Jan C, Rajagopalan R, Bartel DP. A two-hit trigger for siRNA biogenesis in plants. Cell. 2006; 127(3):565\u201377.","journal-title":"Cell"},{"issue":"34","key":"4457_CR21","doi-asserted-by":"publisher","first-page":"15269","DOI":"10.1073\/pnas.1001738107","volume":"107","author":"HM Chen","year":"2010","unstructured":"Chen HM, Chen L-T, Patel K, Li YH, Baulcombe DC, Wu SH. 22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants. Proc Natl Acad Sci. 2010; 107(34):15269\u201374.","journal-title":"Proc Natl Acad Sci"},{"issue":"8","key":"4457_CR22","doi-asserted-by":"publisher","first-page":"997","DOI":"10.1038\/nsmb.1866","volume":"17","author":"JT Cuperus","year":"2010","unstructured":"Cuperus JT, Carbonell A, Fahlgren N, Garcia-Ruiz H, Burke RT, Takeda A, Sullivan CM, Gilbert SD, Montgomery TA, Carrington JC. Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis. Nat Struct Mol Biol. 2010; 17(8):997\u20131003.","journal-title":"Nat Struct Mol Biol"},{"issue":"7","key":"4457_CR23","doi-asserted-by":"publisher","first-page":"2461","DOI":"10.1073\/pnas.1200169109","volume":"109","author":"PA Manavella","year":"2012","unstructured":"Manavella PA, Koenig D, Weigel D. Plant secondary siRNA production determined by microRNA-duplex structure. Proc Natl Acad Sci. 2012; 109(7):2461\u20136.","journal-title":"Proc Natl Acad Sci"},{"issue":"5","key":"4457_CR24","doi-asserted-by":"publisher","first-page":"1555","DOI":"10.1105\/tpc.113.110957","volume":"25","author":"R Xia","year":"2013","unstructured":"Xia R, Meyers BC, Liu Z, Beers EP, Ye S, Liu Z. MicroRNA superfamilies descended from miR390 and their roles in secondary small interfering RNA biogenesis in eudicots. Plant Cell. 2013; 25(5):1555\u201372.","journal-title":"Plant Cell"},{"issue":"24","key":"4457_CR25","doi-asserted-by":"publisher","first-page":"3407","DOI":"10.1101\/gad.1476406","volume":"20","author":"R Rajagopalan","year":"2006","unstructured":"Rajagopalan R, Vaucheret H, Trejo J, Bartel DP. A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev. 2006; 20(24):3407\u201325.","journal-title":"Genes Dev"},{"issue":"9","key":"4457_CR26","doi-asserted-by":"publisher","first-page":"3318","DOI":"10.1073\/pnas.0611119104","volume":"104","author":"HM Chen","year":"2007","unstructured":"Chen HM, Li Y-H, Wu SH. Bioinformatic prediction and experimental validation of a microRNA-directed tandem trans-acting siRNA cascade in Arabidopsis. PNAS. 2007; 104(9):3318\u201323.","journal-title":"PNAS"},{"issue":"23","key":"4457_CR27","doi-asserted-by":"publisher","first-page":"2540","DOI":"10.1101\/gad.177527.111","volume":"25","author":"J Zhai","year":"2011","unstructured":"Zhai J, Jeong D-H, De Paoli E, Park S, Rosen BD, Li Y, Gonz\u00e1lez AJ, Yan Z, Kitto SL, Grusak MA, et al. MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes Dev. 2011; 25(23):2540\u201353.","journal-title":"Genes Dev"},{"issue":"3","key":"4457_CR28","doi-asserted-by":"publisher","first-page":"859","DOI":"10.1105\/tpc.111.095380","volume":"24","author":"PV Shivaprasad","year":"2012","unstructured":"Shivaprasad PV, Chen H-M, Patel K, Bond DM, Santos BA, Baulcombe DC. A microRNA superfamily regulates nucleotide binding site\u2013leucine-rich repeats and other mRNAs. Plant Cell. 2012; 24(3):859\u201374.","journal-title":"Plant Cell"},{"issue":"5","key":"4457_CR29","doi-asserted-by":"publisher","first-page":"1790","DOI":"10.1073\/pnas.1118282109","volume":"109","author":"F Li","year":"2012","unstructured":"Li F, Pignatta D, Bendix C, Brunkard JO, Cohn MM, Tung J, Sun H, Kumar P, Baker B. MicroRNA regulation of plant innate immune receptors. Proc Natl Acad Sci. 2012; 109(5):1790\u20135.","journal-title":"Proc Natl Acad Sci"},{"issue":"2","key":"4457_CR30","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1104\/pp.113.214643","volume":"162","author":"T K\u00e4llman","year":"2013","unstructured":"K\u00e4llman T, Chen J, Gyllenstrand N, Lagercrantz U. A significant fraction of 21-nucleotide small RNA originates from phased degradation of resistance genes in several perennial species. Plant Physiol. 2013; 162(2):741\u201354.","journal-title":"Plant Physiol"},{"issue":"12","key":"4457_CR31","doi-asserted-by":"publisher","first-page":"e84390","DOI":"10.1371\/journal.pone.0084390","volume":"8","author":"QH Zhu","year":"2013","unstructured":"Zhu QH, Fan L, Liu Y, Xu H, Llewellyn D, Wilson I. miR482 regulation of NBS-LRR defense genes during fungal pathogen infection in cotton. PloS ONE. 2013; 8(12):e84390.","journal-title":"PloS ONE"},{"issue":"6","key":"4457_CR32","doi-asserted-by":"publisher","first-page":"R47","DOI":"10.1186\/gb-2012-13-6-r47","volume":"13","author":"R Xia","year":"2012","unstructured":"Xia R, Zhu H, An Y-q, Beers EP, Liu Z. Apple miRNAs and tasiRNAs with novel regulatory networks. Genome Biol. 2012; 13(6):R47.","journal-title":"Genome Biol"},{"issue":"1","key":"4457_CR33","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1186\/1471-2229-12-149","volume":"12","author":"H Zhu","year":"2012","unstructured":"Zhu H, Xia R, Zhao B, An YQ, Dardick CD, Callahan AM, Liu Z. Unique expression, processing regulation, and regulatory network of peach (Prunus persica) miRNAs. BMC Plant Biol. 2012; 12(1):149.","journal-title":"BMC Plant Biol"},{"issue":"2","key":"4457_CR34","doi-asserted-by":"publisher","first-page":"e57359","DOI":"10.1371\/journal.pone.0057359","volume":"8","author":"N Liu","year":"2013","unstructured":"Liu N, Yang J, Guo S, Xu Y, Zhang M. Genome-wide identification and comparative analysis of conserved and novel microRNAs in grafted watermelon by high-throughput sequencing. PloS one. 2013; 8(2):e57359.","journal-title":"PloS one"},{"issue":"1","key":"4457_CR35","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1186\/1471-2164-13-329","volume":"13","author":"G Jagadeeswaran","year":"2012","unstructured":"Jagadeeswaran G, Nimmakayala P, Zheng Y, Gowdu K, Reddy UK, Sunkar R. Characterization of the small RNA component of leaves and fruits from four different cucurbit species. BMC Genomics. 2012; 13(1):329.","journal-title":"BMC Genomics"},{"key":"4457_CR36","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1016\/j.biochi.2014.03.002","volume":"102","author":"J Hu","year":"2014","unstructured":"Hu J, Sun L, Zhu Z, Zheng Y, Xiong W, Ding Y. Characterization of conserved microRNAs from five different cucurbit species using computational and experimental analysis. Biochimie. 2014; 102:137\u201344.","journal-title":"Biochimie"},{"key":"4457_CR37","first-page":"1231","volume":"7","author":"H Li","year":"2016","unstructured":"Li H, Dong Y, Chang J, He J, Chen H, Liu Q, Wei C, Ma J, Zhang Y, Yang J, Zhang X. High-throughput microRNA and mRNA sequencing reveals that microRNAs may be involved in melatonin-mediated cold tolerance in Citrullus lanatus L. Front Plant Sci. 2016; 7:1231.","journal-title":"Front Plant Sci"},{"key":"4457_CR38","doi-asserted-by":"publisher","first-page":"2591","DOI":"10.1007\/s00705-017-3401-6","volume":"162","author":"Y Sun","year":"2017","unstructured":"Sun Y, Niu X, Fan M. Genome-wide identification of cucumber green mottle mosaic virus-responsive microRNAs in watermelon. Arch Virol. 2017; 162:2591\u20132602.","journal-title":"Arch Virol"},{"issue":"3","key":"4457_CR39","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1007\/s12042-016-9173-4","volume":"9","author":"Y Zheng","year":"2016","unstructured":"Zheng Y, Li T, Xu Z, Wai CM, Chen K, Zhang X, Wang S, Ji B, Ming R, Sunkar R. Identification of microRNAs, phasiRNAs and their targets in pineapple. Trop Plant Biol. 2016; 9(3):176\u201386.","journal-title":"Trop Plant Biol"},{"issue":"D1","key":"4457_CR40","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1093\/nar\/gks1005","volume":"41","author":"SW Burge","year":"2013","unstructured":"Burge SW, Daub J, Eberhardt R, Tate J, Barquist L, Nawrocki EP, Eddy SR, Gardner PP, Bateman A. Rfam 11.0: 10 years of RNA families. Nucleic Acids Res. 2013; 41(D1):226\u201332.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"4457_CR41","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1093\/nar\/gkr1175","volume":"40","author":"D Bu","year":"2012","unstructured":"Bu D, Yu K, Sun S, Xie C, Skogerb\u00f8 G, Miao R, Xiao H, Liao Q, Luo H, Zhao G, et al. NONCODE v3. 0: integrative annotation of long noncoding RNAs. Nucleic Acids Res. 2012; 40(D1):210\u20135.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"4457_CR42","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1093\/nar\/gks1219","volume":"41","author":"C Quast","year":"2013","unstructured":"Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Gl\u00f6ckner FO. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013; 41(D1):590\u20136.","journal-title":"Nucleic Acids Res"},{"issue":"suppl_1","key":"4457_CR43","doi-asserted-by":"publisher","first-page":"360","DOI":"10.1093\/nar\/gkh099","volume":"32","author":"S Ouyang","year":"2004","unstructured":"Ouyang S, Buell CR. The TIGR Plant Repeat Databases: a collective resource for the identification of repetitive sequences in plants. Nucleic Acids Res. 2004; 32(suppl_1):360\u20133.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"4457_CR44","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13100-015-0041-9","volume":"6","author":"W Bao","year":"2015","unstructured":"Bao W, Kojima KK, Kohany O. Repbase update, a database of repetitive elements in eukaryotic genomes. Mobile DNA. 2015; 6(1):1.","journal-title":"Mobile DNA"},{"issue":"15","key":"4457_CR45","doi-asserted-by":"publisher","first-page":"1966","DOI":"10.1093\/bioinformatics\/btp336","volume":"25","author":"R Li","year":"2009","unstructured":"Li R, Yu C, Li Y, Lam TW, Yiu S-M, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009; 25(15):1966\u20137.","journal-title":"Bioinformatics"},{"issue":"D1","key":"4457_CR46","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1093\/nar\/gkt1181","volume":"42","author":"A Kozomara","year":"2014","unstructured":"Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014; 42(D1):68\u201373.","journal-title":"Nucleic Acids Res"},{"issue":"13","key":"4457_CR47","doi-asserted-by":"publisher","first-page":"3429","DOI":"10.1093\/nar\/gkg599","volume":"31","author":"IL Hofacker","year":"2003","unstructured":"Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res. 2003; 31(13):3429\u201331.","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"4457_CR48","doi-asserted-by":"publisher","first-page":"3186","DOI":"10.1105\/tpc.108.064311","volume":"20","author":"BC Meyers","year":"2008","unstructured":"Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, et al. Criteria for annotation of plant MicroRNAs. Plant Cell. 2008; 20(12):3186\u201390.","journal-title":"Plant Cell"},{"issue":"1","key":"4457_CR49","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2010","unstructured":"Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010; 26(1):139\u201340.","journal-title":"Bioinformatics"},{"issue":"1","key":"4457_CR50","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1111\/j.1469-8137.2009.02915.x","volume":"184","author":"G Jagadeeswaran","year":"2009","unstructured":"Jagadeeswaran G, Zheng Y, Li Y-F, Shukla LI, Matts J, Hoyt P, Macmil SL, Wiley GB, Roe BA, Zhang W, Sunkar R. Cloning and characterization of small RNAs from Medicago truncatula reveals four novel legume-specific microRNA families. New Phytol. 2009; 184(1):85\u201398.","journal-title":"New Phytol"},{"key":"4457_CR51","doi-asserted-by":"publisher","first-page":"9418","DOI":"10.1038\/s41598-017-09670-8","volume":"7","author":"Y Zheng","year":"2017","unstructured":"Zheng Y, Chen K, Xu Z, Liao P, Zhang X, Liu L, Wei K, Liu D, Li YF, Sunkar R, et al. Small RNA profiles from panax notoginseng roots differing in sizes reveal correlation between mir156 abundances and root biomass levels. Sci Rep. 2017; 7:9418.","journal-title":"Sci Rep"},{"issue":"11","key":"4457_CR52","doi-asserted-by":"publisher","first-page":"1965","DOI":"10.1261\/rna.1706109","volume":"15","author":"E De Paoli","year":"2009","unstructured":"De Paoli E, Dorantes-Acosta A, Zhai J, Accerbi M, Jeong DH, Park S, Meyers BC, Jorgensen RA, Green PJ. Distinct extremely abundant siRNAs associated with cosuppression in petunia. RNA. 2009; 15(11):1965\u201370.","journal-title":"RNA"},{"issue":"1","key":"4457_CR53","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B Methodol. 1995; 57(1):289\u2013300.","journal-title":"J R Stat Soc Ser B Methodol"},{"issue":"4","key":"4457_CR54","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1093\/nar\/gkr1092","volume":"40","author":"Y Zheng","year":"2012","unstructured":"Zheng Y, Li Y-F, Sunkar R, Zhang W. SeqTar: an effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants. Nucleic Acids Res. 2012; 40(4):28\u201328.","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"4457_CR55","doi-asserted-by":"publisher","first-page":"2905","DOI":"10.1093\/molbev\/msv164","volume":"32","author":"R Xia","year":"2015","unstructured":"Xia R, Xu J, Arikit S, Meyers BC. Extensive families of miRNAs and PHAS loci in norway spruce demonstrate the origins of complex phasiRNA networks in seed plants. Mol Biol Evol. 2015; 32(11):2905\u201318.","journal-title":"Mol Biol Evol"},{"issue":"12","key":"4457_CR56","doi-asserted-by":"publisher","first-page":"e113790","DOI":"10.1371\/journal.pone.0113790","volume":"9","author":"Y Zheng","year":"2014","unstructured":"Zheng Y, Wang S, Sunkar R. Genome-wide discovery and analysis of phased small interfering RNAs in chinese sacred lotus. PLoS ONE. 2014; 9(12):e113790.","journal-title":"PLoS ONE"},{"issue":"10","key":"4457_CR57","doi-asserted-by":"publisher","first-page":"3146","DOI":"10.1073\/pnas.1418918112","volume":"112","author":"J Zhai","year":"2015","unstructured":"Zhai J, Zhang H, Arikit S, Huang K, Nan G-L, Walbot V, Meyers BC. Spatiotemporally dynamic, cell-type\u2013dependent premeiotic and meiotic phasiRNAs in maize anthers. Proc Natl Acad Sci. 2015; 112(10):3146\u201351.","journal-title":"Proc Natl Acad Sci"}],"container-title":["BMC Genomics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-018-4457-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12864-018-4457-8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12864-018-4457-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,6]],"date-time":"2024-07-06T16:44:53Z","timestamp":1720284293000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcgenomics.biomedcentral.com\/articles\/10.1186\/s12864-018-4457-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,5]]},"references-count":57,"journal-issue":{"issue":"S2","published-print":{"date-parts":[[2018,5]]}},"alternative-id":["4457"],"URL":"https:\/\/doi.org\/10.1186\/s12864-018-4457-8","relation":{},"ISSN":["1471-2164"],"issn-type":[{"value":"1471-2164","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,5]]},"assertion":[{"value":"9 May 2018","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"111"}}