title: Transcriptome-wide identification and characterization of microRNAs from castor bean (Ricinus communis L.).
abstract: BACKGROUND
  MicroRNAs (miRNAs) are endogenously encoded small RNAs that post-transcriptionally regulate gene expression and play essential roles in numerous developmental and physiological processes. Currently, little information on the transcriptome and tissue-specific expression of miRNAs is available in the model non-edible oilseed crop castor bean (Ricinus communis L.), one of the most important non-edible oilseed crops cultivated worldwide. Recent advances in sequencing technologies have allowed the identification of conserved and novel miRNAs in many plant species. Here, we used high-throughput sequencing technologies to identify and characterize the miRNAs in castor bean.
  
  
  RESULTS
  Five small RNA libraries were constructed for deep sequencing from root tips, leaves, developing seeds (at the initial stage, seed1; and at the fast oil accumulation stage, seed2) and endosperms in castor bean. High-throughput sequencing generated a large number of sequence reads of small RNAs in this study. In total, 86 conserved miRNAs were identified, including 63 known and 23 newly identified. Sixteen miRNA isoform variants in length were found from the conserved miRNAs of castor bean. MiRNAs displayed diverse organ-specific expression levels among five libraries. Combined with criteria for miRNA annotation and a RT-PCR approach, 72 novel miRNAs and their potential precursors were annotated and 20 miRNAs newly identified were validated. In addition, new target candidates for miRNAs newly identified in this study were proposed.
  
  
  CONCLUSIONS
  The current study presents the first high-throughput small RNA sequencing study performed in castor bean to identify its miRNA population. It characterizes and increases the number of miRNAs and their isoforms identified in castor bean. The miRNA expression analysis provides a foundation for understanding castor bean miRNA organ-specific expression patterns. The present study offers an expanded picture of miRNAs for castor bean and other members in the family Euphorbiaceae.
authors.affiliation: Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Xu
authors.forename: Qinghua
authors.initials: Q
authors.lastname: Cui
authors.forename: Fei
authors.initials: F
authors.lastname: Li
authors.forename: Aizhong
authors.initials: A
authors.lastname: Liu
mesh_terms: D002367:Ricinus communis / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000235:genetics
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant
references.citation: Bioresour Technol. 2006 Jun;97(9):1086-91
references.pmid: 15919203
references.citation: Brief Bioinform. 2009 Sep;10(5):490-7
references.pmid: 19332473
references.citation: Cell. 2008 Apr 4;133(1):128-41
references.pmid: 18342362
references.citation: Silence. 2010 Jun 09;1(1):12
references.pmid: 20534119
references.citation: Nucleic Acids Res. 2010 Jan;38(3):981-95
references.pmid: 19942686
references.citation: Methods Mol Biol. 2010;630:49-64
references.pmid: 20300990
references.citation: Cell. 2005 Apr 22;121(2):207-21
references.pmid: 15851028
references.citation: BMC Genomics. 2012 Jul 16;13:310
references.pmid: 22799740
references.citation: BMC Genomics. 2012 Mar 06;13:83
references.pmid: 22394504
references.citation: Mol Biotechnol. 2013 Mar;53(3):257-69
references.pmid: 22388699
references.citation: BMC Genomics. 2012 Apr 06;13:132
references.pmid: 22480283
references.citation: BMC Plant Biol. 2013 Jan 15;13:10
references.pmid: 23320600
references.citation: Development. 2006 Nov;133(21):4211-8
references.pmid: 17021043
references.citation: Science. 2005 Sep 2;309(5740):1567-9
references.pmid: 16141074
references.citation: Plant Cell. 2008 Dec;20(12):3186-90
references.pmid: 19074682
references.citation: PLoS One. 2011;6(11):e27530
references.pmid: 22110666
references.citation: Planta. 2011 Mar;233(3):611-9
references.pmid: 21136073
references.citation: BMC Plant Biol. 2008 Apr 16;8:37
references.pmid: 18416839
references.citation: FEBS Lett. 2005 Oct 31;579(26):5923-31
references.pmid: 16144699
references.citation: PLoS Genet. 2009 Nov;5(11):e1000716
references.pmid: 19936050
references.citation: Cell. 2008 Apr 4;133(1):116-27
references.pmid: 18342361
references.citation: Annu Rev Plant Biol. 2006;57:19-53
references.pmid: 16669754
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D109-11
references.pmid: 14681370
references.citation: Nat Rev Genet. 2012 Apr 18;13(5):358-69
references.pmid: 22510765
references.citation: Int J Biol Sci. 2012;8(3):418-29
references.pmid: 22419887
references.citation: Genes (Basel). 2010 Jun 03;1(1):70-84
references.pmid: 24710011
references.citation: Nat Biotechnol. 2008 Apr;26(4):407-15
references.pmid: 18392026
references.citation: Plant Cell. 2003 Nov;15(11):2730-41
references.pmid: 14555699
references.citation: BMC Plant Biol. 2010 Dec 16;10:278
references.pmid: 21162723
references.citation: Curr Opin Plant Biol. 2009 Feb;12(1):81-6
references.pmid: 18980858
references.citation: BMC Plant Biol. 2012 Feb 13;12:18
references.pmid: 22330773
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8
references.pmid: 17991681
references.citation: RNA. 2009 May;15(5):992-1002
references.pmid: 19307293
references.citation: PLoS One. 2012;7(9):e44385
references.pmid: 22962612
references.citation: Nucleic Acids Res. 2003 Jul 1;31(13):3406-15
references.pmid: 12824337
references.citation: Planta. 2012 Aug;236(2):437-45
references.pmid: 22407387
references.citation: Mol Genet Genomics. 2012 Jul;287(7):555-63
references.pmid: 22643909
references.citation: PLoS One. 2011;6(5):e19523
references.pmid: 21603611
references.citation: PLoS One. 2009 Jul 30;4(7):e6442
references.pmid: 19649244
references.citation: Curr Genomics. 2010 Mar;11(1):14-23
references.pmid: 20808519
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D140-4
references.pmid: 16381832
references.citation: Dev Cell. 2005 Apr;8(4):517-27
references.pmid: 15809034
references.citation: RNA. 2010 May;16(5):991-1006
references.pmid: 20360395
references.citation: Biotechnol Adv. 2008 Sep-Oct;26(5):424-35
references.pmid: 18579331
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D152-7
references.pmid: 21037258