title: Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing.
abstract: BACKGROUND
  MicroRNAs (miRNAs) regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional levels in higher plants. miRNAs and related target genes have been widely studied in model plants such as Arabidopsis and rice; however, the number of identified miRNAs in soybean (Glycine max) is limited, and global identification of the related miRNA targets has not been reported in previous research.
  
  
  RESULTS
  In our study, a small RNA library and a degradome library were constructed from developing soybean seeds for deep sequencing. We identified 26 new miRNAs in soybean by bioinformatic analysis and further confirmed their expression by stem-loop RT-PCR. The miRNA star sequences of 38 known miRNAs and 8 new miRNAs were also discovered, providing additional evidence for the existence of miRNAs. Through degradome sequencing, 145 and 25 genes were identified as targets of annotated miRNAs and new miRNAs, respectively. GO analysis indicated that many of the identified miRNA targets may function in soybean seed development. Additionally, a soybean homolog of Arabidopsis suppressor of gene silencing 3 (AtSGS3) was detected as a target of the newly identified miRNA Soy_25, suggesting the presence of feedback control of miRNA biogenesis.
  
  
  CONCLUSIONS
  We have identified large numbers of miRNAs and their related target genes through deep sequencing of a small RNA library and a degradome library. Our study provides more information about the regulatory network of miRNAs in soybean and advances our understanding of miRNA functions during seed development.
authors.affiliation: State Key Laboratory of Plant Genomics, Genome Biology Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China.
authors.forename: Qing-Xin
authors.initials: QX
authors.lastname: Song
authors.forename: Yun-Feng
authors.initials: YF
authors.lastname: Liu
authors.forename: Xing-Yu
authors.initials: XY
authors.lastname: Hu
authors.forename: Wan-Ke
authors.initials: WK
authors.lastname: Zhang
authors.forename: Biao
authors.initials: B
authors.lastname: Ma
authors.forename: Shou-Yi
authors.initials: SY
authors.lastname: Chen
authors.forename: Jin-Song
authors.initials: JS
authors.lastname: Zhang
mesh_terms: D001483:Base Sequence; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D017343:Genes, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D012322:RNA Precursors / Q000235:genetics; D020871:RNA Stability / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012639:Seeds / Q000196:embryology* / Q000235:genetics*; D013025:Glycine max / Q000196:embryology* / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins; D012322:RNA Precursors; D012333:RNA, Messenger; D018749:RNA, Plant