title: Small RNA and degradome profiling reveals miRNA regulation in the seed germination of ancient eudicot Nelumbo nucifera.
abstract: MicroRNAs (miRNAs) play important roles in plant growth and development. MiRNAs and their targets have been widely studied in model plants, but limited knowledge is available concerning this small RNA population and their targets in sacred lotus (Nelumbo nucifera Gaertn.).
  
  
  
  In this study, a total of 145 known miRNAs belonging to 47 families and 78 novel miRNAs were identified during seed germination using high-throughput small RNA sequencing. Furthermore, some miRNA families which have not yet been reported in monocot or eudicot species were detected in N. nucifera, indicating that these miRNAs was divergence from monocots and core eudicots during evolution. Using degradome sequencing, 2580 targets were detected for all the miRNAs. GO (Gene Ontology) and KEGG pathway analyses showed that many target genes enriched in "regulation of transcription" and involved in "carbohydrate", "amino acid and energy metabolism". Nine miRNAs and three corresponding targets of them were further validated by quantitative RT-PCR.
  
  
  
  The results present here suggested that many miRNAs were involved in the regulation of seed germination of sacred lotus, providing a foundation for future studies of sacred lotus seed longevity. Comparative analysis of miRNAs from different plants also provided insight into the evolutionary gains and losses of miRNAs in plants.
authors: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.|State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.
authors: Jihong
authors: J
authors: Hu
authors: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
authors: Jing
authors: J
authors: Jin
authors: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
authors: Qian
authors: Q
authors: Qian
authors: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
authors: Keke
authors: K
authors: Huang
authors: State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China. yiding@whu.edu.cn.
authors: Yi
authors: Y
authors: Ding
mesh_terms: D019295:Computational Biology / Q000379:methods; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D063990:Gene Ontology; D018525:Germination / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000235:genetics*; D031653:Nelumbo / Q000235:genetics*; D017393:RNA Editing; D020871:RNA Stability; D058727:RNA, Small Untranslated / Q000235:genetics*; D012639:Seeds / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D058727:RNA, Small Untranslated
keywords: Degradome sequencing; Nelumbo nucifera; Quantitative qRT-PCR; Target genes; miRNA