title: Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development.
abstract: As a typical geocarpic plant, peanut embryogenesis and pod development are complex processes involving many gene regulatory pathways and controlled by appropriate hormone level. MicroRNAs (miRNAs) are small non-coding RNAs that play indispensable roles in post-transcriptional gene regulation. Recently, identification and characterization of peanut miRNAs has been described. However, whether miRNAs participate in the regulation of peanut embryogenesis and pod development has yet to be explored.
  
  
  
  In this study, small RNA and degradome libraries from peanut early pod of different developmental stages were constructed and sequenced. A total of 70 known and 24 novel miRNA families were discovered. Among them, 16 miRNA families were legume-specific and 12 families were peanut-specific. 30 known and 10 novel miRNA families were differentially expressed during pod development. In addition, 115 target genes were identified for 47 miRNA families by degradome sequencing. Several new targets that might be specific to peanut were found and further validated by RNA ligase-mediated rapid amplification of 5' cDNA ends (RLM 5'-RACE). Furthermore, we performed profiling analysis of intact and total transcripts of several target genes, demonstrating that SPL (miR156/157), NAC (miR164), PPRP (miR167 and miR1088), AP2 (miR172) and GRF (miR396) are actively modulated during early pod development, respectively.
  
  
  
  Large numbers of miRNAs and their related target genes were identified through deep sequencing. These findings provided new information on miRNA-mediated regulatory pathways in peanut pod, which will contribute to the comprehensive understanding of the molecular mechanisms that governing peanut embryo and early pod development.
authors.affiliation: Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
authors.forename: Chao
authors.initials: C
authors.lastname: Gao
authors.affiliation: Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
authors.forename: Pengfei
authors.initials: P
authors.lastname: Wang
authors.affiliation: Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
authors.forename: Shuzhen
authors.initials: S
authors.lastname: Zhao
authors.affiliation: Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
authors.forename: Chuanzhi
authors.initials: C
authors.lastname: Zhao
authors.affiliation: Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
authors.forename: Han
authors.initials: H
authors.lastname: Xia
authors.affiliation: Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
authors.forename: Lei
authors.initials: L
authors.lastname: Hou
authors.affiliation: Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Ju
authors.affiliation: Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
authors.forename: Ye
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.
authors.forename: Changsheng
authors.initials: C
authors.lastname: Li
authors.affiliation: Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China. xingjunw@hotmail.com.|College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China. xingjunw@hotmail.com.
authors.forename: Xingjun
authors.initials: X
authors.lastname: Wang
mesh_terms: D020413:3' Untranslated Regions; D010367:Arachis / Q000235:genetics* / Q000254:growth & development; D001483:Base Sequence; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks / Q000528:radiation effects; D059014:High-Throughput Nucleotide Sequencing; D008027:Light; D035683:MicroRNAs / Q000737:chemistry / Q000378:metabolism*; D010641:Phenotype; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D020413:3' Untranslated Regions; D035683:MicroRNAs; D010940:Plant Proteins; D012333:RNA, Messenger; D018749:RNA, Plant
keywords: Embryogenesis; High-throughput sequencing; Hormone; Light; Peanut; Pod development; miRNA