title: Deep sequencing and microarray hybridization identify conserved and species-specific microRNAs during somatic embryogenesis in hybrid yellow poplar.
abstract: BACKGROUND
  To date, several studies have indicated a major role for microRNAs (miRNAs) in regulating plant development, but miRNA-mediated regulation of the developing somatic embryo is poorly understood, especially during early stages of somatic embryogenesis in hardwood plants. In this study, Solexa sequencing and miRNA microfluidic chips were used to discover conserved and species-specific miRNAs during somatic embryogenesis of hybrid yellow poplar (Liriodendron tulipifera×L. chinense).
  
  
  RESULTS
  A total of 17,214,153 reads representing 7,421,623 distinct sequences were obtained from a short RNA library generated from small RNAs extracted from all stages of somatic embryos. Through a combination of deep sequencing and bioinformatic analyses, we discovered 83 sequences with perfect matches to known miRNAs from 33 conserved miRNA families and 273 species-specific candidate miRNAs. MicroRNA microarray results demonstrated that many conserved and species-specific miRNAs were expressed in hybrid yellow poplar embryos. In addition, the microarray also detected another 149 potential miRNAs, belonging to 29 conserved families, which were not discovered by deep sequencing analysis. The biological processes and molecular functions of the targets of these miRNAs were predicted by carrying out BLAST search against Arabidopsis thaliana GenBank sequences and then analyzing the results with Gene Ontology.
  
  
  CONCLUSIONS
  Solexa sequencing and microarray hybridization were used to discover 232 candidate conserved miRNAs from 61 miRNA families and 273 candidate species-specific miRNAs in hybrid yellow poplar. In these predicted miRNAs, 64 conserved miRNAs and 177 species-specific miRNAs were detected by both sequencing and microarray hybridization. Our results suggest that miRNAs have wide-ranging characteristics and important roles during all stages of somatic embryogenesis in this economically important species.
authors.affiliation: The Key Laboratory of Forest Genetics and Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing, China.
authors.forename: Tingting
authors.initials: T
authors.lastname: Li
authors.forename: Jinhui
authors.initials: J
authors.lastname: Chen
authors.forename: Shuai
authors.initials: S
authors.lastname: Qiu
authors.forename: Yanjuan
authors.initials: Y
authors.lastname: Zhang
authors.forename: Pengkai
authors.initials: P
authors.lastname: Wang
authors.forename: Liwei
authors.initials: L
authors.lastname: Yang
authors.forename: Ye
authors.initials: Y
authors.lastname: Lu
authors.forename: Jisen
authors.initials: J
authors.lastname: Shi
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D017124:Conserved Sequence; D003433:Crosses, Genetic; D005816:Genetic Complementation Test; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D031567:Liriodendron / Q000235:genetics*; D035683:MicroRNAs / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D063245:Plant Development; D010944:Plants / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics*
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant