High-throughput sequencing of RNA silencing-associated small RNAs in olive (Olea europaea L.)

• Published in: PloS one 2011-11, Vol.6 (11), p.e27916-e27916
• Main Authors: Donaire, Livia, Pedrola, Laia, Rosa, Raúl de la, Llave, César
• Format: Article
• Language: English
• Subjects: Acids; Analysis; Arabidopsis; Arabidopsis thaliana; Base Sequence; Biology; Conserved Sequence - genetics; Flowers & plants; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Gene Regulatory Networks - genetics; Gene sequencing; Genes; Genomes; Genomics; Heterochromatin; High-Throughput Nucleotide Sequencing - methods; Hybridization; Identification; Integrity; Interactive control; MicroRNA; MicroRNAs; MicroRNAs - genetics; MicroRNAs - metabolism; miRNA; Molecular Sequence Data; Next-generation sequencing; Nucleotides; Olea - genetics; Olea - growth & development; Olea europaea; Polymorphism, Genetic; Reproducibility of Results; Reverse Transcriptase Polymerase Chain Reaction; Ribonucleic acid; RNA; RNA Interference; RNA polymerase; RNA, Plant - genetics; RNA-mediated interference; Sequence Analysis, RNA; Shoots; siRNA; Time Factors; Transcription factors; Transportation networks
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0027916

Small RNAs (sRNAs) of 20 to 25 nucleotides (nt) in length maintain genome integrity and control gene expression in a multitude of developmental and physiological processes. Despite RNA silencing has been primarily studied in model plants, the advent of high-throughput sequencing technologies has enabled profiling of the sRNA component of more than 40 plant species. Here, we used deep sequencing and molecular methods to report the first inventory of sRNAs in olive (Olea europaea L.). sRNA libraries prepared from juvenile and adult shoots revealed that the 24-nt class dominates the sRNA transcriptome and atypically accumulates to levels never seen in other plant species, suggesting an active role of heterochromatin silencing in the maintenance and integrity of its large genome. A total of 18 known miRNA families were identified in the libraries. Also, 5 other sRNAs derived from potential hairpin-like precursors remain as plausible miRNA candidates. RNA blots confirmed miRNA expression and suggested tissue- and/or developmental-specific expression patterns. Target mRNAs of conserved miRNAs were computationally predicted among the olive cDNA collection and experimentally validated through endonucleolytic cleavage assays. Finally, we use expression data to uncover genetic components of the miR156, miR172 and miR390/TAS3-derived trans-acting small interfering RNA (tasiRNA) regulatory nodes, suggesting that these interactive networks controlling developmental transitions are fully operational in olive.