title: Identification and characterization of the microRNA transcriptome of a moth orchid Phalaenopsis aphrodite.
abstract: Orchids display unique phenotypes, functional characteristics and ecological adaptations that are not found in model plants. In this study, we aimed to characterize the microRNA (miRNA) transcriptome and identify species- and tissue-specific miRNAs in Phalaenopsis aphrodite. After data filtering and cleanup, a total of 59,387,374 reads, representing 1,649,996 unique reads, were obtained from four P. aphrodite small RNA libraries. A systematic bioinformatics analysis pipeline was developed that can be used for miRNA and precursor mining, and target gene prediction in non-model plants. A total of 3,251 unique reads for 181 known plant miRNAs (belonging to 88 miRNA families), 23 new miRNAs and 91 precursors were identified. All the miRNA star sequences (miRNA*), the complementary strands of miRNA that from miRNA/miRNA* duplexes, of the predicted new miRNAs were detected in our small RNA libraries, providing additional evidence for their existence as new miRNAs in P. aphrodite. Furthermore, 240 potential miRNA-targets that appear to be involved in many different biological activities and molecular functions, especially transcription factors, were identified, suggesting that miRNAs can impact multiple processes in P. aphrodite. We also verified the cleavage sites for six targets using RNA ligase-mediated rapid amplification of 5' ends assay. The results provide valuable information about the composition, expression and function of miRNA in P. aphrodite, and will aid functional genomics studies of orchids.
authors.affiliation: Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan, ytchao@gate.sinica.edu.tw.
authors.forename: Ya-Ting
authors.initials: YT
authors.lastname: Chao
authors.forename: Chun-Lin
authors.initials: CL
authors.lastname: Su
authors.forename: Wen-Han
authors.initials: WH
authors.lastname: Jean
authors.forename: Wan-Chieh
authors.initials: WC
authors.lastname: Chen
authors.forename: Yao-Chien Alex
authors.initials: YC
authors.lastname: Chang
authors.forename: Ming-Che
authors.initials: MC
authors.lastname: Shih
mesh_terms: D001483:Base Sequence; D016000:Cluster Analysis; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D020411:Oligonucleotide Array Sequence Analysis; D029595:Orchidaceae / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D012322:RNA Precursors / Q000235:genetics; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012689:Sequence Homology, Nucleic Acid; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins; D012322:RNA Precursors; D018749:RNA, Plant