title: Computational identification of conserved microRNAs and their targets from expression sequence tags of blueberry (Vaccinium corybosum).
abstract: MicroRNAs (miRNAs) are a class of endogenous, approximately 21nt in length, non-coding RNA, which mediate the expression of target genes primarily at post-transcriptional levels. miRNAs play critical roles in almost all plant cellular and metabolic processes. Although numerous miRNAs have been identified in the plant kingdom, the miRNAs in blueberry, which is an economically important small fruit crop, still remain totally unknown. In this study, we reported a computational identification of miRNAs and their targets in blueberry. By conducting an EST-based comparative genomics approach, 9 potential vco-miRNAs were discovered from 22,402 blueberry ESTs according to a series of filtering criteria, designated as vco-miR156-5p, vco-miR156-3p, vco-miR1436, vco-miR1522, vco-miR4495, vco-miR5120, vco-miR5658, vco-miR5783, and vco-miR5986. Based on sequence complementarity between miRNA and its target transcript, 34 target ESTs from blueberry and 70 targets from other species were identified for the vco-miRNAs. The targets were found to be involved in transcription, RNA splicing and binding, DNA duplication, signal transduction, transport and trafficking, stress response, as well as synthesis and metabolic process. These findings will greatly contribute to future research in regard to functions and regulatory mechanisms of blueberry miRNAs.
authors.affiliation: a College of Plant Science; Jilin University; Changchun, Jilin, PR China.
authors.forename: Xuyan
authors.initials: X
authors.lastname: Li
authors.forename: Yanming
authors.initials: Y
authors.lastname: Hou
authors.forename: Li
authors.initials: L
authors.lastname: Zhang
authors.forename: Wenhao
authors.initials: W
authors.lastname: Zhang
authors.forename: Chen
authors.initials: C
authors.lastname: Quan
authors.forename: Yuhai
authors.initials: Y
authors.lastname: Cui
authors.forename: Shaomin
authors.initials: S
authors.lastname: Bian
mesh_terms: D001483:Base Sequence; D029798:Blueberry Plants / Q000235:genetics* / Q000378:metabolism; D019295:Computational Biology; D017124:Conserved Sequence; D020224:Expressed Sequence Tags; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D018749:RNA, Plant / Q000737:chemistry / Q000235:genetics*; D015398:Signal Transduction / Q000235:genetics
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant
keywords: Expression sequence tags; blueberry; comparative genomics; miRNA targets; microRNAs