title: High-throughput sequencing-based genome-wide identification of microRNAs expressed in developing cotton seeds.
abstract: MicroRNAs (miRNAs) have been shown to play critical regulatory roles in gene expression in cotton. Although a large number of miRNAs have been identified in cotton fibers, the functions of miRNAs in seed development remain unexplored. In this study, a small RNA library was constructed from cotton seeds sampled at 15 days post-anthesis (DPA) and was subjected to high-throughput sequencing. A total of 95 known miRNAs were detected to be expressed in cotton seeds. The expression pattern of these identified miRNAs was profiled and 48 known miRNAs were differentially expressed between cotton seeds and fibers at 15 DPA. In addition, 23 novel miRNA candidates were identified in 15-DPA seeds. Putative targets for 21 novel and 87 known miRNAs were successfully predicted and 900 expressed sequence tag (EST) sequences were proposed to be candidate target genes, which are involved in various metabolic and biological processes, suggesting a complex regulatory network in developing cotton seeds. Furthermore, miRNA-mediated cleavage of three important transcripts in vivo was validated by RLM-5' RACE. This study is the first to show the regulatory network of miRNAs that are involved in developing cotton seeds and provides a foundation for future studies on the specific functions of these miRNAs in seed development.
authors.affiliation: Laboratory of Plant Molecular Biology, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
authors.forename: YanMei
authors.initials: Y
authors.lastname: Wang
authors.forename: Yan
authors.initials: Y
authors.lastname: Ding
authors.forename: DingWei
authors.initials: D
authors.lastname: Yu
authors.forename: Wei
authors.initials: W
authors.lastname: Xue
authors.forename: JinYuan
authors.initials: J
authors.lastname: Liu
mesh_terms: D001483:Base Sequence; D020869:Gene Expression Profiling / Q000379:methods; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D018745:Genome, Plant / Q000235:genetics*; D003368:Gossypium / Q000235:genetics* / Q000254:growth & development; D059014:High-Throughput Nucleotide Sequencing; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010940:Plant Proteins / Q000235:genetics; D012639:Seeds / Q000235:genetics* / Q000254:growth & development; D012689:Sequence Homology, Nucleic Acid; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins