title: Identification and Characterization of miRNAs in Chondrus crispus by High-Throughput Sequencing and Bioinformatics Analysis.
abstract: Chondrus crispus, an economically and medicinally important red alga, is a medicinally active substance and important for anti-tumor research. In this study, 117 C. crispus miRNAs (108 conserved and 9 novel) were identified from 2,416,181 small-RNA reads using high-throughput sequencing and bioinformatics methods. According to the BLAST search against the miRBase database, these miRNAs belonged to 110 miRNA families. Sequence alignment combined with homology searching revealed both the conservation and diversity of predicted potential miRNA families in different plant species. Four and 19 randomly selected miRNAs were validated by northern blotting and stem-loop quantitative real-time reverse transcription polymerase chain reaction detection, respectively. The validation rates (75% and 94.7%) demonstrated that most of the identified miRNAs could be credible. A total of 160 potential target genes were predicted and functionally annotated by Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis. We also analyzed the interrelationship of miRNAs, miRNA-target genes and target genes in C. crispus by constructing a Cytoscape network. The 117 miRNAs identified in our study should supply large quantities of information that will be important for red algae small RNA research.
authors.affiliation: School of Life Science, Shanxi University, Taiyuan 030006, China.
authors.forename: Fan
authors.initials: F
authors.lastname: Gao
authors.affiliation: School of Life Science, Shanxi University, Taiyuan 030006, China.
authors.forename: FangRu
authors.initials: F
authors.lastname: Nan
authors.affiliation: College of Shanxi Physical Technology, Taiyuan 030006, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Song
authors.affiliation: School of Life Science, Shanxi University, Taiyuan 030006, China.
authors.forename: Jia
authors.initials: J
authors.lastname: Feng
authors.affiliation: School of Life Science, Shanxi University, Taiyuan 030006, China.
authors.forename: JunPing
authors.initials: J
authors.lastname: Lv
authors.affiliation: School of Life Science, Shanxi University, Taiyuan 030006, China.
authors.forename: ShuLian
authors.initials: S
authors.lastname: Xie
mesh_terms: D044723:Chondrus / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D035683:MicroRNAs / Q000235:genetics*; D010940:Plant Proteins / Q000235:genetics; D018749:RNA, Plant / Q000235:genetics; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D035683:MicroRNAs; D010940:Plant Proteins; D018749:RNA, Plant