title: Small RNA Sequencing Based Identification of MiRNAs in Daphnia magna.
abstract: Small RNA molecules are short, non-coding RNAs identified for their crucial role in post-transcriptional regulation. A well-studied example includes miRNAs (microRNAs) which have been identified in several model organisms including the freshwater flea and planktonic crustacean Daphnia. A model for epigenetic-based studies with an available genome database, the identification of miRNAs and their potential role in regulating Daphnia gene expression has only recently garnered interest. Computational-based work using Daphnia pulex, has indicated the existence of 45 miRNAs, 14 of which have been experimentally verified. To extend this study, we took a sequencing approach towards identifying miRNAs present in a small RNA library isolated from Daphnia magna. Using Perl codes designed for comparative genomic analysis, 815,699 reads were obtained from 4 million raw reads and run against a database file of known miRNA sequences. Using this approach, we have identified 205 putative mature miRNA sequences belonging to 188 distinct miRNA families. Data from this study provides critical information necessary to begin an investigation into a role for these transcripts in the epigenetic regulation of Daphnia magna.
authors.affiliation: Abant İzzet Baysal University, Faculty of Art and Science, Department of Chemistry, Bolu, Turkey.
authors.forename: Ercan Selçuk
authors.initials: ES
authors.lastname: Ünlü
authors.affiliation: Mississippi State University, Department of Biological Sciences, Mississippi State, Starkville, Mississippi, United States of America.
authors.forename: Donna M
authors.initials: DM
authors.lastname: Gordon
authors.affiliation: Abant İzzet Baysal University, Faculty of Art and Science, Department of Biology, Bolu, Turkey.
authors.forename: Murat
authors.initials: M
authors.lastname: Telli
mesh_terms: D000818:Animals; D001483:Base Sequence; D019295:Computational Biology; D017124:Conserved Sequence; D003621:Daphnia / Q000235:genetics*; D057890:Epigenomics; D005786:Gene Expression Regulation; D035683:MicroRNAs / Q000737:chemistry*; D008969:Molecular Sequence Data; D017423:Sequence Analysis, RNA / Q000379:methods
chemical_list: D035683:MicroRNAs