Northwest Fisheries Science Center

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Document Type: Journal Article
Center: NWFSC
Document ID: 7458
Title: In silico prediction and in vivo validation of Daphnia pulex microRNAs
Author: Shuai Chen, Garrett McKinney, Krista M. Nichols, Maria Sepulveda
Publication Year: 2014
Journal: PLoS ONE
Volume: 9
Pages: e83708
DOI: 10.1371/journal.pone.0083708
Keywords: Gene expression

 Daphnia pulex, the crustacean with the first sequenced genome, is an important organism that has been widely used in ecological and toxicological research. MicroRNAs (miRNAs) are 21–25 nucleotide small non-coding RNAs that are involved in a myriad of physiological processes. In this research, we predicted 75 D. pulex miRNAs by sequence homology and secondary structure identification from the full genome sequence. Fourteen predicted miRNAs were selected for quantitative real time polymerase chain reaction (RT-PCR) validation. Out of these, eight (mir-8, mir-9, mir-12, mir-92, mir-100, mir-133, mir-153 and mir-283) were successfully amplified and validated. Next, expression levels were quantified at three different life stages (days 4, 8 and 12 of age) using U6 spliceosomal RNA as a reference gene. The expression of mir-8, mir-9, mir-12, mir-92 and mir-100 significantly differed across time suggesting these microRNAs might play a critical role during D. pulex development. This is the first study to identify and validate miRNAs in D. pulex, which is an important first step in further studies that evaluate their roles in development and response to environmental and ecological stimuli.

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Theme: Recovery and rebuilding of marine and coastal species
Foci: Characterize the population biology of species, and develop and improve methods for predicting the status of populations.