Comprehensive identification and profiling of Chinese shrimp (Fenneropenaeus chinensis) microRNAs in response to high pH stress using Hiseq2000 sequencing

Abstract

pH has a great impact on the distribution, growth, behaviour and physiology in many aquatic animals. MicroRNAs (miRNAs), a class of small non-coding RNAs play essential roles in animal responses to environmental stress. In this study, we constructed two small RNA (sRNA) libraries from control (pH 7.4) and high pH (9.4) treated shrimp to identify high pH stress-responsive miRNAs. Using deep sequencing, we identified 72 (3 conserved and 69 novel) up- and 4 (2 conserved and 2 novel) down-regulated miRNAs from high pH challenged shrimp hepatopancreas. Gene Ontology annotations and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that these target transcripts were implicated in a broad range of biological processes and various metabolic pathways. Moreover, we validated the expression patterns of selected miRNAs and their target genes by qRT-PCR. The present work adds new insights into the large-scale identification and characterization of Fenneropenaeus chinensis miRNAs and their potential targets and represents a foundation for underlying mechanisms of animal responses to high pH stress at post-transcriptional level.