Bioinformatics analysis of hemocyte miRNAs of scallop Chlamys farreri against acute viral necrobiotic virus (AVNV)

The sustainable development of the scallop Chlamys farreri industry in China is hindered by mass mortality mainly caused by a novel pathogen known as acute viral necrosis virus (AVNV). A better understanding of host-virus interactions, especially those at the molecular level, may facilitate the prevention and cure of AVNV infections. MicroRNAs (miRNAs) represent a class of small RNA molecules involved in several biological processes, including mediating host-pathogen responses. In this study, two hemocyte small RNA libraries were constructed from control (control library, CL) and AVNV-infected (infection library, IL) C. farreri for high throughput sequencing using Solexa technology. Acquired data were further used to identify conserved and novel miRNAs, screen differentially expressed miRNAs, and predict their target genes through bioinformatics analysis. Solexa sequencing produced 19,485,719 and 20,594,513 clean reads representing 2,248,814 and 1,510,256 unique small RNAs from CL and IL, respectively. A total of 57 conserved miRNAs were identified in both libraries, among which only two were unique to IL. Novel miRNA prediction using the Crassostrea gigas genome as a reference revealed 11 candidate miRNAs, 10 of which were validated by RT-PCR. Differential expression (p < 0.001) between libraries was observed in 37 miRNAs, among which 30 and 7 miRNAs were up- and downregulated, respectively. Expression differences were further confirmed by qRT-PCR. A sequence homology search against available C. farreri ESTs showed that these differentially expressed miRNAs may target 177 genes involved in a broad range of biological processes including immune defense and stress response. This study is the first to characterize C. farreri miRNAs and miRNA expression profiles in response to AVNV infection by deep sequencing. The results presented here will deepen our understanding of the pathogenesis of AVNV at the molecular level and provide new insights into the molecular basis of host-pathogen interactions in C. farreri.