Identification of differential mRNA and lncRNA expression in AcMNPV-infected Sf9 cells

Abstract

Sf9Sf9 are the ovarian cells of Spodoptera frugiperda that is the host of Autographa californica multiple nucleopolyhedrovirus (AcMNPV), and hence can serve as an effective test vehicle to understand the AcMNPV infection mechanism. In this study, through high-throughput sequencing technology using samples collected from Sf9 cells at different time points after AcMNPV infection, 3463 pieces of time-series differentially expressed RNA (1,200 mRNA and 2,263 lncRNA) are identified and justified by experimental verification of randomly selected samples from them, proving the validity of the bioinformatical analysis on this topic. Functional enrichment analysis and target prediction are performed on those differentially expressed RNA, from which the major functional enrichment distribution of those differentially expressed mRNA is derived. It has been found that the differential genes are mainly in the cellular anatomical entity and intracellular in terms of the cellular component, and in the binding and catalytic activity in terms of the molecular function. Also, the differential mRNA are mainly concentrated in global and overview maps, signal transduction, infectious diseases, and viral, etc. Moreover, those mRNA targeted by lncRNA are predicted. The correlation between those differentially expressed lncRNA and mRNA indicates that lncRNA is very likely playing an important role in the interaction between virus and host. Aided by an advanced co-expression analysis approach, the “hub” RNA is also identified. The study in this work pave the way for further analyzing and understanding how AcMNPV escapes from the host’s immunity, manipulates the host to realize the self-multiplication, and realizes the timely conversion between its two particle forms, laying the foundation for uncovering the host’s immune response process.