Abstract
Small interfering RNAs (siRNAs) and microRNAs (miRNAs) are two classes of small RNAs (sRNAs) that are critical for virus-host interplay via the RNA interference (RNAi) pathway. One virus-derived siRNA and numerous miRNAs has been reported for the double-stranded DNA virus white spot syndrome virus (WSSV), however, the expression profiles of these different types of sRNAs have not been assessed. Here, by sequencing the sRNAs and mRNAs of WSSV-infected Chinese shrimp (Fenneropenaeus chinensis), we found that the viral transcripts were universally targeted by WSSV-derived siRNAs, supporting a pivotal role for RNAi in the anti-viral immunity of shrimp. The genesis of WSSV-derived siRNAs was associated with long RNA structures. Moreover, by separating miRNAs from siRNAs, 12 WSSV miRNAs were identified. Investigation of conserved viral miRNA targets in different host species indicated the involvement of viral miRNAs in host immune responses. Collectively, our data provide new insights into the role of the RNAi pathway in the interplay between DNA viruses and crustaceans.
Highlights
The origins of small interfering RNAs (siRNAs) and miRNA differ. miRNA biogenesis starts in the nucleus, wherein a primary miRNA is transcribed and processed into shorter hairpin RNAs by Drosha
After removing small RNA (sRNA) that aligned with host mRNAs, the latent infection (LI) cephalothorax sample provided 1,664 unique sRNAs that aligned with the white spot syndrome virus (WSSV) genome
Virus-derived sRNAs have been detected in animals infected with various viruses[14,18]
Summary
The origins of siRNA and miRNA differ. miRNA biogenesis starts in the nucleus, wherein a primary miRNA (pri-miRNA) is transcribed and processed into shorter hairpin RNAs (precursor miRNAs or pre-miRNAs) by Drosha. RNAi provides vital anti-viral defense for the host[14] In this defense, viral dsRNA is recognized by Dicer[2] and cleaved into vsiRNAs VsiRNA was originally thought to be confined to RNA viruses with dsRNA genomes or replication intermediates that are targeted by host Dicer. Genome-wide siRNA production has recently been discovered in DNA viruses that infect plants and insects[17,18,22,23,24,25]. With the capability to infect a wide range of crustaceans, including shrimp, crab, and crayfish, WSSV is a major pathogen in shrimp aquaculture and has caused serious losses worldwide since the 1990s27 It differs profoundly from all presently known viruses and is the sole representative of the Nimaviridae family[28,29]. The deep-sequencing technique has the potential to discriminate between miRNAs and siRNAs33, their differences have not been addressed in WSSV
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