Comparative transcriptome and potential antiviral signaling pathways analysis of the gills in the red swamp crayfish, Procambarus clarkii infected with White Spot Syndrome Virus (WSSV)

Abstract

Red swamp crayfish is an important model organism for research of the invertebrate innate immunity mechanism. Its excellent disease resistance against bacteria, fungi, and viruses is well-known. However, the antiviral mechanisms of crayfish remain unclear. In this study, we obtained high-quality sequence reads from normal and white spot syndrome virus (WSSV)-challenged crayfish gills. For group normal (GN), 39,390,280 high-quality clean reads were randomly assembled to produce 172,591 contigs; whereas, 34,011,488 high-quality clean reads were randomly assembled to produce 182,176 contigs for group WSSV-challenged (GW). After GO annotations analysis, a total of 35,539 (90.01%), 14,931 (37.82%), 28,221 (71.48%), 25,290 (64.05%), 15,595 (39.50%), and 13,848 (35.07%) unigenes had significant matches with sequences in the Nr, Nt, Swiss-Prot, KEGG, COG and GO databases, respectively. Through the comparative analysis between GN and GW, 12,868 genes were identified as differentially up-regulated DEGs, and 9,194 genes were identified as differentially down-regulated DEGs. Ultimately, these DEGs were mapped into different signaling pathways, including three important signaling pathways related to innate immunity responses. These results could provide new insights into crayfish antiviral immunity mechanism.

Temporal changes in transcriptome profile provide insights of White Spot Syndrome Virus infection in Litopenaeus vannamei

“…To date many transcriptomic studies have reported changes in GE resulting from WSSV infection, but so far these studies were limited on a single time point 9,14–19,21 , providing no insight into dynamic changes in GE happening during the course of infection. The use of TC analysis allowed us to identify genes with significant differences between treatments and between different time points that were subsequently mapped to identify altered cellular processes or pathways during WSSV infection.…”

“…4), further suggesting an involvement of ABC transporter as entry mechanism or host defensive mechanism in initial stages of infection. In addition, Du and Jin 19 and Chen et al . 17 found GE changes in ABC transporters after WSSV infection in red swamp crayfish gills and whiteleg shrimp hepatopancreas: interestingly, while in whiteleg shrimp hepatopancreas ABC transporters were down-regulated, in red swamp crayfish gills ABC were upregulated, suggesting that an important difference exists between these two tissues.…”

“…Therefore, in order to fully understand the mechanism of infection it is essential to characterize these dynamic changes in GE. Hitherto, the vast majority of available transcriptomic studies focussed on comparing GE between infected and control animals at a single time point 9,14–19 , therefore providing no insight on how GE in host and pathogen is changing with time. In order to improve our knowledge on the dynamic interaction between host and pathogen with time, we used an RNA sequencing (RNA-seq) approach to contrast GE changes in gills of L. vannamei at different stages of infection, namely 1.5, 18 and 56 hours-post-infection (hpi), between WSSV-challenged shrimps and control shrimps.…”

China’s most typical nonferrous organic-metal facilities own specific microbial communities

“…PICRUSt analyses predicted the potential function in each community for functional profiles of bacterial communities. Sequences of 13 NMMFs samples were used to carry out functional annotation tasks, including categorized with COG functional annotation 58 . NSTI characterized the accuracy of PICRUSt, with lower values indicating a higher accuracy 40 , 59 .…”

Transcriptome analysis of Macrobrachium rosenbergii intestines under the white spot syndrome virus and poly (I:C) challenges

“…In freshwater crayfish P . clarkii , spliceosome was also on the list of potential antiviral signaling pathways [ 28 ]. Similarly, in RNA-seq analysis of M .…”