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.

Figure 1. Gene ontology (GO) classification of transcripts from the two gill samples (GN and GW). The three main GO categories include biological process (blue), cellular component (red), and molecular function (green).

Figure 2. Cluster of orthologous groups (COG) classification of putative proteins.

Figure 3. Comparative analysis of the gene expression levels for two transcript libraries between normal (GN) and WSSV-challenged (GW) crayfish gills. Red dots represent transcripts significantly up-regulated in GW, while green dots represent significantly down-regulated transcripts. The parameters “FDR ≤ 0.001” and “| log2 Ratio| ≥ 1” were used as the threshold to judge the significance of gene expression differences.

Figure 4. Gene ontology (GO) classification analysis of differentially expressed genes (DEGs) between GN and GW. The three main GO categories include biological process (blue), cellular component (red), and molecular function (green).

Figure 5. Significant differentially expressed genes (DEGs) identified by KEGG as involved in the apoptosis signaling pathway. Red boxes indicate significantly increased expression, green boxes indicate significantly decreased expression and blue boxes indicate unchanged expression.

Figure 6. Significant differentially expressed genes (DEGs) identified by KEGG involved in the melanogenesis signaling pathway. Red boxes indicate significantly increased expression, green boxes indicate significantly decreased expression, and black boxes indicate unchanged expression.

Figure 7. Significant differentially expressed genes (DEGs) identified by KEGG involved in the Toll-like receptors (TLRs) signaling pathway. Red boxes indicate significantly increased expression, green boxes indicate significantly decreased expression, and black boxes indicate unchanged expression.