Transcriptomic Analysis of Resistant and Susceptible Bombyx mori Strains Following BmNPV Infection Provides Insights into the Antiviral Mechanisms

Abstract

Purpose. To decipher transcriptomic changes and related genes with potential functions against Bombyx mori nucleopolyhedrovirus infection and to increase the understanding of the enhanced virus resistance of silkworm on the transcriptomic level. Methods. We assembled and annotated transcriptomes of the Qiufeng (susceptible to infection) and QiufengN (resistant to infection) strains and performed comparative analysis in order to decipher transcriptomic changes and related genes with potential functions against BmNPV infection. Results. A total of 78,408 SNPs were identified in the Qiufeng strain of silkworm and 56,786 SNPs were identified in QiufengN strain. Besides, novel AS events were found in these 2 strains. In addition, 1,728 DEGs were identified in the QiufengN strain compared with Qiufeng strain. These DEGs were involved in GO terms related to membrane, metabolism, binding and catalytic activity, cellular processes, and organismal systems. The highest levels of gene representation were found in oxidative phosphorylation, phagosome, TCA cycle, arginine and proline metabolism, and pyruvate metabolism. Additionally, COG analysis indicated that DEGs were involved in "amino acid transport and metabolism" and "carbohydrate transport and metabolism." Conclusion. We identified a series of major pathological changes in silkworm following infection and several functions were related to the antiviral mechanisms of silkworm.

Figure 1

Saturation curve of transcriptomic sequencing reads for samples and single nucleotide polymorphism (SNP) density distribution. (a) Saturation curve of transcriptomic sequencing reads for samples of the silkworm strains QiufengN and Qiufeng. Red line, samples of the Qiufeng strain; green line, samples of the QiufengN strain. (b) SNP density distribution of the QiufengN and Qiufeng strain. T01 indicates the sample of Qiufeng strain. T02 indicates the sample of QiufengN strain.

Figure 2

Identification of differentially expressed genes (DEGs). (a) Heat map of DEGs between QiufengN and Qiufeng strains. Columns indicate different samples. Rows represent different DEGs. Different colors indicate the gene expression levels in the samples that measured as log₂ (FPKM + 1). (b) MA plot of DEGs. Red points represent genes without differential expression. Green points indicate DEGs. FC, fold change. FPKM, fragments per kilobase of transcript.

Figure 3

Gene Ontology (GO) classification of DEGs.

Figure 4

KEGG enrichment analysis of DEGs. (a) Histogram representation of KEGG pathways of DEGs. x-axis represents the number and percentage of DEGs enriched in a specific pathway. y-axis indicates the KEGG pathways. (b) Scatter diagram of KEGG pathways. The x-axis “enrichment factor” indicates the ratio of the proportion of all genes annotated to a pathway to the proportion of the DEGs annotated to a pathway. Less enrichment factor indicates more significance of the DEGs being annotated to the pathway. Q-value represents corrected P value. Thus, the point near the top left corner in the figure had more significance.

Figure 5

Histogram representation of clusters of orthologous groups (COG) classification of DEGs. The y-axis “Frequency” indicates the number of genes in a specific function cluster. The figure keys show a description of the 25 function categories that were functionally classified by genes.